diff --git a/counts.json b/counts.json index 9f0414c..e638348 100644 --- a/counts.json +++ b/counts.json @@ -2326,16 +2326,16 @@ "2csfastq_1csfastq": 1, "2ft": 2, "2ndscore": 1, - "2to3": 3709, - "2to3-3.10": 819, - "2to3-3.11": 270, + "2to3": 3713, + "2to3-3.10": 820, + "2to3-3.11": 271, "2to3-3.12": 226, "2to3-3.4": 6, "2to3-3.5": 103, "2to3-3.6": 342, "2to3-3.7": 383, "2to3-3.8": 577, - "2to3-3.9": 652, + "2to3-3.9": 654, "3EdgeTests": 1, "3_1_filter_mapQ_for_sam.pl": 1, "3seq": 1, @@ -2419,8 +2419,8 @@ "AminoExtract": 2, "AmpliGone": 1, "AmpliconSuite-pipeline.py": 1, - "AnalyseDists": 50, - "AnalyseSeqs": 50, + "AnalyseDists": 51, + "AnalyseSeqs": 51, "AnnotSV": 1, "AnnotateInexactHomology": 1, "AnnotateInexactHomologyBedpe": 1, @@ -2966,7 +2966,7 @@ "FEELnc_pipeline.sh": 1, "FEELnc_tpLevel2gnLevelClassification.R": 1, "FEELnc_tpLevel2gnLevelClassification.R.bak": 1, - "FET.pl": 45, + "FET.pl": 46, "FEW.pl": 6, "FFEval": 2, "FGAP": 1, @@ -3296,7 +3296,7 @@ "KatComp": 1, "KatGC": 1, "KinamineY-shaker": 1, - "Kinfold": 59, + "Kinfold": 60, "Kmasker": 1, "KmerCount.py": 1, "KmerFilter": 5, @@ -3710,8 +3710,8 @@ "PCoA_bubble.py": 1, "PDBFUNCS.pm": 2, "PERsim": 1, - "PF00225_full.blocks.txt": 9, - "PF00225_seed.blocks.txt": 9, + "PF00225_full.blocks.txt": 10, + "PF00225_seed.blocks.txt": 10, "PFAM_dat_parser.pl": 1, "PFAMtoGoParser.pl": 1, "PGDSpider2-cli": 1, @@ -3929,7 +3929,7 @@ "QueueingSystem.dll": 1, "QuickDeconvolution": 1, "QuickSNP.py": 1, - "R": 4666, + "R": 4667, "R-scape": 2, "R-scape-sim": 2, "R-scape-sim-nobps": 2, @@ -3959,19 +3959,19 @@ "RKP.py": 1, "RLPipes": 1, "RM2Bed.py": 13, - "RNA2Dfold": 57, + "RNA2Dfold": 58, "RNADigestor": 2, - "RNALalifold": 57, - "RNALfold": 59, + "RNALalifold": 58, + "RNALfold": 60, "RNAMassCalculator": 1, - "RNAPKplex": 57, + "RNAPKplex": 58, "RNAPhylo": 1, "RNARedPrint": 1, "RNARedPrintSampler.py": 1, "RNARedPrintStructure.py": 1, "RNA_fragment_size.py": 3, - "RNAaliduplex": 59, - "RNAalifold": 59, + "RNAaliduplex": 60, + "RNAalifold": 60, "RNAalishapes": 1, "RNAalishapes_eval_macrostate": 1, "RNAalishapes_eval_microstate": 1, @@ -4047,32 +4047,32 @@ "RNAcentralHTTPRequest-bin": 1, "RNAclust.pl": 1, "RNAcode": 2, - "RNAcofold": 59, - "RNAdistance": 59, - "RNAdos": 42, - "RNAduplex": 59, + "RNAcofold": 60, + "RNAdistance": 60, + "RNAdos": 43, + "RNAduplex": 60, "RNAeffective": 1, - "RNAeval": 59, - "RNAfold": 58, - "RNAforester": 59, - "RNAheat": 59, + "RNAeval": 60, + "RNAfold": 59, + "RNAforester": 60, + "RNAheat": 60, "RNAhybrid": 1, - "RNAinverse": 59, + "RNAinverse": 60, "RNAlien": 1, "RNAlien-bin": 1, "RNAlienScan": 1, "RNAlienScan-bin": 1, "RNAlienStatistics": 1, "RNAlienStatistics-bin": 1, - "RNAlocmin": 50, - "RNAmultifold": 27, - "RNApaln": 59, - "RNAparconv": 57, - "RNApdist": 59, - "RNAplex": 57, - "RNAplfold": 59, - "RNAplot": 59, - "RNApvmin": 52, + "RNAlocmin": 51, + "RNAmultifold": 28, + "RNApaln": 60, + "RNAparconv": 58, + "RNApdist": 60, + "RNAplex": 58, + "RNAplfold": 60, + "RNAplot": 60, + "RNApvmin": 53, "RNAshapes": 4, "RNAshapes_eval_macrostate": 1, "RNAshapes_eval_microstate": 1, @@ -4143,11 +4143,11 @@ "RNAshapes_subopt_nodangle_window": 1, "RNAshapes_subopt_overdangle": 1, "RNAshapes_subopt_overdangle_window": 1, - "RNAsnoop": 57, + "RNAsnoop": 58, "RNAsnp": 1, "RNAsoup": 1, - "RNAsubopt": 59, - "RNAup": 59, + "RNAsubopt": 60, + "RNAup": 60, "RNAz": 3, "RNAz.pm": 4, "RNPxlSearch": 2, @@ -4264,7 +4264,7 @@ "Rprof": 1, "Rsample": 5, "Rsample-smp": 5, - "Rscript": 4667, + "Rscript": 4668, "RunTHetA.py": 1, "SAGE": 1, "SAMMPileUpReader.py": 1, @@ -4462,7 +4462,7 @@ "SpectraSTSearchAdapter": 2, "SpliceAwareAligner": 1, "SpliceMap": 1, - "SplicedAlignment.pm": 14, + "SplicedAlignment.pm": 15, "SplicingToBed": 1, "SplitBamByCell": 1, "SplitClusters.pl": 1, @@ -4540,7 +4540,7 @@ "THESIAS": 1, "TICCalculator": 2, "TIR-Learner": 1, - "TMalign": 19, + "TMalign": 20, "TMscore": 6, "TNS": 2, "TOBIAS": 2, @@ -4692,7 +4692,7 @@ "XS": 1, "XTandemAdapter": 2, "XXmotif": 5, - "Xcalcmem.sh": 12, + "Xcalcmem.sh": 13, "XrayPrep": 6, "YamlDotNet.dll": 1, "ZOL": 1, @@ -4948,8 +4948,8 @@ "a3m_extract": 4, "a3m_reduce": 4, "a5toa4": 1, - "a_sample_mt.sh": 30, - "aa2nonred.pl": 12, + "a_sample_mt.sh": 31, + "aa2nonred.pl": 13, "aa_comp_calculator.py": 1, "aa_recoder.py": 1, "aacon": 1, @@ -5048,7 +5048,7 @@ "acc2gtdb_tax.py": 1, "acc2locus": 2, "accession_retrieve": 1, - "accn-at-a-time": 272, + "accn-at-a-time": 273, "accurate_bkp.py": 1, "acdc": 26, "acdc-filter-fasta-by-name.awk": 1, @@ -5061,7 +5061,7 @@ "acdvalid": 25, "ace.pl": 56, "ace2contig": 2, - "ace2sam": 517, + "ace2sam": 519, "aci": 1, "aclocal.bak": 11, "acountry": 4272, @@ -5128,7 +5128,7 @@ "add_metadata_tree.py": 6, "add_missing_mates.pl": 1, "add_mz": 2, - "add_name_to_gff3.pl": 9, + "add_name_to_gff3.pl": 10, "add_pancore_matrices.pl": 1, "add_pangenome_matrices.pl": 1, "add_pb_seq.pl": 1, @@ -5144,23 +5144,23 @@ "add_tradis_tags": 2, "add_transcript_feature_to_gtf.py": 1, "add_xray": 6, - "addadapters.sh": 30, + "addadapters.sh": 31, "addindel.py": 1, "addles": 6, "addr2line": 8, "addrg": 1, "addsnv.py": 1, - "addssu.sh": 29, + "addssu.sh": 30, "addsv.py": 1, "addtit.pl": 2, "adf_checker.pl": 1, "adhocfilelist": 1, - "adig": 4548, + "adig": 4551, "adjustPeakFile.pl": 5, "adjustRedunGroupFile.pl": 5, "adjustScanRankerScoreByGroup": 2, "adjust_seq_orientation.py": 1, - "adjusthomopolymers.sh": 29, + "adjusthomopolymers.sh": 30, "admixture": 1, "adptSim": 1, "adt": 2, @@ -5271,7 +5271,7 @@ "agrvate": 1, "agtsampleinforw.dll": 2, "ahmm-s": 1, - "ahost": 4548, + "ahost": 4551, "airr-tools": 5, "akita_data.py": 1, "akita_data_read.py": 1, @@ -5314,7 +5314,7 @@ "align-cache.2.11.0": 10, "align-cache.3": 2, "align-cache.3.0.0": 2, - "align-columns": 215, + "align-columns": 216, "align-ema.smk": 1, "align-families.py": 1, "align-info": 22, @@ -5378,7 +5378,7 @@ "alignoth": 1, "aligns_to": 1, "alignstats": 1, - "alimask": 181, + "alimask": 182, "alistat": 4, "all-interval": 2, "allVsAll.sh": 2, @@ -5403,12 +5403,12 @@ "alleyoop": 1, "allneeded": 1, "allo": 1, - "alltoall.sh": 27, + "alltoall.sh": 28, "aln-seqs.pl": 4, "aln2basecnt": 1, "aln2bed.pl": 2, "aln2fa.pl": 4, - "aln2wig": 9, + "aln2wig": 10, "alncut": 2, "alnpi": 2, "alnsel.pl": 4, @@ -5438,7 +5438,7 @@ "amdgpu-arch": 1, "ame": 13, "amgr": 1, - "amino-acid-composition": 303, + "amino-acid-composition": 304, "aminoextract": 2, "amk_ccc": 2, "amk_fft2": 2, @@ -5496,10 +5496,10 @@ "analyze_primers.py": 1, "analyze_probe_coverage.py": 1, "analyze_schema.py": 1, - "analyzeaccession.sh": 29, - "analyzegenes.sh": 29, + "analyzeaccession.sh": 30, + "analyzegenes.sh": 30, "analyzer": 1, - "analyzesketchresults.sh": 27, + "analyzesketchresults.sh": 28, "anamed": 1, "ananse": 1, "anansnake": 1, @@ -5549,7 +5549,7 @@ "annotate.py": 39, "annotate.pyc": 1, "annotateBAM.py": 1, - "annotateBed": 274, + "annotateBed": 275, "annotateBed_2way.pl": 1, "annotateInteractions.pl": 5, "annotatePeaks.pl": 5, @@ -5785,7 +5785,7 @@ "apply_mdae": 1, "apply_to_db.py": 1, "applygeo": 37, - "applyvariants.sh": 29, + "applyvariants.sh": 30, "appspam": 1, "apr-1-config": 3, "aprfinder": 1, @@ -5804,7 +5804,7 @@ "ar01_accret.py": 1, "arachne2ctg": 2, "arachne2scaff": 2, - "aragorn": 34, + "aragorn": 35, "arara": 1, "arb": 2, "arb_2_ascii": 4, @@ -5870,12 +5870,12 @@ "arcasHLA": 1, "archer": 1, "architeuthis": 1, - "archive-ncbinlp": 27, - "archive-nihocc": 27, - "archive-nmcds": 27, - "archive-pmc": 27, - "archive-pubmed": 302, - "archive-taxonomy": 27, + "archive-ncbinlp": 28, + "archive-nihocc": 28, + "archive-nmcds": 28, + "archive-pmc": 28, + "archive-pubmed": 303, + "archive-taxonomy": 28, "archive_directory.py": 2, "archosv": 2, "archspec": 10, @@ -5886,9 +5886,9 @@ "argnorm": 1, "argparse2tool": 1, "argparse2tool_check_path": 1, - "args2slice": 27, + "args2slice": 28, "args_oap": 1, - "aria2c": 23, + "aria2c": 24, "ariba": 3, "arlatex": 1, "array-as-vcf": 1, @@ -5937,7 +5937,7 @@ "ase-gui": 3, "ase-info": 3, "ase-run": 3, - "aserver": 444, + "aserver": 446, "asession": 3, "asgal": 1, "asgal_BitVector.py": 1, @@ -5963,8 +5963,8 @@ "asn2ff": 1, "asn2gb": 2, "asn2idx": 1, - "asn2ref": 27, - "asn2xml": 216, + "asn2ref": 28, + "asn2xml": 217, "asndhuff": 1, "asntool": 1, "asp-cp": 87, @@ -6025,17 +6025,17 @@ "attr": 44, "augment-bam": 1, "augur": 1, - "augustify.py": 9, - "augustus": 15, - "augustus2browser.pl": 14, - "augustus2gbrowse.pl": 14, + "augustify.py": 10, + "augustus": 16, + "augustus2browser.pl": 15, + "augustus2gbrowse.pl": 15, "augustus_to_proteindb.rb": 1, "auriclass": 1, "auspice": 1, "authorindex": 1, - "autoAug.pl": 14, - "autoAugPred.pl": 14, - "autoAugTrain.pl": 14, + "autoAug.pl": 15, + "autoAugPred.pl": 15, + "autoAugTrain.pl": 15, "autoRun.pathInfo": 5, "autoTrinotate.pl": 1, "auto_collapse_pops.py": 1, @@ -6069,7 +6069,7 @@ "autometa-taxonomy-majority-vote": 2, "autometa-unclustered-recruitment": 2, "autometa-update-databases": 2, - "autopoint": 5297, + "autopoint": 5298, "autoreconf.bak": 10, "autoscan.bak": 10, "autoupdate.bak": 10, @@ -6083,7 +6083,7 @@ "avgEpsGrid": 2, "aviary": 1, "avro": 13, - "awk": 100, + "awk": 101, "aws": 6, "aws-create-elastic-blast-janitor-role.sh": 1, "aws-delete-elastic-blast-janitor-role.sh": 1, @@ -6119,7 +6119,7 @@ "axt_to_lav.py": 59, "axt_to_maf.py": 59, "b2": 2, - "b2ct": 52, + "b2ct": 53, "b2sum": 83, "b2w": 1, "bFst": 31, @@ -6225,7 +6225,7 @@ "bam2fna": 3, "bam2fq.py": 3, "bam2gtf.py": 1, - "bam2hints": 15, + "bam2hints": 16, "bam2msa": 3, "bam2nuc": 2, "bam2occupancy": 1, @@ -6247,19 +6247,19 @@ "bam2starch_slurm-float128": 14, "bam2starch_slurm-megarow": 14, "bam2starch_slurm-typical": 14, - "bam2wig": 14, + "bam2wig": 15, "bam2wig.py": 3, "bamAlignCleaner": 1, "bamCompare": 11, "bamCoverage": 11, "bamFlags": 3, "bamPEFragmentSize": 11, - "bamToBed": 274, + "bamToBed": 275, "bamToBw.pl": 3, - "bamToFastq": 274, - "bamToGBrowse.pl": 89, + "bamToFastq": 275, + "bamToGBrowse.pl": 90, "bamToPsl": 1, - "bamToWig.py": 11, + "bamToWig.py": 12, "bam_accuracy.py": 1, "bam_add_tags": 3, "bam_alignment_length.py": 1, @@ -6371,7 +6371,7 @@ "bamtofastq": 3, "bamtofastq.py": 1, "bamtofastq_dir": 1, - "bamtools": 48, + "bamtools": 49, "bamtools-2.4.0": 3, "bamtools-2.4.1": 4, "bamutils": 1, @@ -6405,7 +6405,7 @@ "baredSC_2d": 1, "barriers": 2, "barriers-RNA2": 1, - "barrnap": 34, + "barrnap": 35, "barrnap.py": 1, "barseqcount": 1, "bart": 1, @@ -6421,8 +6421,8 @@ "baseCalling_Matrix_merger": 1, "base_evolve": 2, "basecall_network.py": 1, - "baseml": 69, - "basemlg": 69, + "baseml": 70, + "basemlg": 70, "basename": 84, "basenc": 81, "basenji_annot_chr.py": 1, @@ -6516,32 +6516,32 @@ "bazel-scan.py": 10, "bbAnalyze": 4, "bbFilter": 4, - "bbcms.sh": 29, - "bbcountunique.sh": 30, + "bbcms.sh": 30, + "bbcountunique.sh": 31, "bbcrisprfinder.sh": 1, - "bbduk.sh": 30, - "bbest.sh": 30, + "bbduk.sh": 31, + "bbest.sh": 31, "bbf": 4, - "bbfakereads.sh": 30, + "bbfakereads.sh": 31, "bbglm": 1, "bbl2bib": 1, - "bbmap.sh": 30, - "bbmapskimmer.sh": 30, - "bbmask.sh": 30, - "bbmerge-auto.sh": 30, - "bbmerge.sh": 30, + "bbmap.sh": 31, + "bbmapskimmer.sh": 31, + "bbmask.sh": 31, + "bbmerge-auto.sh": 31, + "bbmerge.sh": 31, "bbmergegapped.sh": 1, - "bbnorm.sh": 30, + "bbnorm.sh": 31, "bbqc.sh": 1, - "bbrealign.sh": 30, - "bbrename.sh": 30, - "bbsketch.sh": 30, + "bbrealign.sh": 31, + "bbrename.sh": 31, + "bbsketch.sh": 31, "bbsort.sh": 1, - "bbsplit.sh": 30, - "bbsplitpairs.sh": 30, - "bbstats.sh": 30, - "bbversion.sh": 30, - "bbwrap.sh": 30, + "bbsplit.sh": 31, + "bbsplitpairs.sh": 31, + "bbstats.sh": 31, + "bbversion.sh": 31, + "bbwrap.sh": 31, "bc": 27, "bcalm": 5, "bcbio-prioritize": 1, @@ -6576,7 +6576,7 @@ "beav_db": 1, "bed-to-bigBed": 1, "bed12-to-gtf": 3, - "bed12ToBed6": 274, + "bed12ToBed6": 275, "bed2DtoUCSCbed.pl": 5, "bed2associated_genes.py": 1, "bed2bedGraph.pl": 1, @@ -6595,10 +6595,10 @@ "bedGraphPack": 1, "bedGraphToBigWig": 18, "bedSort": 2, - "bedToBam": 274, + "bedToBam": 275, "bedToBigBed": 18, "bedToGenePred": 6, - "bedToIgv": 274, + "bedToIgv": 275, "bed_bigwig_profile.py": 59, "bed_build_windows.py": 59, "bed_complement.py": 59, @@ -6621,7 +6621,7 @@ "bedextract-megarow": 14, "bedextract-typical": 14, "bedgovcf": 1, - "bedgraph2wig.pl": 14, + "bedgraph2wig.pl": 15, "bedgraphtobigwig": 1, "bedmap": 14, "bedmap-float128": 14, @@ -6633,12 +6633,12 @@ "bedops-typical": 14, "bedoverlap": 1, "bedparse": 2, - "bedpeToBam": 274, + "bedpeToBam": 275, "bedpeToBam.py": 1, "bedpeToBed12.py": 1, "bedtk": 2, "bedtobigbed": 1, - "bedtools": 274, + "bedtools": 275, "bedutils": 1, "bedx-to-bedy": 3, "beeline": 6, @@ -6664,7 +6664,7 @@ "beta_diversity.py": 4, "beta_diversity_through_plots.py": 1, "beta_significance.py": 1, - "between-two-genes": 303, + "between-two-genes": 304, "bf.sh": 1, "bfc": 1, "bfconvert": 1, @@ -6679,7 +6679,7 @@ "bgenFileInfo": 1, "bgenix": 1, "bgreat": 4, - "bgzip": 714, + "bgzip": 716, "bgzip.pl": 4, "bgziptabix": 31, "bialign.py": 1, @@ -6845,7 +6845,7 @@ "bl-pileup-stats": 1, "bl-randomize": 1, "bl-threshold": 1, - "bl2seq": 34, + "bl2seq": 35, "bl2seq_unit_test": 5, "black": 11, "black-hole": 2, @@ -6864,7 +6864,7 @@ "blast2lca": 1, "blast2rma": 1, "blast2sam": 1, - "blast2sam.pl": 517, + "blast2sam.pl": 519, "blastMapAnalyzer2.pl": 1, "blastMining": 1, "blastMining_lca.sh": 1, @@ -6874,7 +6874,7 @@ "blast_check_pair.pl": 1, "blast_filter.pl": 1, "blast_format_unit_test": 5, - "blast_formatter": 337, + "blast_formatter": 338, "blast_names_mapping.tsv": 1, "blast_outfmt6_replace_trans_id_w_gene_symbol.pl": 1, "blast_report": 21, @@ -6885,16 +6885,16 @@ "blast_to_link.sh": 1, "blast_unit_test": 5, "blast_wrapper.py": 1, - "blastall": 34, + "blastall": 35, "blastbesties": 1, "blastcl3": 1, - "blastclust": 34, - "blastdb_aliastool": 337, + "blastclust": 35, + "blastdb_aliastool": 338, "blastdb_convert": 21, "blastdb_format_unit_test": 5, "blastdb_path": 21, - "blastdbcheck": 337, - "blastdbcmd": 337, + "blastdbcheck": 338, + "blastdbcmd": 338, "blastdbcp": 55, "blastdiag_unit_test": 5, "blastengine_unit_test": 5, @@ -6902,38 +6902,38 @@ "blastfilter_unit_test": 5, "blasthits_unit_test": 5, "blastinput_unit_test": 5, - "blastn": 337, - "blastn_vdb": 50, + "blastn": 338, + "blastn_vdb": 51, "blastoptions_unit_test": 5, - "blastp": 337, - "blastpgp": 34, + "blastp": 338, + "blastpgp": 35, "blastsetup_unit_test": 5, - "blastx": 337, + "blastx": 338, "blastzWrapper": 1, "blat": 19, - "blat2gbrowse.pl": 14, + "blat2gbrowse.pl": 15, "blat2gtf.pl": 5, - "blat2hints.pl": 14, + "blat2hints.pl": 15, "blat2nucmer": 2, "blaze": 1, "blend": 1, "bleties": 1, "blobtools": 2, "blobtools-build_nodesdb": 2, - "block2prfl.pl": 14, + "block2prfl.pl": 15, "blockbuster.x": 3, "blockclust": 1, "blockclust.py": 1, "blockclust_plot.r": 1, "blocksplit": 1, "bloom_query": 1, - "bloomfilter.sh": 29, - "bloomfilterparser.sh": 9, + "bloomfilter.sh": 30, + "bloomfilterparser.sh": 10, "blossom5": 1, "blossom_randGraph.py": 1, "blosum62.fas": 2, - "blst2gm": 27, - "blst2tkns": 215, + "blst2gm": 28, + "blst2tkns": 216, "bmaToLinks.pl": 1, "bmfilter": 4, "bmge": 1, @@ -6987,7 +6987,7 @@ "bowtie2-inspect-l": 114, "bowtie2-inspect-s": 114, "bowtie2_stuff.py": 2, - "bowtie2sam.pl": 517, + "bowtie2sam.pl": 519, "bowtie_PE_separate_then_join.pl": 1, "bowtie_mapper.sh": 1, "box": 1, @@ -6995,12 +6995,12 @@ "boxplot_ng": 1, "bp": 2, "bp-analyze": 1, - "bp_aacomp": 52, + "bp_aacomp": 53, "bp_aacomp.pl": 73, "bp_biofetch_genbank_proxy.pl": 73, - "bp_bioflat_index": 52, + "bp_bioflat_index": 53, "bp_bioflat_index.pl": 73, - "bp_biogetseq": 52, + "bp_biogetseq": 53, "bp_biogetseq.pl": 73, "bp_blast2tree.pl": 73, "bp_bulk_load_gff.pl": 73, @@ -7008,107 +7008,107 @@ "bp_classify_hits_kingdom.pl": 73, "bp_composite_LD.pl": 73, "bp_das_server.pl": 73, - "bp_dbsplit": 52, + "bp_dbsplit": 53, "bp_dbsplit.pl": 73, "bp_download_query_genbank.pl": 73, "bp_einfo": 3, "bp_export_proteins.py": 1, "bp_export_tags.py": 1, - "bp_extract_feature_seq": 52, + "bp_extract_feature_seq": 53, "bp_extract_feature_seq.pl": 73, "bp_fast_load_gff.pl": 73, "bp_fasta_prepare.py": 1, - "bp_fastam9_to_table": 52, + "bp_fastam9_to_table": 53, "bp_fastam9_to_table.pl": 73, - "bp_fetch": 52, + "bp_fetch": 53, "bp_fetch.pl": 73, - "bp_filter_search": 52, + "bp_filter_search": 53, "bp_filter_search.pl": 73, - "bp_find-blast-matches": 52, + "bp_find-blast-matches": 53, "bp_find-blast-matches.pl": 51, "bp_flanks.pl": 73, - "bp_gccalc": 52, + "bp_gccalc": 53, "bp_gccalc.pl": 73, "bp_genbank2gff.pl": 73, - "bp_genbank2gff3": 52, + "bp_genbank2gff3": 53, "bp_genbank2gff3.pl": 73, "bp_genbank_ref_extractor": 3, "bp_generate_histogram.pl": 73, "bp_heterogeneity_test.pl": 73, "bp_hivq.pl": 73, - "bp_hmmer_to_table.pl": 98, - "bp_index": 52, + "bp_hmmer_to_table.pl": 99, + "bp_index": 53, "bp_index.pl": 73, "bp_load_gff.pl": 73, - "bp_local_taxonomydb_query": 52, + "bp_local_taxonomydb_query": 53, "bp_local_taxonomydb_query.pl": 73, - "bp_make_mrna_protein": 52, + "bp_make_mrna_protein": 53, "bp_make_mrna_protein.pl": 73, "bp_mapped_tags.py": 1, - "bp_mask_by_search": 52, + "bp_mask_by_search": 53, "bp_mask_by_search.pl": 73, "bp_meta_gff.pl": 73, - "bp_mrtrans": 52, + "bp_mrtrans": 53, "bp_mrtrans.pl": 73, - "bp_mutate": 52, + "bp_mutate": 53, "bp_mutate.pl": 73, "bp_netinstall.pl": 73, - "bp_nexus2nh": 52, + "bp_nexus2nh": 53, "bp_nexus2nh.pl": 73, - "bp_nrdb": 52, + "bp_nrdb": 53, "bp_nrdb.pl": 73, - "bp_oligo_count": 52, + "bp_oligo_count": 53, "bp_oligo_count.pl": 73, - "bp_pairwise_kaks": 66, + "bp_pairwise_kaks": 67, "bp_pairwise_kaks.pl": 22, - "bp_parse_hmmsearch.pl": 98, + "bp_parse_hmmsearch.pl": 99, "bp_parse_tags.py": 1, - "bp_process_gadfly": 52, + "bp_process_gadfly": 53, "bp_process_gadfly.pl": 73, - "bp_process_sgd": 52, + "bp_process_sgd": 53, "bp_process_sgd.pl": 73, "bp_process_wormbase.pl": 73, "bp_query_entrez_taxa.pl": 73, "bp_remote_blast.pl": 76, - "bp_revtrans-motif": 52, + "bp_revtrans-motif": 53, "bp_revtrans-motif.pl": 73, "bp_search2BSML.pl": 22, - "bp_search2alnblocks": 52, + "bp_search2alnblocks": 53, "bp_search2alnblocks.pl": 73, - "bp_search2gff": 52, + "bp_search2gff": 53, "bp_search2gff.pl": 73, - "bp_search2table": 52, + "bp_search2table": 53, "bp_search2table.pl": 73, - "bp_search2tribe": 52, + "bp_search2tribe": 53, "bp_search2tribe.pl": 73, - "bp_seq_length": 52, + "bp_seq_length": 53, "bp_seq_length.pl": 73, - "bp_seqconvert": 52, + "bp_seqconvert": 53, "bp_seqconvert.pl": 73, - "bp_seqcut": 52, + "bp_seqcut": 53, "bp_seqcut.pl": 73, "bp_seqfeature_delete.pl": 73, "bp_seqfeature_gff3.pl": 73, "bp_seqfeature_load.pl": 73, - "bp_seqpart": 52, + "bp_seqpart": 53, "bp_seqpart.pl": 73, - "bp_seqret": 52, + "bp_seqret": 53, "bp_seqret.pl": 73, - "bp_seqretsplit": 52, + "bp_seqretsplit": 53, "bp_seqretsplit.pl": 73, - "bp_split_seq": 52, + "bp_split_seq": 53, "bp_split_seq.pl": 73, - "bp_sreformat": 52, + "bp_sreformat": 53, "bp_sreformat.pl": 73, - "bp_taxid4species": 52, + "bp_taxid4species": 53, "bp_taxid4species.pl": 73, - "bp_taxonomy2tree": 52, + "bp_taxonomy2tree": 53, "bp_taxonomy2tree.pl": 73, - "bp_translate_seq": 52, + "bp_translate_seq": 53, "bp_translate_seq.pl": 73, - "bp_tree2pag": 52, + "bp_tree2pag": 53, "bp_tree2pag.pl": 73, - "bp_unflatten_seq": 52, + "bp_unflatten_seq": 53, "bp_unflatten_seq.pl": 73, "bpcomp": 1, "bpipe": 4, @@ -7151,7 +7151,7 @@ "broad_utils.py": 1, "brockman_pipeline": 1, "brooklyn_plot": 1, - "brotli": 434, + "brotli": 435, "browse": 18, "bs_call": 2, "bs_seeker2-align.py": 1, @@ -7166,7 +7166,7 @@ "bseqc2": 4, "bseqc2mbiasplot.R": 4, "bsmap": 5, - "bsmp2info": 7, + "bsmp2info": 8, "bsp2sam.py": 1, "bsrate": 1, "bsseeker2bismark.pl": 1, @@ -7231,7 +7231,7 @@ "build_chr_gene_alignment_index.pl": 1, "build_database.py": 1, "build_db_functions.jl": 2, - "build_env_setup.sh": 253, + "build_env_setup.sh": 254, "build_fasta.smk": 1, "build_fusion_annot_db_index.pl": 1, "build_genomeBG": 2, @@ -7252,16 +7252,16 @@ "bundlelinks": 2, "bundler": 19, "bunwarpj": 4, - "bunzip2": 6676, + "bunzip2": 6681, "burden_test_vase": 1, "burst_linux_DB12": 1, "burst_linux_DB15": 1, - "busco": 2, + "busco": 3, "busco_configurator.py": 1, "buscolite": 1, "bustools": 2, "bvop": 1, - "bwa": 168, + "bwa": 169, "bwa-mem2": 7, "bwa-mem2.avx": 7, "bwa-mem2.avx2": 7, @@ -7303,16 +7303,16 @@ "bxStats.py": 1, "bxcl_seqqc": 1, "bxtools": 1, - "bzcat": 6676, - "bzcmp": 6676, - "bzdiff": 6676, - "bzegrep": 6676, - "bzfgrep": 6676, - "bzgrep": 6676, - "bzip2": 6676, - "bzip2recover": 6676, - "bzless": 6676, - "bzmore": 6676, + "bzcat": 6681, + "bzcmp": 6681, + "bzdiff": 6681, + "bzegrep": 6681, + "bzfgrep": 6681, + "bzgrep": 6681, + "bzip2": 6681, + "bzip2recover": 6681, + "bzless": 6681, + "bzmore": 6681, "c++": 5, "c++filt": 8, "c-index-test": 8, @@ -7329,7 +7329,7 @@ "cPecanLibTests": 1, "cPecanModifyHmm": 1, "cPecanRealign": 1, - "c_rehash": 7823, + "c_rehash": 7828, "ca2ace.pl": 3, "ca2ctg": 2, "ca2mates": 2, @@ -7403,7 +7403,7 @@ "cage-classify.py": 1, "cagee": 1, "cai": 26, - "cairo-trace": 5140, + "cairo-trace": 5142, "cairosvg": 6, "cal": 13, "calD": 1, @@ -7416,10 +7416,10 @@ "calc_prob.py": 1, "calc_probe_hit_from_sam.py": 1, "calcdatarange": 2, - "calcmem.sh": 30, + "calcmem.sh": 31, "calcprobs.py": 1, "calcs": 1, - "calctruequality.sh": 30, + "calctruequality.sh": 31, "calculAllelicBalance.sh": 1, "calculate-bed-overlap": 1, "calculate-cnv": 1, @@ -7462,13 +7462,13 @@ "call_program.py": 1, "call_sbatch.py": 1, "callerpp": 1, - "callgenes.sh": 29, + "callgenes.sh": 30, "calling_functions.jl": 2, "callingcardstools": 1, - "callpeaks.sh": 30, + "callpeaks.sh": 31, "callstate": 1, - "callvariants.sh": 30, - "callvariants2.sh": 30, + "callvariants.sh": 31, + "callvariants2.sh": 31, "cameo": 4, "camlhmp": 2, "camlhmp-blast": 1, @@ -7507,7 +7507,7 @@ "capnpc-capnp": 56, "capnpc-cython": 1, "capri_eval": 1, - "captoinfo": 7755, + "captoinfo": 7760, "captus_assembly": 1, "caqc.pl": 3, "caqc_help.ini": 3, @@ -7626,22 +7626,22 @@ "ccsmeth": 1, "cct": 41, "cctk": 1, - "cd-hit": 46, - "cd-hit-2d": 46, - "cd-hit-2d-para.pl": 46, - "cd-hit-454": 46, - "cd-hit-clstr_2_blm8.pl": 45, - "cd-hit-div": 46, - "cd-hit-div.pl": 46, + "cd-hit": 47, + "cd-hit-2d": 47, + "cd-hit-2d-para.pl": 47, + "cd-hit-454": 47, + "cd-hit-clstr_2_blm8.pl": 46, + "cd-hit-div": 47, + "cd-hit-div.pl": 47, "cd-hit-dup": 1, - "cd-hit-est": 47, - "cd-hit-est-2d": 46, + "cd-hit-est": 48, + "cd-hit-est-2d": 47, "cd-hit-lap": 1, - "cd-hit-para.pl": 46, + "cd-hit-para.pl": 47, "cda2dcm": 1, - "cdbfasta": 12, + "cdbfasta": 13, "cdbg-ops": 1, - "cdbyank": 12, + "cdbyank": 13, "cdhit-compare": 1, "cdhit-parser": 1, "cdhit_cluster.sh": 1, @@ -7656,7 +7656,7 @@ "cdscan": 1, "ceas": 2, "ceasBW": 1, - "cegma2gff.pl": 14, + "cegma2gff.pl": 15, "cegma2zff": 1, "ceinutil.py": 6, "celery": 4, @@ -7788,10 +7788,10 @@ "checkFlowframe.R": 1, "checkHierarchy.py": 1, "checkNUCmer.pl": 1, - "checkParamArchive.pl": 14, + "checkParamArchive.pl": 15, "checkPeakFile.pl": 5, "checkTagBias.pl": 5, - "checkUTR": 14, + "checkUTR": 15, "check_BDBHs.pl": 1, "check_all_snv": 1, "check_all_snv_dir": 1, @@ -7863,7 +7863,7 @@ "chexalign": 1, "chexmix": 1, "chgrp": 84, - "chi2": 69, + "chi2": 70, "chimChe": 3, "chimera": 3, "chimerascan-exclude-transcriptome-events": 2, @@ -7901,7 +7901,7 @@ "chown": 84, "chroder": 1, "chromRegionLength.r": 1, - "chrom_sizes.pl": 89, + "chrom_sizes.pl": 90, "chromap": 1, "chromatiblock": 1, "chromograph": 1, @@ -7945,10 +7945,10 @@ "circulocov": 1, "cirdna": 25, "cirtap": 1, - "cit2pmid": 27, + "cit2pmid": 28, "civicpy": 1, "cjk-gs-integrate": 1, - "cjpeg": 5786, + "cjpeg": 5789, "ckeygen": 1, "cksum": 84, "claMLST": 1, @@ -8041,7 +8041,7 @@ "clean": 1, "clean-hairpins": 1, "cleanAtac": 3, - "cleanDOSfasta.pl": 14, + "cleanDOSfasta.pl": 15, "cleanMe.pl": 1, "cleanPolishes": 3, "cleanUpPeakFile.pl": 5, @@ -8055,11 +8055,11 @@ "cleanmap.awk": 1, "cleanme.pl": 1, "cleanpp.sh": 3, - "cleanup-blastdb-volumes.py": 264, + "cleanup-blastdb-volumes.py": 265, "cleanup-coverage.py": 2, "cleanup-stale-gcp-resources.py": 1, "cleanup.py": 1, - "clear": 7755, + "clear": 7760, "clearCNV": 1, "clearcut": 1, "cleric": 1, @@ -8109,54 +8109,54 @@ "closest-features-float128": 14, "closest-features-megarow": 14, "closest-features-typical": 14, - "closestBed": 274, + "closestBed": 275, "closest_residues": 1, "cloudgene.yaml": 1, "clove": 1, "clp": 104, "clsify": 1, - "clstr2tree.pl": 46, - "clstr2txt.pl": 46, - "clstr2xml.pl": 46, - "clstr_cut.pl": 46, - "clstr_list.pl": 45, - "clstr_list_sort.pl": 45, - "clstr_merge.pl": 46, - "clstr_merge_noorder.pl": 46, - "clstr_quality_eval.pl": 46, - "clstr_quality_eval_by_link.pl": 46, - "clstr_reduce.pl": 46, - "clstr_renumber.pl": 46, - "clstr_rep.pl": 46, - "clstr_reps_faa_rev.pl": 46, - "clstr_rev.pl": 46, - "clstr_select.pl": 46, - "clstr_select_rep.pl": 46, - "clstr_size_histogram.pl": 46, - "clstr_size_stat.pl": 46, - "clstr_sort_by.pl": 46, - "clstr_sort_prot_by.pl": 46, - "clstr_sql_tbl.pl": 46, - "clstr_sql_tbl_sort.pl": 46, + "clstr2tree.pl": 47, + "clstr2txt.pl": 47, + "clstr2xml.pl": 47, + "clstr_cut.pl": 47, + "clstr_list.pl": 46, + "clstr_list_sort.pl": 46, + "clstr_merge.pl": 47, + "clstr_merge_noorder.pl": 47, + "clstr_quality_eval.pl": 47, + "clstr_quality_eval_by_link.pl": 47, + "clstr_reduce.pl": 47, + "clstr_renumber.pl": 47, + "clstr_rep.pl": 47, + "clstr_reps_faa_rev.pl": 47, + "clstr_rev.pl": 47, + "clstr_select.pl": 47, + "clstr_select_rep.pl": 47, + "clstr_size_histogram.pl": 47, + "clstr_size_stat.pl": 47, + "clstr_sort_by.pl": 47, + "clstr_sort_prot_by.pl": 47, + "clstr_sql_tbl.pl": 47, + "clstr_sql_tbl_sort.pl": 47, "clumpMaker": 3, - "clumpify.sh": 30, + "clumpify.sh": 31, "clust": 1, "clust-greedy": 1, "clust-mst": 1, "clust_fcc": 1, "clustal2link": 2, "clustal_to_alma.py": 1, - "clustalo": 31, - "clustalw": 76, - "clustalw2": 77, + "clustalo": 32, + "clustalw": 77, + "clustalw2": 78, "clustalw2fasta": 13, "clustalw2phylip": 13, "cluster": 204, "cluster-picker": 2, "cluster2bed.pl": 5, "cluster2bedgraph.pl": 5, - "clusterAndSplitGenes.pl": 14, - "clusterBed": 274, + "clusterAndSplitGenes.pl": 15, + "clusterBed": 275, "clusterGenes": 1, "clusterHeatmap.R": 1, "clusterSnps": 2, @@ -8182,20 +8182,20 @@ "clxdo": 24, "cmake": 11, "cmake_install.cmake": 1, - "cmalign": 56, + "cmalign": 57, "cmaple": 1, "cmaple-aa": 1, "cmark": 54, "cmasker": 1, "cmat": 1, - "cmbuild": 56, - "cmcalibrate": 56, - "cmconvert": 56, + "cmbuild": 57, + "cmcalibrate": 57, + "cmconvert": 57, "cmd.py": 1, "cmdstan_model": 2, - "cmemit": 56, + "cmemit": 57, "cmetindex": 11, - "cmfetch": 56, + "cmfetch": 57, "cmfinder": 1, "cmfinder.pl": 1, "cmfinder04": 1, @@ -8203,7 +8203,7 @@ "cmip": 2, "cmp": 1, "cmp_bed.py": 1, - "cmpfillin": 58, + "cmpfillin": 59, "cmpgenome": 1, "cmpgenome_combine_snp": 1, "cmpgenome_dir": 1, @@ -8216,15 +8216,15 @@ "cmph": 1, "cmph5tools.py": 2, "cmpr.pl": 2, - "cmpress": 56, - "cmscan": 56, + "cmpress": 57, + "cmscan": 57, "cmsd": 1, - "cmsearch": 56, + "cmsearch": 57, "cmsearch-deoverlap.pl": 1, "cmsearchToBed": 1, "cmsearchToBed-bin": 1, "cmsip": 1, - "cmstat": 56, + "cmstat": 57, "cmtime": 24, "cnasim": 1, "cnitool": 4, @@ -8259,7 +8259,7 @@ "codcmp": 25, "codcopy": 25, "codecov": 2, - "codeml": 69, + "codeml": 70, "coderet": 25, "codes_bufr_filter": 1, "codes_count": 1, @@ -8325,7 +8325,7 @@ "combine": 4, "combine-assembled-files.sh": 1, "combine-subexons": 1, - "combine-uid-lists": 27, + "combine-uid-lists": 28, "combineAndAnnotateReferences.pl": 1, "combineFile": 2, "combineFragandDBGraph_fastg.py": 1, @@ -8367,7 +8367,7 @@ "common.go": 14, "common_errors_from_bam": 1, "common_functions.py": 2, - "commonkmers.sh": 30, + "commonkmers.sh": 31, "community": 6, "compPlot.Rmd": 1, "compRatio.R": 1, @@ -8403,7 +8403,7 @@ "compare_gff3_to_chado": 1, "compare_gos.py": 9, "compare_intervals_exact.pl": 2, - "compare_masking.pl": 11, + "compare_masking.pl": 12, "compare_miso": 1, "compare_motif.pl": 1, "compare_predictions_to_phages.py": 2, @@ -8414,24 +8414,24 @@ "compare_trajectories.py": 1, "compare_vcfs": 1, "comparecounts.py": 1, - "comparegff.sh": 29, + "comparegff.sh": 30, "comparem": 1, "comparem2": 1, - "comparesketch.sh": 30, - "comparessu.sh": 27, - "comparevcf.sh": 30, + "comparesketch.sh": 31, + "comparessu.sh": 28, + "comparevcf.sh": 31, "comparison.sh": 1, "compile-et.pl": 43, "compile-rpbp-models": 2, "compile.bat": 22, "compile.make": 22, - "compileSpliceCands": 12, + "compileSpliceCands": 13, "compile_STARE_Linux.sh": 1, "compile_STARE_macOS.sh": 1, - "compile_et": 5833, + "compile_et": 5837, "compiled_table.py": 1, "compleasm": 1, - "complementBed": 274, + "complementBed": 275, "complete-ant-cmd.pl": 1, "complete_locus": 1, "completion.bash": 1, @@ -8454,7 +8454,7 @@ "compute-prior-dist": 13, "compute-uniform-priors": 13, "computeCoverageStat": 3, - "computeFlankingRegion.pl": 12, + "computeFlankingRegion.pl": 13, "computeGCBias": 11, "computeMatrix": 11, "computeMatrixOperations": 11, @@ -8504,7 +8504,7 @@ "conda-skeleton": 3, "conda-verify": 1, "conda2solv": 24, - "conda_build.sh": 270, + "conda_build.sh": 271, "condenseBedGraph.pl": 5, "condense_workflow.py": 1, "condiga": 1, @@ -8519,7 +8519,7 @@ "config.py": 1, "config.sh": 1, "configManta.py": 1, - "config_data": 64, + "config_data": 65, "config_parser.py": 1, "configure": 1, "configureESTmapper.pl": 3, @@ -8542,12 +8542,12 @@ "cons2fasta.pl": 5, "consEntropy": 2, "consambig": 25, - "consect.sh": 30, + "consect.sh": 31, "consel": 1, "consense": 10, "consensus": 4, "consensus.py": 8, - "consensus.sh": 29, + "consensus.sh": 30, "consensus.smk": 1, "consensus_aDNA.py": 7, "consensus_tree.py": 1, @@ -8600,11 +8600,11 @@ "conv-template": 17, "convbkmk": 1, "convert": 76, - "convert-caffe2-to-onnx": 44, + "convert-caffe2-to-onnx": 45, "convert-ccds-to-bed": 3, "convert-fasta-to-v2.pl": 3, "convert-mirdeep2-fasta.py": 1, - "convert-onnx-to-caffe2": 44, + "convert-onnx-to-caffe2": 45, "convert-readcount-file.py": 1, "convert-regions": 2, "convert-sam-for-rsem": 1, @@ -8612,7 +8612,7 @@ "convert2bed-float128": 14, "convert2bed-megarow": 14, "convert2bed-typical": 14, - "convert2blastmask": 337, + "convert2blastmask": 338, "convert2snns": 2, "convertCoordinates.pl": 5, "convertFastaQualToFastQ.rb": 1, @@ -8726,13 +8726,13 @@ "copycat.3.0.0": 2, "copyfile.sh": 1, "copylink": 1, - "copymat": 34, + "copymat": 35, "coral": 1, "core-only.pl": 1, "core_diversity_analyses.py": 1, "core_methods.py": 1, "core_overlap_plot.py": 1, - "corelist": 1711, + "corelist": 1713, "corepack": 12, "coreprocess.pl": 3, "coresnpfilter": 1, @@ -8792,14 +8792,14 @@ "count_seq": 1, "count_seqs.py": 1, "count_table_fields.pl": 1, - "countbarcodes.sh": 30, + "countbarcodes.sh": 31, "countbarcodes2.sh": 1, "countduplicates.sh": 1, "counterr": 1, - "countgc.sh": 30, + "countgc.sh": 31, "counts_in_region": 3, "countsam": 1, - "countsharedlines.sh": 30, + "countsharedlines.sh": 31, "cov.R": 1, "cov2lr.pl": 1, "covToWig.py": 1, @@ -8815,7 +8815,7 @@ "coverage.py": 1, "coverage2cytosine": 2, "coverage3": 2, - "coverageBed": 274, + "coverageBed": 275, "coverage_estimator.py": 1, "coverage_from_bam": 1, "coverage_from_fastx": 1, @@ -8839,9 +8839,9 @@ "cp2k_run": 1, "cp2k_shell.ssmp": 1, "cpack": 11, - "cpan": 1711, + "cpan": 1713, "cpancover": 6, - "cpanm": 244, + "cpanm": 245, "cpat.py": 1, "cpeinutil.py": 6, "cpgcdifenrich": 1, @@ -8901,7 +8901,7 @@ "create-orf-profiles": 2, "create-priors": 13, "create-read-length-orf-profiles": 2, - "createAugustusJoblist.pl": 14, + "createAugustusJoblist.pl": 15, "createBackboneMFA": 4, "createChargeFile.pl": 2, "createChemistryHeader.py": 1, @@ -8926,7 +8926,7 @@ "create_custom_transcriptome_fa.pl": 1, "create_data": 1, "create_datauri": 2, - "create_dbs.py": 3, + "create_dbs.py": 4, "create_edge_matrix.py": 1, "create_end_pairs.perl": 1, "create_end_pairs.pl": 1, @@ -8988,8 +8988,8 @@ "croo": 1, "crossEntropy": 1, "crossSampleOverview.py": 1, - "crossblock.sh": 30, - "crosscontaminate.sh": 30, + "crossblock.sh": 31, + "crosscontaminate.sh": 31, "crossmap": 3, "crossrates.pl": 2, "crosstable_gene_ids": 1, @@ -9035,7 +9035,7 @@ "csv2rdf": 33, "csv2tsv": 1, "csv2xlsx": 1, - "csv2xml": 215, + "csv2xml": 216, "csvExtractBorders": 1, "csvFrags2text": 1, "csv_to_tsv": 1, @@ -9043,7 +9043,7 @@ "ct-energy": 3, "ct-ng.config": 1, "ct2bp": 1, - "ct2db": 52, + "ct2db": 53, "ct2dot": 5, "ct2rnaml": 3, "ct_boxplot_ng": 1, @@ -9075,7 +9075,7 @@ "cuffquant": 2, "cuppa": 1, "cuppa-chart": 1, - "cups-config": 199, + "cups-config": 201, "curare": 1, "curare_wizard": 1, "curate_chemical_data": 1, @@ -9083,8 +9083,8 @@ "curate_spatial_data": 1, "curate_universe": 1, "curesim": 2, - "curl": 5123, - "curl-config": 5945, + "curl": 5124, + "curl-config": 5948, "curlywhirly": 1, "curve_keygen": 70, "cusp": 25, @@ -9104,11 +9104,11 @@ "cutadapt": 36, "cuteSV": 2, "cutgextract": 25, - "cutgff.sh": 29, + "cutgff.sh": 30, "cutoff.r": 1, "cutoff.r.bak": 1, "cutot": 1, - "cutprimers.sh": 30, + "cutprimers.sh": 31, "cutqc": 1, "cutseq": 25, "cuttlefish": 2, @@ -9234,7 +9234,7 @@ "datasets": 3, "datasets-cli": 2, "datashader": 1, - "datatool": 337, + "datatool": 338, "datavzrd": 2, "date": 84, "datma.py": 1, @@ -9258,23 +9258,23 @@ "db2search": 2, "dbSNP_idx": 2, "dbTestScript": 1, - "db_archive": 123, - "db_checkpoint": 123, - "db_convert": 101, - "db_deadlock": 123, - "db_dump": 123, + "db_archive": 124, + "db_checkpoint": 124, + "db_convert": 102, + "db_deadlock": 124, + "db_dump": 124, "db_exclude.locs.tsv": 1, "db_graph.jl": 2, - "db_hotbackup": 123, - "db_load": 123, - "db_log_verify": 123, - "db_printlog": 123, - "db_recover": 123, - "db_replicate": 123, - "db_stat": 123, - "db_tuner": 123, - "db_upgrade": 123, - "db_verify": 123, + "db_hotbackup": 124, + "db_load": 124, + "db_log_verify": 124, + "db_printlog": 124, + "db_recover": 124, + "db_replicate": 124, + "db_stat": 124, + "db_tuner": 124, + "db_upgrade": 124, + "db_verify": 124, "dba": 3, "dbcanLight": 1, "dbcanLight-hmmparser": 1, @@ -9287,9 +9287,9 @@ "dbifasta": 25, "dbiflat": 25, "dbigcg": 25, - "dbilogstrip": 112, - "dbiprof": 112, - "dbiproxy": 112, + "dbilogstrip": 113, + "dbiprof": 113, + "dbiproxy": 113, "dbkit_create.py": 1, "dbkit_extract.py": 1, "dbkit_merge.py": 1, @@ -9416,7 +9416,7 @@ "decode_sam_flag": 1, "decompose": 1, "decompose.py": 2, - "decontaminate.sh": 30, + "decontaminate.sh": 31, "decorate": 1, "decoyFASTA": 2, "decoyFastaGenerator.pl": 2, @@ -9424,9 +9424,9 @@ "dedup": 1, "dedupDiscordantsMultiPass.py": 1, "dedup_FLNC_per_cluster.py": 1, - "dedupe.sh": 30, - "dedupe2.sh": 30, - "dedupebymapping.sh": 30, + "dedupe.sh": 31, + "dedupe2.sh": 31, + "dedupebymapping.sh": 31, "deduplicate": 3, "deduplicate.py": 1, "deduplicate_bismark": 2, @@ -9461,7 +9461,7 @@ "dehomopolymerate": 1, "deinterleave_fastq.sh": 2, "del01_delete_db_entries.py": 1, - "del_from_prfl.pl": 14, + "del_from_prfl.pl": 15, "del_parse.py": 1, "delaunay": 144, "deldup": 1, @@ -9476,7 +9476,7 @@ "deltaBS.pl": 1, "delta_filter_wrapper.py": 5, "delta_unit_test": 5, - "deltablast": 337, + "deltablast": 338, "deltapd": 1, "demes": 5, "demesdraw": 1, @@ -9498,12 +9498,12 @@ "demux_isoseq2_no_genome.py": 1, "demux_isoseq_no_genome.py": 1, "demux_isoseq_with_genome.py": 1, - "demuxbyname.sh": 30, + "demuxbyname.sh": 31, "demuxbyname2.sh": 3, "demuxlet": 1, "dendro.R": 1, "dendrogram": 1, - "dendropy-format": 50, + "dendropy-format": 51, "deno": 1, "denoise_wrapper.py": 1, "denoiser.py": 1, @@ -9518,7 +9518,7 @@ "denovo_static.py": 1, "densitree": 1, "density": 25, - "depinfo": 7, + "depinfo": 8, "depot": 1, "deprecated_decorator.py": 1, "depth.py": 1, @@ -9527,7 +9527,7 @@ "depth_calc.py": 1, "depth_estim_from_vcf.sh": 1, "depythontex": 1, - "derb": 5862, + "derb": 5866, "derep_stuff.py": 2, "deripcal": 1, "derna": 1, @@ -9601,7 +9601,7 @@ "diagtool": 4, "dialign-tx": 6, "dialign2-2": 3, - "diamond": 101, + "diamond": 102, "diamond_alignment.sh": 1, "diamond_makedb.sh": 1, "dicey": 1, @@ -9613,7 +9613,7 @@ "diff_iso_usage": 1, "diff_motif": 1, "diffacto": 1, - "difference-uid-lists": 27, + "difference-uid-lists": 28, "difference_from_first_TSS_script_mordor.r": 1, "difference_from_first_TSS_script_mordor_chrom_wide.r": 1, "differentialBindingAffinity_multipleSNPs": 1, @@ -9652,7 +9652,7 @@ "dirmngr-client": 2, "dirname": 84, "dirseq": 2, - "disambiguate-nucleotides": 215, + "disambiguate-nucleotides": 216, "disco": 17, "disco.cfg": 1, "disco_2.cfg": 1, @@ -9660,7 +9660,7 @@ "discrete": 2, "discrete-mi": 4, "disentangle_organelle_assembly.py": 1, - "diskbench.sh": 30, + "diskbench.sh": 31, "dispatch_srvr": 3, "display": 75, "display_rate_matrix": 2, @@ -9693,7 +9693,7 @@ "django-admin": 4, "django-admin.py": 3, "django-admin.pyc": 1, - "djpeg": 5786, + "djpeg": 5789, "dkfzbiasfilter.py": 1, "dkfzbiasfilter_summarize.py": 1, "dlcoal_to_dlcpar": 1, @@ -9804,15 +9804,15 @@ "download-db.sh": 9, "download-dfam.py": 1, "download-entities.pl": 2, - "download-ncbi-data": 288, + "download-ncbi-data": 289, "download-ncbi-genomes": 1, - "download-ncbi-software": 215, + "download-ncbi-software": 216, "download-ncbi-taxa.sh": 1, "download-ncbi-taxmaps": 1, "download-ncbi-taxonomy": 1, - "download-pmc": 27, - "download-pubmed": 302, - "download-sequence": 302, + "download-pmc": 28, + "download-pubmed": 303, + "download-sequence": 303, "download-spatypes.sh": 1, "download-srr-files": 3, "download-taxonomy.sh": 1, @@ -9828,7 +9828,7 @@ "download_behst_data.sh": 1, "download_chromhmm_data.sh": 1, "download_database.sh": 1, - "download_eggnog_data.py": 3, + "download_eggnog_data.py": 4, "download_fasta_database": 1, "download_generate_bberg_ref_files.pl": 1, "download_genomes_ncbi.pl": 1, @@ -9913,7 +9913,7 @@ "drtext": 25, "drttest": 1, "drugbank": 1, - "ds2pme": 27, + "ds2pme": 28, "dsCompareCurves": 1, "dsComputeBEDDensity": 1, "dsComputeGCCoverage": 1, @@ -10050,7 +10050,7 @@ "dupre": 1, "dupsifter": 1, "dust": 13, - "dustmasker": 337, + "dustmasker": 338, "dv_call_variants.py": 1, "dv_make_examples.py": 1, "dv_postprocess_variants.py": 1, @@ -10114,7 +10114,7 @@ "eaddress": 88, "eagle": 1, "earlGrey": 1, - "easel": 154, + "easel": 155, "easy-fuse": 1, "easy.py": 1, "easy_install": 1727, @@ -10139,7 +10139,7 @@ "ecodbtaxstat": 1, "ecofind": 1, "ecogrep": 1, - "ecommon.sh": 215, + "ecommon.sh": 216, "econtact": 88, "ecotag": 1, "ecotaxspecificity": 1, @@ -10175,9 +10175,9 @@ "edonr256-hash": 9, "edonr512-hash": 9, "eel": 1, - "efetch": 303, + "efetch": 304, "effectivet3": 1, - "efilter": 303, + "efilter": 304, "efishent": 1, "efn": 1, "efn2": 6, @@ -10193,8 +10193,8 @@ "eigenstrat_database_tools": 1, "eigenstrat_rename_snps": 1, "eigenstrat_snp_coverage": 1, - "einfo": 303, - "einsi": 105, + "einfo": 304, + "einsi": 106, "einverted": 25, "eject": 13, "eklipseHeader.png": 1, @@ -10222,7 +10222,7 @@ "elfedit": 8, "elgato_report.py": 1, "eliminateBadSuperReadsUsingList": 1, - "elink": 303, + "elink": 304, "elm2meme": 13, "elprep": 1, "elsize": 6, @@ -10232,7 +10232,7 @@ "email.sh": 1, "emailWhoever.pl": 1, "email_validator": 2, - "emapper.py": 3, + "emapper.py": 4, "embl-api-validator": 1, "embossdata": 25, "embossupdate": 25, @@ -10259,8 +10259,8 @@ "enano": 1, "enasearch": 1, "enc": 1, - "enc2xs": 1711, - "encguess": 1711, + "enc2xs": 1713, + "encguess": 1713, "encode2var": 1, "encode_dir": 1, "encode_exclude_loci": 1, @@ -10294,22 +10294,22 @@ "env": 84, "env-execute": 6843, "env.yml": 1, - "env_parallel": 104, - "env_parallel.ash": 104, - "env_parallel.bash": 104, - "env_parallel.csh": 104, - "env_parallel.dash": 104, - "env_parallel.fish": 104, - "env_parallel.ksh": 104, - "env_parallel.mksh": 104, - "env_parallel.pdksh": 104, - "env_parallel.sh": 104, - "env_parallel.tcsh": 104, - "env_parallel.zsh": 104, + "env_parallel": 105, + "env_parallel.ash": 105, + "env_parallel.bash": 105, + "env_parallel.csh": 105, + "env_parallel.dash": 105, + "env_parallel.fish": 105, + "env_parallel.ksh": 105, + "env_parallel.mksh": 105, + "env_parallel.pdksh": 105, + "env_parallel.sh": 105, + "env_parallel.tcsh": 105, + "env_parallel.zsh": 105, "environment.yml": 1, "envpath": 3, "envset.cmd": 1, - "envsubst": 5297, + "envsubst": 5298, "eoulsan.sh": 1, "epa-ng": 4, "epestfind": 25, @@ -10325,7 +10325,7 @@ "epimuller-define": 1, "epimuller-draw": 1, "epimuller-parse": 1, - "epost": 303, + "epost": 304, "eprimer3": 25, "eprimer32": 25, "eproxy": 88, @@ -10361,39 +10361,39 @@ "errorEstimate": 6, "error_corrected2frg": 1, "ervdetective": 1, - "esample": 288, + "esample": 289, "esbuild": 1, "esd2esi": 12, "esdcompat": 12, - "esearch": 303, + "esearch": 304, "esh": 1, "esimsa": 1, "eskrim": 1, - "esl-afetch": 171, + "esl-afetch": 172, "esl-alidepair.pl": 2, - "esl-alimanip": 169, - "esl-alimap": 169, - "esl-alimask": 169, - "esl-alimerge": 169, - "esl-alipid": 169, - "esl-alirev": 169, - "esl-alistat": 169, - "esl-compalign": 169, - "esl-compstruct": 169, - "esl-construct": 169, - "esl-histplot": 169, - "esl-mask": 169, - "esl-mixdchlet": 154, - "esl-reformat": 171, - "esl-selectn": 169, - "esl-seqrange": 169, - "esl-seqstat": 169, - "esl-sfetch": 169, - "esl-shuffle": 169, - "esl-ssdraw": 169, + "esl-alimanip": 170, + "esl-alimap": 170, + "esl-alimask": 170, + "esl-alimerge": 170, + "esl-alipid": 170, + "esl-alirev": 170, + "esl-alistat": 170, + "esl-compalign": 170, + "esl-compstruct": 170, + "esl-construct": 170, + "esl-histplot": 170, + "esl-mask": 170, + "esl-mixdchlet": 155, + "esl-reformat": 172, + "esl-selectn": 170, + "esl-seqrange": 170, + "esl-seqstat": 170, + "esl-sfetch": 170, + "esl-shuffle": 170, + "esl-ssdraw": 170, "esl-ssplit.pl": 2, - "esl-translate": 169, - "esl-weight": 169, + "esl-translate": 170, + "esl-weight": 170, "espell": 88, "espgen": 6, "espgen.py": 6, @@ -10410,7 +10410,7 @@ "est_abundance.py": 4, "est_depth": 1, "est_depth_dir": 1, - "estherfilter.sh": 30, + "estherfilter.sh": 31, "estimate-mer-threshold": 3, "estimate-metagene-profile-bayes-factors": 3, "estimate-orf-bayes-factors": 2, @@ -10427,25 +10427,26 @@ "estscan": 1, "estwise": 3, "estwisedb": 3, - "esummary": 303, + "esummary": 304, "esvee": 1, "etandem": 25, "ete": 2, "ete3": 61, "eternafold": 1, "etex": 1, - "etraining": 15, + "etraining": 16, "eufindtRNA": 14, "eugene.sh": 1, "eukcc": 1, "eutils-config": 1, "eva-sub-cli.py": 1, "eval.pl": 3, - "evalCGP.pl": 14, + "eval.py": 1, + "evalCGP.pl": 15, "eval_alignment.pl": 1, "eval_ann": 1, - "eval_dualdecomp.pl": 14, - "eval_multi_gtf.pl": 12, + "eval_dualdecomp.pl": 15, + "eval_multi_gtf.pl": 13, "eval_predictions": 2, "evaluate-sv-predictions": 2, "evaluate_assembly_using_mapping.py": 1, @@ -10467,7 +10468,7 @@ "eviplot.py": 1, "evol": 3, "evoluzer": 1, - "evolver": 69, + "evolver": 70, "exact-tandems": 57, "exactSNP": 6, "examine": 1, @@ -10483,7 +10484,7 @@ "excise_precursors.pl": 1, "excise_precursors_iterative_final.pl": 1, "excl_seqs": 2, - "exclude-uid-lists": 288, + "exclude-uid-lists": 289, "exclude_N": 1, "exclude_loci": 1, "exclude_loci_backup": 1, @@ -10493,7 +10494,7 @@ "exeSeq": 1, "exec-plugins.sh": 1, "exec_annotation": 2, - "executeTestCGP.py": 9, + "executeTestCGP.py": 10, "executor": 11, "exiftool": 1, "existDB": 5, @@ -10501,16 +10502,16 @@ "exon_utils": 1, "exonerate": 12, "exonerate-server": 12, - "exonerate2hints.pl": 14, + "exonerate2hints.pl": 15, "exoniphy": 2, - "exoniphyDb2hints.pl": 14, + "exoniphyDb2hints.pl": 15, "exonpairs": 2, "exp_up_ensg.pl": 7, "expam": 1, "expam_limit": 1, "expand": 84, - "expand-current": 288, - "expandCols": 274, + "expand-current": 289, + "expandCols": 275, "expand_fastq": 1, "expand_links.pl": 7, "expand_refseq_isoforms.pl": 1, @@ -10521,13 +10522,13 @@ "exploc_p": 4, "explode.py": 20, "explode_fasta.pl": 1, - "explodetree.sh": 30, + "explodetree.sh": 31, "explore_database.py": 1, "explore_thresholds": 1, "exporTPP.pl": 2, "export-itol.pl": 1, "export2graphlan.py": 1, - "export2sam.pl": 517, + "export2sam.pl": 519, "exportTools.sh": 1, "export_mitochondrial_contigs.py": 1, "export_norm_data": 1, @@ -10573,7 +10574,7 @@ "extract-sv-reads": 1, "extract-transcript-to-gene-map-from-trinity": 1, "extract.py": 1, - "extractAnno.py": 9, + "extractAnno.py": 10, "extractBCITrees": 4, "extractBK_bam.sh": 1, "extractBiG-SCAPEclusters.py": 1, @@ -10593,7 +10594,7 @@ "extractSoftclipped": 1, "extractSplitReads_BwaMem": 1, "extractSplitReads_BwaMem.py": 1, - "extractTranscriptEnds.pl": 14, + "extractTranscriptEnds.pl": 15, "extractUnmapped": 3, "extractUnmappedSubreads.py": 1, "extract_GO_assignments_from_Trinotate_xls.pl": 1, @@ -10689,7 +10690,7 @@ "ezez4makefile_v4.pl": 1, "ezez4qsub_vx1.pl": 1, "ezez_vx1.pl": 1, - "f2py": 2084, + "f2py": 2087, "f2py2": 135, "f2py2.7": 135, "f2py3": 1595, @@ -10725,7 +10726,7 @@ "faSize": 1, "faSplit": 1, "faToNib": 8, - "faToTwoBit": 34, + "faToTwoBit": 35, "faToVcf": 3, "fa_coords": 11, "fab": 2, @@ -10747,7 +10748,7 @@ "faithpd": 2, "fakealigner": 7, "faker": 2, - "faketime": 17, + "faketime": 18, "faketree": 7, "falco": 2, "falcon-bench": 4, @@ -10792,7 +10793,7 @@ "fast5_subset": 13, "fast5seek": 1, "fastANI": 27, - "fastBlockSearch": 15, + "fastBlockSearch": 16, "fastSimBac": 1, "fast_circ.py": 1, "fast_convert": 1, @@ -10815,7 +10816,7 @@ "fasta-most": 13, "fasta-nr": 4, "fasta-re-match": 8, - "fasta-sanitize.pl": 316, + "fasta-sanitize.pl": 318, "fasta-shuffle-letters": 13, "fasta-splitter": 1, "fasta-strip-identifier": 2, @@ -10852,7 +10853,7 @@ "fasta2tab.pl": 5, "fasta2upper": 1, "fasta36": 7, - "fastaFromBed": 274, + "fastaFromBed": 275, "fastaToCA": 3, "fastaToRead": 1, "fasta_base_content.py": 2, @@ -10898,7 +10899,7 @@ "fastachecksum": 12, "fastaclean": 13, "fastaclip": 12, - "fastacmd": 34, + "fastacmd": 35, "fastacomposition": 12, "fastadiff": 12, "fastadigest.py": 2, @@ -11147,15 +11148,15 @@ "fax2tiff": 5296, "fba": 1, "fc": 1, - "fc-cache": 5342, - "fc-cat": 5342, - "fc-conflist": 4859, - "fc-list": 5342, - "fc-match": 5342, - "fc-pattern": 5342, - "fc-query": 5342, - "fc-scan": 5342, - "fc-validate": 5342, + "fc-cache": 5344, + "fc-cat": 5344, + "fc-conflist": 4861, + "fc-list": 5344, + "fc-match": 5344, + "fc-pattern": 5344, + "fc-query": 5344, + "fc-scan": 5344, + "fc-validate": 5344, "fc_actg_coordinate": 1, "fc_calc_cutoff": 1, "fc_consensus": 1, @@ -11236,12 +11237,12 @@ "fermi2.pl": 2, "fetch": 4, "fetch-extras": 73, - "fetch-local": 27, - "fetch-nmcds": 27, - "fetch-pmc": 27, - "fetch-pubmed": 302, + "fetch-local": 28, + "fetch-nmcds": 28, + "fetch-pmc": 28, + "fetch-pubmed": 303, "fetch-tax.pl": 1, - "fetch-taxonomy": 27, + "fetch-taxonomy": 28, "fetchChromSizes": 5, "fetchEnaLibraryFastqs.sh": 1, "fetchFastq.sh": 1, @@ -11251,7 +11252,7 @@ "fetch_file": 29, "fetch_mrh_data": 1, "fetch_ucsc.py": 1, - "fetchproks.sh": 29, + "fetchproks.sh": 30, "fetchseq": 6, "ff2ftbl": 1, "ff2ftbl.py": 1, @@ -11274,8 +11275,8 @@ "ffprobe": 10, "ffq": 1, "ffreqboot": 2, - "fftns": 105, - "fftnsi": 105, + "fftns": 106, + "fftnsi": 106, "fftw-wisdom": 167, "fftw-wisdom-to-conf": 167, "fftwf-wisdom": 167, @@ -11320,18 +11321,18 @@ "filter-alignments.py": 1, "filter-bam": 2, "filter-bam-by-ids": 3, - "filter-columns": 203, - "filter-genbank": 27, + "filter-columns": 204, + "filter-genbank": 28, "filter-gff": 1, "filter-nonunique-peptide-matches": 2, "filter-positions.pl": 1, - "filter-ppx.pl": 14, - "filter-record": 27, + "filter-ppx.pl": 15, + "filter-record": 28, "filter-sort": 1, "filter-stage-1.prl": 5, "filter-stage-2.prl": 5, "filter-stats.pl": 1, - "filter-stop-words": 303, + "filter-stop-words": 304, "filter-stoptags.py": 7, "filter-table": 12, "filter-variations": 2, @@ -11339,7 +11340,7 @@ "filter.pl.bak": 1, "filter.py": 3, "filterBXBAM.py": 1, - "filterBam": 15, + "filterBam": 16, "filterCNV": 1, "filterChrom.py": 1, "filterCirc.awk": 1, @@ -11349,28 +11350,28 @@ "filterESTsimple": 3, "filterFrags": 1, "filterGenemark.pl": 3, - "filterGenes.pl": 14, - "filterGenesIn.pl": 12, - "filterGenesIn_mRNAname.pl": 14, + "filterGenes.pl": 15, + "filterGenesIn.pl": 13, + "filterGenesIn_mRNAname.pl": 15, "filterGenesIn_mRNAname.pl.patch": 2, - "filterGenesOut_mRNAname.pl": 14, + "filterGenesOut_mRNAname.pl": 15, "filterGottcha.pl": 1, "filterHits": 1, - "filterInFrameStopCodons.pl": 14, + "filterInFrameStopCodons.pl": 15, "filterIntronsFindStrand.pl": 3, "filterListBy.pl": 5, "filterMRNA": 3, - "filterMaf.pl": 14, + "filterMaf.pl": 15, "filterNULL": 3, "filterOverlap": 3, - "filterPSL.pl": 14, + "filterPSL.pl": 15, "filterPeakview.py": 1, "filterPolishes": 3, "filterQuality.py": 1, "filterReads.py": 1, "filterShortReads.py": 1, - "filterShrimp.pl": 14, - "filterSpliceHints.pl": 14, + "filterShrimp.pl": 15, + "filterSpliceHints.pl": 15, "filterSpliceSiteCircles.pl": 1, "filterSqMass.py": 1, "filterTADsAndCPs.pl": 5, @@ -11468,30 +11469,30 @@ "filter_vep": 2, "filter_vep.pl": 1, "filter_with_microbes_and_remapping.pl": 1, - "filterassemblysummary.sh": 30, - "filterbarcodes.sh": 30, - "filterbycoverage.sh": 30, - "filterbyname.sh": 30, - "filterbysequence.sh": 30, - "filterbytaxa.sh": 30, - "filterbytile.sh": 30, + "filterassemblysummary.sh": 31, + "filterbarcodes.sh": 31, + "filterbycoverage.sh": 31, + "filterbyname.sh": 31, + "filterbysequence.sh": 31, + "filterbytaxa.sh": 31, + "filterbytile.sh": 31, "filterfa": 10, "filterfa.o": 10, "filterfiles.py": 1, "filterfrg": 2, "filterjuncbyROCarguNonCanonical": 1, - "filterlines.sh": 30, + "filterlines.sh": 31, "filterlinks": 2, "filteroriginalfusion": 1, "filterout-bam": 1, - "filterqc.sh": 29, + "filterqc.sh": 30, "filterremappedfusion": 1, - "filtersam.sh": 30, - "filtersilva.sh": 27, - "filtersubs.sh": 30, + "filtersam.sh": 31, + "filtersilva.sh": 28, + "filtersubs.sh": 31, "filtertest": 3, "filtertranslate": 1, - "filtervcf.sh": 30, + "filtervcf.sh": 31, "filtlong": 1, "fimo": 13, "finalFusion": 1, @@ -11508,7 +11509,7 @@ "find-all-symbols": 2, "find-compounds.pl": 1, "find-duplicate-reads": 2, - "find-in-gene": 215, + "find-in-gene": 216, "find-knots.py": 7, "find-mango-assembly.sh": 1, "find-mango-home": 1, @@ -11528,7 +11529,7 @@ "findGOtxt.pl": 5, "findGapsInCoverageOfPacbios": 1, "findGenesInIntrons.pl": 2, - "findGffNamesInFasta.pl": 12, + "findGffNamesInFasta.pl": 13, "findHiCCompartments.pl": 5, "findHiCDomains.pl": 5, "findHiCInteractionsByChr.pl": 5, @@ -11543,7 +11544,7 @@ "findPeaks": 5, "findRedundantBLAT.pl": 5, "findRegionsExclusivelyInGroup": 1, - "findRepetitiveProtSeqs.py": 4, + "findRepetitiveProtSeqs.py": 5, "findRestSite": 2, "findTADsAndLoops.pl": 5, "findTADsAndLoopsFromRelMatrix": 5, @@ -11618,7 +11619,7 @@ "fitsverify": 1, "fitter": 1, "fix-all-bed-files": 3, - "fix-sqn-date": 16, + "fix-sqn-date": 17, "fixACE4consed.tcl": 1, "fixBX.py": 1, "fixErrors": 2, @@ -11635,8 +11636,8 @@ "fix_chirality": 1, "fix_consensus_from_vcf.pl": 1, "fix_gtf_ids.py": 3, - "fix_in_frame_stop_codon_genes.py": 11, - "fix_joingenes_gtf.pl": 11, + "fix_in_frame_stop_codon_genes.py": 12, + "fix_joingenes_gtf.pl": 12, "fix_map_ordering": 3, "fix_side_chain": 2, "fix_sonar.py": 1, @@ -11646,7 +11647,7 @@ "fixfasta": 1, "fixfastq": 2, "fixfrg": 2, - "fixgaps.sh": 29, + "fixgaps.sh": 30, "fixlib": 2, "fixqt4headers.pl": 241, "fixremdcouts.py": 6, @@ -11657,7 +11658,7 @@ "flaimapper": 1, "flair": 1, "flake8": 4, - "flankBed": 274, + "flankBed": 275, "flanker": 1, "flapjack": 1, "flash": 16, @@ -11721,7 +11722,7 @@ "font-awesome-to-png": 2, "font2c": 3, "fontinst": 1, - "fonttools": 408, + "fonttools": 409, "fop": 1, "forceOneClusterPerPairMem.py": 1, "forest.py": 1, @@ -11738,9 +11739,9 @@ "format_sintax.py": 1, "format_xml.pl": 1, "format_xml.pl.bak": 1, - "formatdb": 34, + "formatdb": 35, "formatlist": 1, - "formatrpsdb": 34, + "formatrpsdb": 35, "formcon": 2, "forwardGenomics.R": 1, "forwardGenomics_fullAnalysis.R": 1, @@ -11813,7 +11814,7 @@ "freec": 1, "freec2bed.pl": 1, "freec2circos.pl": 1, - "freetype-config": 5849, + "freetype-config": 5852, "freeze_graph": 25, "freq2group.pl": 5, "frequency.py": 1, @@ -11827,7 +11828,7 @@ "frg2fastq": 2, "frg2ta": 2, "frgs2clones": 3, - "fribidi": 4021, + "fribidi": 4022, "frictionless": 1, "frm_admin": 1, "frm_purged": 1, @@ -11848,7 +11849,7 @@ "from_unionbed_to_ratio_per_window_CC0": 1, "fs": 1, "fsa": 1, - "fsa2xml": 7, + "fsa2xml": 8, "fsc": 1, "fsc.bat": 1, "fseq": 1, @@ -11956,22 +11957,22 @@ "funannotate": 1, "funcannot": 1, "functions.py": 1, - "fungalrelease.sh": 30, + "fungalrelease.sh": 31, "funnel": 1, "funpack": 49, "funr": 1, "funzip": 25, "fuse": 1, - "fuse-ranges": 215, - "fuse-segments": 203, - "fuse.sh": 30, + "fuse-ranges": 216, + "fuse-segments": 204, + "fuse.sh": 31, "fusion-bloom": 1, "fusion-bloom.makefile": 1, "fusion_finder.py": 1, "fusion_report": 1, "fusioncatcher-to-CG": 2, "fusionsam2junc_filteranchor_newfmt": 1, - "futurize": 240, + "futurize": 241, "fuzznuc": 25, "fuzzpro": 25, "fuzztran": 25, @@ -12230,33 +12231,33 @@ "gatk3": 5, "gatk3-register": 3, "gatk_to_gvcf": 1, - "gawk": 100, + "gawk": 101, "gawk-4.1.3": 1, "gawk-4.2.1": 2, "gawk-5.0.0": 1, "gawk-5.0.1": 6, "gawk-5.1.0": 64, "gawk-5.2.2": 1, - "gawk-5.3.0": 25, - "gawkbug": 26, + "gawk-5.3.0": 26, + "gawkbug": 27, "gb2fas": 1, "gb2fasta": 1, - "gbSmallDNA2gff.pl": 14, + "gbSmallDNA2gff.pl": 15, "gbase": 2, - "gbf2fsa": 27, - "gbf2info": 7, - "gbf2ref": 27, - "gbf2xml": 302, + "gbf2fsa": 28, + "gbf2info": 8, + "gbf2ref": 28, + "gbf2xml": 303, "gbf2xml.bak": 1, "gbfalncut": 2, "gbfcut": 2, - "gbff2gff.sh": 29, + "gbff2gff.sh": 30, "gbk2faa.pl": 2, "gbkviz_webapp": 1, "gbmunge": 1, "gbnsr6": 6, - "gbrowse.conf": 14, - "gbrowseold2gff3.pl": 14, + "gbrowse.conf": 15, + "gbrowseold2gff3.pl": 15, "gbsx": 1, "gc": 201, "gc-assembler": 1, @@ -12379,6 +12380,7 @@ "gemBS": 1, "gemini": 1, "gemma": 1, + "gempipe": 1, "gen-reliab-dot.pl": 4, "genFlowOverview.py": 1, "genFm9": 2, @@ -12401,20 +12403,20 @@ "genbank_to": 1, "genblastG": 1, "genbox": 1, - "genbrk": 5862, - "gencfu": 5862, + "genbrk": 5866, + "gencfu": 5866, "genclust": 1, - "gencnval": 5862, + "gencnval": 5866, "gencode_extract_relevant_gtf_exons.pl": 1, "gencode_singleton_unit_test": 5, "genconf": 1, "gencore": 1, "gencove": 1, "gendb": 13, - "gendict": 5862, + "gendict": 5866, "gendist": 10, "gene2protein.db3": 2, - "gene2range": 203, + "gene2range": 204, "gene2xml": 1, "geneAssociationZscore.py": 1, "geneBody_coverage.py": 3, @@ -12492,7 +12494,7 @@ "generate_mtbd": 1, "generate_params_from_workflow.py": 1, "generate_plot": 3, - "generate_plot.py": 5, + "generate_plot.py": 6, "generate_primers_denovo.py": 1, "generate_qscoremtx.sh": 1, "generate_random_graph.pl": 4, @@ -12534,8 +12536,8 @@ "genome-complexity-fast": 2, "genome-to-blast-db": 1, "genome2cg": 1, - "genomeCoverageBed": 274, - "genomeCoverageBed.pl": 89, + "genomeCoverageBed": 275, + "genomeCoverageBed.pl": 90, "genomeOntology": 5, "genome_LenFilter_stats.pl": 3, "genome_anno.py": 2, @@ -12572,7 +12574,7 @@ "genotyphi.py": 1, "genpcz": 2, "genpept2gsi.pl": 2, - "genrb": 5862, + "genrb": 5866, "genreflex": 3, "genremdinputs.py": 6, "genrestr": 4, @@ -12616,8 +12618,8 @@ "getAbundance": 1, "getAccssnTaxID": 1, "getAlignmentWindows": 4, - "getAnnoFasta.pl": 14, - "getAnnoFastaFromJoingenes.py": 12, + "getAnnoFasta.pl": 15, + "getAnnoFastaFromJoingenes.py": 13, "getBamAvgChromDepth.pl": 1, "getChrLengths.pl": 5, "getConfidenceDensity": 1, @@ -12647,7 +12649,7 @@ "getInfo": 1, "getLengthStatisticsForKUnitigsFile.perl": 1, "getLikelyAdapters.pl": 5, - "getLinesMatching.pl": 12, + "getLinesMatching.pl": 13, "getMappableRegions": 5, "getMappingStats.pl": 5, "getMeanAndStdevByGCCount.perl": 1, @@ -12658,7 +12660,7 @@ "getOntology.R": 1, "getOntology.py": 1, "getOrthologList": 4, - "getOverlap": 274, + "getOverlap": 275, "getPartOfPromoter.pl": 5, "getPatch": 2, "getPeakTags": 5, @@ -12667,7 +12669,7 @@ "getRCChrom.rb": 1, "getRandomReads.pl": 5, "getRepeatMaskerBatch.pl": 15, - "getSeq": 14, + "getSeq": 15, "getSeq_genome_wN": 1, "getSeq_genome_woN": 1, "getSequenceForClosedGaps.perl": 1, @@ -12733,7 +12735,7 @@ "get_introns_from_ensembl.pl": 1, "get_kmers.py": 1, "get_lmas_data.sh": 1, - "get_loci_from_gb.pl": 9, + "get_loci_from_gb.pl": 10, "get_longest_ORF_per_transcript.pl": 5, "get_longest_isoform.py": 2, "get_lowest_common_ancestor.pl": 1, @@ -12775,8 +12777,8 @@ "get_sequence_type": 1, "get_sequences_for_meme.py": 1, "get_simple_cycs.py": 1, - "get_species_taxids.sh": 302, - "get_species_taxids.sh.bak": 297, + "get_species_taxids.sh": 303, + "get_species_taxids.sh.bak": 298, "get_standard_headers": 1, "get_stats_summary.pl": 1, "get_subontology_from.pl": 1, @@ -12837,7 +12839,7 @@ "getpbchemistry": 1, "getpbchemistry_dir": 1, "getpub": 1, - "getreads.sh": 30, + "getreads.sh": 31, "getreadsbyname": 1, "getreadsbyname_bak": 1, "getreadsbyref": 1, @@ -12847,9 +12849,9 @@ "getscu": 1, "getsize": 13, "getsnvfreq_by_interval": 1, - "gettext": 5297, - "gettext.sh": 5297, - "gettextize": 5297, + "gettext": 5298, + "gettext.sh": 5298, + "gettextize": 5298, "getuniqgenomealign": 1, "getuniqgenomealign_interval": 1, "getuniqgenomealign_sample_names": 1, @@ -12881,10 +12883,10 @@ "gff2bed.pl": 1, "gff2bed.py": 1, "gff2embl": 1, - "gff2gbSmallDNA.pl": 14, + "gff2gbSmallDNA.pl": 15, "gff2gff.py": 65, "gff2pos.pl": 5, - "gff2ps_mycustom": 14, + "gff2ps_mycustom": 15, "gff2seq": 2, "gff2starch": 14, "gff2starch-float128": 14, @@ -12908,7 +12910,7 @@ "gff3_to_embl": 1, "gff3_to_gtf.pl": 1, "gff3sort.pl": 2, - "gffGetmRNA.pl": 14, + "gffGetmRNA.pl": 15, "gffToBed": 1, "gffToVcf": 1, "gff_check": 10, @@ -12949,20 +12951,20 @@ "gi-compile-repository": 13, "gi-decompile-typelib": 13, "gi-inspect-typelib": 13, - "gi2ancestors.sh": 30, - "gi2taxid.sh": 30, + "gi2ancestors.sh": 31, + "gi2taxid.sh": 31, "gid-taxid": 1, "gie": 41, - "gif2h5": 547, + "gif2h5": 548, "gif2hdf": 125, - "gif2rgb": 756, + "gif2rgb": 758, "gif2tiff": 189, "gif2webp": 354, - "gifbuild": 756, - "gifclrmp": 756, + "gifbuild": 758, + "gifclrmp": 758, "gifecho": 39, "giffilter": 25, - "giffix": 756, + "giffix": 758, "gifinto": 39, "gifmaker.py": 20, "gifrop": 1, @@ -12973,15 +12975,15 @@ "gifrop_pannotate.R": 1, "gifrop_plots.R": 1, "gifsponge": 25, - "giftext": 756, + "giftext": 758, "giftogd2": 237, - "giftool": 756, + "giftool": 758, "gigrnd.py": 1, "gil2bin": 1, "gimbleprep": 1, "gimme": 4, - "gimme_taxa.py": 7, - "ginsi": 105, + "gimme_taxa.py": 8, + "ginsi": 106, "gio": 1547, "gio-launch-desktop": 668, "gio-querymodules": 1659, @@ -12996,7 +12998,7 @@ "git2": 15, "git2_cli": 7, "git_test.py": 1, - "gitable.sh": 30, + "gitable.sh": 31, "gitk": 30, "give_pathways": 1, "gkmpredict": 1, @@ -13027,11 +13029,11 @@ "glnexus_cli": 1, "glob_res.pl": 1, "global.json": 1, - "glpsol": 235, + "glpsol": 236, "glsearch36": 7, "gm": 2, - "gm2ranges": 27, - "gm2segs": 27, + "gm2ranges": 28, + "gm2segs": 28, "gmap": 13, "gmap.nosimd": 8, "gmap.sse42": 11, @@ -13210,7 +13212,7 @@ "gottcha2.py": 1, "gottcha_db.pl": 1, "gout": 1, - "gp2othergp.pl": 14, + "gp2othergp.pl": 15, "gpart": 1, "gpg": 2, "gpg-agent": 2, @@ -13229,15 +13231,15 @@ "gpgtar": 2, "gpgv": 2, "gplas.sh": 1, - "gpmetis": 58, + "gpmetis": 59, "gprof": 8, "gpustat": 6, "gql-cli": 2, "gqt": 1, "grabix": 3, "grabpars": 1, - "grademerge.sh": 30, - "gradesam.sh": 30, + "grademerge.sh": 31, + "gradesam.sh": 31, "grafimo": 1, "graftM": 2, "grako": 5, @@ -13253,7 +13255,7 @@ "graph_simplification.py": 1, "graphanalyzer.py": 1, "graphbin": 1, - "graphchk": 58, + "graphchk": 59, "graphdump": 3, "graphembed": 2, "graphlan.py": 1, @@ -13319,7 +13321,7 @@ "groopm": 1, "groot": 2, "groovy_script": 4, - "groupBy": 274, + "groupBy": 275, "groupSequences.pl": 5, "group_ORF_sequences.py": 1, "group_bp_reads.pl": 1, @@ -13348,9 +13350,9 @@ "gsf": 1, "gsf-office-thumbnailer": 1, "gsf-vba-dump": 1, - "gsl-config": 4558, - "gsl-histogram": 4558, - "gsl-randist": 4558, + "gsl-config": 4559, + "gsl-histogram": 4559, + "gsl-randist": 4559, "gslj": 105, "gslp": 105, "gsnap": 11, @@ -13361,7 +13363,7 @@ "gsnapl.sse42": 11, "gsnd": 105, "gsort": 5, - "gss-client": 5833, + "gss-client": 5837, "gss-server": 2, "gst-completion-helper": 1, "gst-device-monitor-1.0": 234, @@ -13384,16 +13386,16 @@ "gtester": 1657, "gtester-report": 1657, "gtf-to-bed12": 3, - "gtf2aa.pl": 12, + "gtf2aa.pl": 13, "gtf2bed": 15, "gtf2bed-float128": 14, "gtf2bed-megarow": 14, "gtf2bed-typical": 14, - "gtf2bed.pl": 15, + "gtf2bed.pl": 16, "gtf2bed12": 1, "gtf2featureAnnotation.R": 1, "gtf2genetab": 1, - "gtf2gff.pl": 14, + "gtf2gff.pl": 15, "gtf2gff.pl.origexit": 2, "gtf2revcom.pl": 1, "gtf2starch": 14, @@ -13423,7 +13425,7 @@ "gtftools": 1, "gtfutils": 1, "gth": 3, - "gth2gtf.pl": 12, + "gth2gtf.pl": 13, "gthclean.sh": 3, "gthcleanrec.sh": 3, "gthconsensus": 3, @@ -13519,7 +13521,7 @@ "gunc": 1, "gunicorn": 6, "gunzip": 18, - "guppy": 21, + "guppy": 22, "guppy_basecaller": 1, "gushr.py": 1, "gustaf": 2, @@ -13585,39 +13587,39 @@ "h264dec": 10, "h264enc": 10, "h2load": 3929, - "h2ph": 1711, - "h2xs": 1711, + "h2ph": 1713, + "h2xs": 1713, "h4_ncdump": 125, "h4_ncgen": 125, "h4cc": 125, "h4redeploy": 125, - "h52gif": 547, - "h5c++": 547, - "h5cc": 552, - "h5clear": 531, - "h5copy": 547, - "h5debug": 547, - "h5delete": 88, - "h5diff": 547, - "h5dump": 549, - "h5fc": 534, - "h5format_convert": 531, - "h5fuse.sh": 56, - "h5import": 547, - "h5jam": 547, - "h5ls": 547, - "h5mkgrp": 547, + "h52gif": 548, + "h5c++": 548, + "h5cc": 553, + "h5clear": 532, + "h5copy": 548, + "h5debug": 548, + "h5delete": 89, + "h5diff": 548, + "h5dump": 550, + "h5fc": 535, + "h5format_convert": 532, + "h5fuse.sh": 57, + "h5import": 548, + "h5jam": 548, + "h5ls": 548, + "h5mkgrp": 548, "h5pcc": 3, "h5perf": 3, - "h5perf_serial": 547, + "h5perf_serial": 548, "h5pfc": 3, - "h5redeploy": 547, - "h5repack": 547, - "h5repart": 547, - "h5stat": 547, - "h5tools_test_utils": 36, - "h5unjam": 547, - "h5watch": 531, + "h5redeploy": 548, + "h5repack": 548, + "h5repart": 548, + "h5stat": 548, + "h5tools_test_utils": 37, + "h5unjam": 548, + "h5watch": 532, "hAMRoaster": 1, "h_num": 1, "haarz.x": 1, @@ -13643,7 +13645,7 @@ "hal2fasta": 1, "hal2maf": 1, "hal2mafMP.py": 1, - "hal2maf_split.pl": 14, + "hal2maf_split.pl": 15, "hal4dExtract": 1, "hal4dExtractTest": 1, "halAddToBranch": 1, @@ -13759,11 +13761,11 @@ "haystack_pipeline": 1, "haystack_run_test": 1, "haystack_tf_activity_plane": 1, - "hb-info": 288, - "hb-ot-shape-closure": 5083, - "hb-shape": 5083, - "hb-subset": 4647, - "hb-view": 5040, + "hb-info": 290, + "hb-ot-shape-closure": 5085, + "hb-shape": 5085, + "hb-subset": 4649, + "hb-view": 5042, "hbvblast.sh": 1, "hca-matrix-downloader": 1, "hca-mtx-to-10x": 1, @@ -13806,7 +13808,7 @@ "helicos-load.3": 2, "helicos-load.3.0.0": 2, "helixturnhelix": 25, - "helpMod.pm": 14, + "helpMod.pm": 15, "helper_functions.py": 1, "helpers.py": 3, "helpviewer": 6, @@ -13817,7 +13819,7 @@ "hg2hg_net": 1, "hgGcPercent": 3, "hgvs-shell": 1, - "hgvs2spdi": 215, + "hgvs2spdi": 216, "hhalign": 4, "hhalign_omp": 4, "hhblits": 4, @@ -13951,49 +13953,49 @@ "hmm-assembler.pl": 2, "hmm-info": 2, "hmm2gff.py": 1, - "hmm_mapper.py": 3, + "hmm_mapper.py": 4, "hmm_process.py": 2, - "hmm_server.py": 3, + "hmm_server.py": 4, "hmm_train": 2, "hmm_tweak": 2, "hmm_vali.py": 2, "hmm_view": 2, - "hmm_worker.py": 3, - "hmmalign": 187, + "hmm_worker.py": 4, + "hmmalign": 188, "hmmalign2": 6, - "hmmbuild": 187, + "hmmbuild": 188, "hmmbuild2": 6, - "hmmc2": 13, + "hmmc2": 14, "hmmcalibrate2": 6, - "hmmconvert": 181, + "hmmconvert": 182, "hmmconvert2": 6, - "hmmemit": 181, + "hmmemit": 182, "hmmemit2": 6, "hmmer2filtered_best.py": 1, "hmmer2gff": 1, "hmmer_utils.py": 1, "hmmeralign": 7, "hmmerbuild": 7, - "hmmerfm-exactmatch": 13, - "hmmfetch": 181, + "hmmerfm-exactmatch": 14, + "hmmfetch": 182, "hmmfetch2": 6, "hmmgs": 5, "hmmindex2": 6, "hmmlib_to_sqlite3.py": 2, - "hmmlogo": 181, + "hmmlogo": 182, "hmmpair": 1, "hmmpfam2": 6, - "hmmpgmd": 181, + "hmmpgmd": 182, "hmmpgmd_shard": 153, - "hmmpress": 181, - "hmmscan": 181, + "hmmpress": 182, + "hmmscan": 182, "hmmscan-parser.py": 1, "hmmscan_parser.py": 2, - "hmmsearch": 181, + "hmmsearch": 182, "hmmsearch2": 6, "hmmsearch_run.py": 2, - "hmmsim": 181, - "hmmstat": 181, + "hmmsim": 182, + "hmmstat": 182, "hmnfusion": 1, "hmnqc": 1, "hmoment": 25, @@ -14002,7 +14004,7 @@ "hmtnote": 1, "hocort": 1, "holoviews": 2, - "homGeneMapping": 15, + "homGeneMapping": 16, "homePage.Rmd": 1, "homer": 5, "homer2": 5, @@ -14068,11 +14070,11 @@ "htseq-count": 22, "htseq-count-barcodes": 14, "htseq-qa": 22, - "htsfile": 710, + "htsfile": 712, "htsget": 2, "htsinfer": 1, "httpcfg": 15, - "httpx": 21, + "httpx": 22, "hubward": 1, "hug": 1, "huge-count.pl": 1, @@ -14131,21 +14133,21 @@ "humann_unpack_pathways": 1, "humid": 1, "hv-pipeline.py": 1, - "hwloc-annotate": 72, + "hwloc-annotate": 74, "hwloc-assembler": 2, "hwloc-assembler-remote": 2, - "hwloc-bind": 72, - "hwloc-calc": 72, - "hwloc-compress-dir": 72, - "hwloc-diff": 72, + "hwloc-bind": 74, + "hwloc-calc": 74, + "hwloc-compress-dir": 74, + "hwloc-diff": 74, "hwloc-distances": 2, - "hwloc-distrib": 72, - "hwloc-gather-cpuid": 70, - "hwloc-gather-topology": 72, - "hwloc-info": 72, - "hwloc-ls": 72, - "hwloc-patch": 72, - "hwloc-ps": 72, + "hwloc-distrib": 74, + "hwloc-gather-cpuid": 72, + "hwloc-gather-topology": 74, + "hwloc-info": 74, + "hwloc-ls": 74, + "hwloc-patch": 74, + "hwloc-ps": 74, "hyb_analyze": 1, "hyb_check": 1, "hyb_eval": 1, @@ -14205,16 +14207,16 @@ "icctrans": 1, "ice": 2, "ice_pbdagcon2.py": 1, - "icecreamfinder.sh": 29, - "icecreamgrader.sh": 29, - "icecreammaker.sh": 29, + "icecreamfinder.sh": 30, + "icecreamgrader.sh": 30, + "icecreammaker.sh": 30, "icescreen": 1, "ichar": 1, "icon-font-to-png": 2, "iconv": 5462, - "icu-config": 5862, - "icuexportdata": 2077, - "icuinfo": 5862, + "icu-config": 5866, + "icuexportdata": 2081, + "icuinfo": 5866, "id": 84, "id_conserved_regions.pl": 1, "idba": 10, @@ -14245,25 +14247,25 @@ "idfetch": 1, "idiag-socket-details": 13, "idle": 332, - "idle3": 3378, - "idle3.10": 819, - "idle3.11": 270, + "idle3": 3382, + "idle3.10": 820, + "idle3.11": 271, "idle3.12": 226, "idle3.4": 6, "idle3.5": 103, "idle3.6": 342, "idle3.7": 383, "idle3.8": 577, - "idle3.9": 652, + "idle3.9": 654, "idlj": 117, - "idmatrix.sh": 30, - "idn": 30, - "idn2": 277, + "idmatrix.sh": 31, + "idn": 31, + "idn2": 278, "idpAssemble": 2, "idpQonvert": 2, "idpQuery": 2, "idr": 1, - "idtree.sh": 30, + "idtree.sh": 31, "idxdepth": 1, "iep": 25, "ifCNV": 1, @@ -14389,7 +14391,7 @@ "imode_gcc": 2, "imodview": 2, "imove": 2, - "impala": 34, + "impala": 35, "impg": 1, "import": 75, "import-html-template": 13, @@ -14453,7 +14455,7 @@ "infer_bp_v4.pl": 1, "infer_experiment.py": 3, "infer_sv.pl": 1, - "infinitesites": 69, + "infinitesites": 70, "inflate_denoiser_output.py": 1, "influx_i": 1, "influx_i.py": 1, @@ -14464,12 +14466,12 @@ "infoalign": 25, "infoassembly": 25, "infobase": 25, - "infocmp": 7755, + "infocmp": 7760, "inforesidue": 25, "informant.py": 1, "infoseq": 25, - "infotocap": 7755, - "ini2xml": 27, + "infotocap": 7760, + "ini2xml": 28, "init_Trinotate_sqlite_db.pl": 1, "init_db.sh": 1, "initdb": 47, @@ -14530,7 +14532,7 @@ "installpackages.R": 1, "installvst": 15, "instance_events": 29, - "instmodsh": 1711, + "instmodsh": 1713, "int_seqs_to_char_strings.py": 59, "intake": 1, "intake-server": 1, @@ -14561,12 +14563,12 @@ "interop_plot_qscore_histogram": 4, "interop_plot_sample_qc": 4, "interop_summary": 4, - "interpolate_sam.pl": 517, + "interpolate_sam.pl": 519, "interprophet.rb": 1, "interproscan.sh": 1, "intersect": 5, - "intersect-uid-lists": 301, - "intersectBed": 274, + "intersect-uid-lists": 302, + "intersectBed": 275, "intersectFiles.py": 2, "intersectGenomicSets.py": 1, "intersect_assembly_errors": 1, @@ -14587,7 +14589,7 @@ "intron_exon_reads.pyc": 1, "inv": 2, "invert-pubmed": 1, - "invertkey.sh": 30, + "invertkey.sh": 31, "invgeod": 39, "invoke": 2, "involucro": 2, @@ -14631,17 +14633,17 @@ "ipkdump-dna": 1, "ipopt": 1, "ipopt_sens": 1, - "ippeveprinter": 199, - "ipptool": 199, + "ippeveprinter": 201, + "ipptool": 201, "ipr_update_gff": 1, "iprscan2gff3": 1, "iptest": 53, "iptest2": 7, "iptest3": 46, "ipyrad": 1, - "ipython": 97, + "ipython": 99, "ipython2": 7, - "ipython3": 90, + "ipython3": 92, "ipython3.10": 1, "ipython3.9": 4, "iqkm": 1, @@ -14701,7 +14703,7 @@ "isql": 1, "iss": 2, "isutf8": 3, - "isympy": 32, + "isympy": 33, "it.cpython-36m-x86_64-linux-gnu.so": 1, "it.so": 1, "iterate": 2, @@ -14787,7 +14789,7 @@ "jack_zombie": 12, "jackd": 25, "jackdiff": 1, - "jackhmmer": 181, + "jackhmmer": 182, "jackknifed_beta_diversity.py": 1, "jaffa-assembly": 1, "jaffa-direct": 1, @@ -14798,8 +14800,8 @@ "jamo-normalize": 1, "jannovar": 1, "jaotc": 310, - "jar": 542, - "jarsigner": 542, + "jar": 544, + "jarsigner": 544, "jasmine": 3, "jasmine.jar": 1, "jasmine_igv.jar": 1, @@ -14810,21 +14812,21 @@ "jaspscan": 25, "jass": 1, "jass_preprocessing": 1, - "java": 542, + "java": 544, "java-rmi.cgi": 112, - "javac": 542, - "javadoc": 542, + "javac": 544, + "javadoc": 544, "javah": 112, - "javap": 542, + "javap": 544, "javareconf": 1, "jbig2dec": 1, "jbrowse": 1, "jcast": 1, - "jcmd": 542, - "jconsole": 542, - "jdb": 542, - "jdeprscan": 433, - "jdeps": 541, + "jcmd": 544, + "jconsole": 544, + "jdb": 544, + "jdeprscan": 435, + "jdeps": 543, "je": 2, "jellyfish": 47, "jemalloc-config": 14, @@ -14832,21 +14834,21 @@ "jembossctl": 25, "jeprof": 14, "jf_aligner": 1, - "jfr": 377, + "jfr": 379, "jgiDwnld": 2, "jgi_gc": 1, "jgi_summarize_bam_contig_depths": 6, "jgoslin": 1, "jhat": 112, - "jhsdb": 433, - "jimage": 433, - "jinfo": 542, + "jhsdb": 435, + "jimage": 435, + "jinfo": 544, "jiv": 5, "jjs": 420, - "jlink": 433, + "jlink": 435, "jlpm": 3, - "jmap": 542, - "jmod": 433, + "jmap": 544, + "jmod": 435, "jmztab-m": 1, "job-shop": 1, "jobTreeKill": 2, @@ -14856,57 +14858,57 @@ "jobTreeStatus": 2, "jobTreeTest_Dependencies.py": 1, "join": 84, - "join-into-groups-of": 303, + "join-into-groups-of": 304, "join-long-chromosomes": 3, "join.pl": 1, "join.pl.bak": 1, "joinFiles.pl": 5, "joinIntervals.awk": 1, "joinKUnitigs_v3": 1, - "joinPeptides.pl": 14, - "join_aug_pred.pl": 14, + "joinPeptides.pl": 15, + "join_aug_pred.pl": 15, "join_columnar_files.py": 2, "join_mega_reads_trim.onepass.nomatch.pl": 1, "join_mega_reads_trim.onepass.pl": 1, "join_mega_reads_trim.onepass.ref.pl": 1, "join_mega_reads_trim.onepass.rna.pl": 1, - "join_mult_hints.pl": 14, + "join_mult_hints.pl": 15, "join_paired_ends.py": 1, "join_sam.sh": 1, "join_spades_fastg_by_blast.py": 1, - "joingenes": 15, + "joingenes": 16, "joint-indels": 1, "joint-parsimony": 1, "jp.py": 101, - "jpackage": 123, + "jpackage": 125, "jpeg2hdf": 125, - "jpegtran": 5786, - "jpgicc": 1007, + "jpegtran": 5789, + "jpgicc": 1010, "jpredapi": 1, - "jps": 542, + "jps": 544, "jq": 307, "jronn": 1, - "jrunscript": 542, + "jrunscript": 544, "js-beautify": 1, "jsadebugd": 112, "jscan": 1, "jsearch": 1, - "jshell": 433, + "jshell": 435, "json2gff": 1, - "json2xml": 215, + "json2xml": 216, "json_collect_data_source.py": 1, - "json_pp": 1711, - "json_xs": 361, + "json_pp": 1713, + "json_xs": 362, "jsondiff": 9, - "jsonl2xml": 27, + "jsonl2xml": 28, "jsonpatch": 9, "jsonpath.py": 1, "jsonpath_ng": 1, "jsonpointer": 12, "jsonschema": 215, - "jstack": 542, - "jstat": 542, - "jstatd": 542, + "jstack": 544, + "jstat": 544, + "jstatd": 544, "juicer": 1, "juicer_shortform2pairs.pl": 22, "julia": 6, @@ -14954,17 +14956,17 @@ "jupyter-troubleshoot": 148, "jupyter-trust": 141, "just-first-key": 20, - "just-top-hits": 7, + "just-top-hits": 8, "just_blast_test.pl": 1, - "jwebserver": 40, - "k5srvutil": 5833, + "jwebserver": 42, + "k5srvutil": 5837, "k8": 166, "k8-Linux": 1, "k_means": 1, "k_means_coefficient": 1, "k_neighbors": 1, "k_neighbors_coefficient": 1, - "kadmin": 5833, + "kadmin": 5837, "kadmin.local": 2, "kadmind": 2, "kaiju": 4, @@ -14992,7 +14994,7 @@ "kanji-config-updmap-sys": 1, "kanji-config-updmap-user": 1, "kanji-fontmap-creator": 1, - "kapastats.sh": 29, + "kapastats.sh": 30, "kaptive.py": 2, "kar": 20, "kar+": 2, @@ -15034,7 +15036,7 @@ "kchashmgr": 2, "kchashtest": 2, "kclangctest": 2, - "kcompress.sh": 30, + "kcompress.sh": 31, "kcpolymgr": 2, "kcpolytest": 2, "kcprototest": 2, @@ -15058,20 +15060,20 @@ "kdbmeta.3.0.0": 2, "kdbmeta.3.0.3": 1, "kdbmeta.3.1.0": 1, - "kdestroy": 5833, + "kdestroy": 5837, "kea-config": 37, "keep-header": 1, "keep-ribo-periodic": 1, - "keepbestcopy.sh": 29, + "keepbestcopy.sh": 30, "kegg_charter.py": 1, "kegg_pathway_map.py": 1, "keggcharter.py": 1, "keggpathway_map.py": 1, "keyFreq": 1, - "keyctl": 2463, + "keyctl": 2467, "keygen": 1, "keyring": 10, - "keytool": 542, + "keytool": 544, "kget": 18, "kget.2": 18, "kget.2.10.0": 1, @@ -15084,7 +15086,7 @@ "kgwasflow": 1, "khash.h": 1, "khipu": 1, - "khist.sh": 30, + "khist.sh": 31, "kid": 1, "kidc": 1, "kill": 95, @@ -15099,10 +15101,10 @@ "kinSimRiboswitch": 1, "king": 1, "kingfisher": 1, - "kinit": 5833, + "kinit": 5837, "kinship-read": 1, "kinshipDecompose": 1, - "kinwalker": 52, + "kinwalker": 53, "kipoi": 2, "kissnp2": 1, "kissplice": 1, @@ -15112,7 +15114,7 @@ "kitsch": 10, "kitsune": 1, "kleborate": 1, - "klist": 5833, + "klist": 5837, "kma": 19, "kma_index": 19, "kma_shm": 19, @@ -15138,16 +15140,16 @@ "kmer_nt_stuff_threader.py": 2, "kmer_repeat_counter.py": 2, "kmercounter": 1, - "kmercountexact.sh": 30, - "kmercountmulti.sh": 30, + "kmercountexact.sh": 31, + "kmercountmulti.sh": 31, "kmercoverage": 1, - "kmercoverage.sh": 30, - "kmerfilterset.sh": 29, + "kmercoverage.sh": 31, + "kmerfilterset.sh": 30, "kmerfinder.py": 1, "kmergenie": 1, - "kmerlimit.sh": 29, - "kmerlimit2.sh": 29, - "kmerposition.sh": 26, + "kmerlimit.sh": 30, + "kmerlimit2.sh": 30, + "kmerposition.sh": 27, "kmers": 2, "kmers_for_component.py": 1, "kmers_for_component_back.py": 1, @@ -15161,7 +15163,7 @@ "kmtricks": 1, "kmtricks-socks": 1, "kmtricksp": 1, - "kmutate.sh": 24, + "kmutate.sh": 25, "kneaddata": 1, "kneaddata_bowtie2_discordant_pairs": 1, "kneaddata_build_database": 1, @@ -15200,7 +15202,7 @@ "kp1mer_to_kmer.py": 1, "kp2np.py": 1, "kpal": 2, - "kpasswd": 5833, + "kpasswd": 5837, "kpileup.py": 1, "kprop": 2, "kpropd": 2, @@ -15247,7 +15249,7 @@ "krakenuniq-report": 1, "krakenuniq-translate": 1, "krakmeopen": 1, - "krb5-config": 5833, + "krb5-config": 5837, "krb5-send-pr": 2, "krb5kdc": 2, "kreport2krona.py": 3, @@ -15263,9 +15265,9 @@ "kseq_split": 1, "ksnp": 1, "kssd": 1, - "ksu": 5833, + "ksu": 5837, "ksw": 1, - "kswitch": 5833, + "kswitch": 5837, "ktClassifyBLAST": 17, "ktClassifyHits": 13, "ktGetContigMagnitudes": 17, @@ -15296,12 +15298,12 @@ "ktserver": 2, "kttimedmgr": 2, "kttimedtest": 2, - "ktutil": 5833, + "ktutil": 5837, "ktutilmgr": 2, "ktutilserv": 2, "ktutiltest": 2, "kubectl": 1, - "kvno": 5833, + "kvno": 5837, "kwip": 2, "kwip-stats": 2, "l4p-tmpl": 32, @@ -15419,7 +15421,7 @@ "lefse_plot_features.py": 1, "lefse_plot_res.py": 1, "lefse_run.py": 1, - "legacy_blast.pl": 337, + "legacy_blast.pl": 338, "legsta": 1, "lemon-0.x-to-1.x.sh": 4, "lemur": 1, @@ -15453,8 +15455,8 @@ "libclair3.cpython-36m-x86_64-linux-gnu.so": 1, "libclair3.o": 1, "libclair3.so": 1, - "libdeflate-gunzip": 4153, - "libdeflate-gzip": 4153, + "libdeflate-gunzip": 4157, + "libdeflate-gzip": 4157, "libdrawgram.so": 5, "libdrawtree.so": 5, "libfile.pl": 1, @@ -15463,9 +15465,9 @@ "libiomp5md.dll": 1, "liblist.pl": 1, "liblist.pl.bak": 1, - "libnetcfg": 1711, - "libpng-config": 5903, - "libpng16-config": 5903, + "libnetcfg": 1713, + "libpng-config": 5906, + "libpng16-config": 5906, "libpypy-c.so": 1, "libpypy-c.so.debug": 1, "libpypy3-c.so.debug": 3, @@ -15498,7 +15500,7 @@ "lily-glyph-commands": 1, "lily-image-commands": 1, "lily-rebuild-pdfs": 1, - "lilypad.sh": 29, + "lilypad.sh": 30, "lima": 1, "lima-undo": 1, "lin.pl": 1, @@ -15524,11 +15526,11 @@ "link_ssv.py": 1, "linkage2allegro": 1, "linkhsp_unit_test": 5, - "linkicc": 1007, + "linkicc": 1010, "linknets": 2, "links2sql.pl": 7, - "linksBed": 274, - "linsi": 105, + "linksBed": 275, + "linsi": 106, "linux32": 13, "linux64": 13, "linx": 1, @@ -15657,7 +15659,7 @@ "load-overlaps": 2, "load-spark-env.cmd": 6, "load-spark-env.sh": 6, - "load2sqlitedb": 14, + "load2sqlitedb": 15, "loadBalanceMers.pl": 1, "loadChemistry.py": 1, "loadCorrectedReads": 6, @@ -15673,7 +15675,7 @@ "load_prokaryotes": 1, "load_prokaryotes.py": 1, "load_remote_mapping_file.py": 1, - "loadreads.sh": 30, + "loadreads.sh": 31, "locARNAGraphClust.pl": 1, "localAssemblyDBG.py": 1, "localAssemblyIRO.py": 1, @@ -15723,7 +15725,7 @@ "logging_config.ini": 1, "logging_utils.py": 1, "logistic_regression": 1, - "loglog.sh": 30, + "loglog.sh": 31, "logname": 84, "long-orfs": 2, "long-to-linked-pe": 2, @@ -15753,7 +15755,7 @@ "lorma.sh": 1, "lotus2": 1, "low-cov-multisample.py": 1, - "lp_solve": 14, + "lp_solve": 15, "lpconvert": 1, "lprodump": 43, "lprsetup.sh": 105, @@ -15793,8 +15795,8 @@ "lsmem": 13, "lsns": 13, "lss3": 29, - "lstopo": 72, - "lstopo-no-graphics": 72, + "lstopo": 74, + "lstopo-no-graphics": 74, "ltqnorm.pl": 1, "ltqnorm.pl.bak": 1, "ltr_finder": 3, @@ -15825,31 +15827,31 @@ "lut_pdiffCI.dat": 4, "lut_pdiffInRegion.dat": 4, "lwarpmk": 1, - "lwp-download": 197, - "lwp-dump": 197, - "lwp-mirror": 197, - "lwp-request": 197, + "lwp-download": 198, + "lwp-dump": 198, + "lwp-mirror": 198, + "lwp-request": 198, "lyner": 1, "lz4": 3522, "lz4_decompress": 2, "lz4c": 3521, "lz4cat": 3521, - "lzcat": 7581, - "lzcmp": 7581, - "lzdiff": 7581, - "lzegrep": 7581, - "lzfgrep": 7581, - "lzgrep": 7581, - "lzless": 7581, - "lzma": 7581, - "lzmadec": 7581, - "lzmainfo": 7581, - "lzmore": 7581, + "lzcat": 7586, + "lzcmp": 7586, + "lzdiff": 7586, + "lzegrep": 7586, + "lzfgrep": 7586, + "lzgrep": 7586, + "lzless": 7586, + "lzma": 7586, + "lzmadec": 7586, + "lzmainfo": 7586, + "lzmore": 7586, "lzop_build_offset_table.py": 59, "m-party": 1, "m-tx": 1, "m2fmt_tier_hits.pl": 1, - "m2gmetis": 58, + "m2gmetis": 59, "m2r2": 1, "m4": 5, "m5tofa": 1, @@ -15899,7 +15901,7 @@ "maf-join": 11, "maf-sort": 11, "maf-swap": 11, - "maf2conswig.pl": 14, + "maf2conswig.pl": 15, "maf2daa": 1, "maf2fasta": 1, "maf2fasta.pl": 1, @@ -15962,20 +15964,20 @@ "maf_translate_chars.py": 59, "maf_truncate.py": 59, "maf_word_frequency.py": 59, - "mafft": 106, - "mafft-distance": 105, - "mafft-einsi": 105, - "mafft-fftns": 105, - "mafft-fftnsi": 105, - "mafft-ginsi": 105, - "mafft-homologs.rb": 105, - "mafft-linsi": 105, - "mafft-nwns": 105, - "mafft-nwnsi": 105, - "mafft-profile": 105, - "mafft-qinsi": 105, - "mafft-sparsecore.rb": 103, - "mafft-xinsi": 105, + "mafft": 107, + "mafft-distance": 106, + "mafft-einsi": 106, + "mafft-fftns": 106, + "mafft-fftnsi": 106, + "mafft-ginsi": 106, + "mafft-homologs.rb": 106, + "mafft-linsi": 106, + "mafft-nwns": 106, + "mafft-nwnsi": 106, + "mafft-profile": 106, + "mafft-qinsi": 106, + "mafft-sparsecore.rb": 104, + "mafft-xinsi": 106, "mafft.yaml": 1, "mag-improve": 36, "mag2gfa": 1, @@ -16005,7 +16007,7 @@ "main_html_generator.py": 1, "makblk.pl": 4, "makdbs": 4, - "make": 4160, + "make": 4161, "make-barcodes.awk": 1, "make-cluster.R": 1, "make-conf": 2, @@ -16048,7 +16050,7 @@ "makeHKY": 2, "makeHiCWashUfile.pl": 5, "makeIgnoreList": 1, - "makeMatchLists.pl": 14, + "makeMatchLists.pl": 15, "makeMetaGeneProfile.pl": 5, "makeMultiWigHub.pl": 5, "makeNBaitsPerBinFile.py": 1, @@ -16068,7 +16070,7 @@ "makeTagDirectory": 5, "makeTree": 1, "makeUCSCfile": 5, - "makeUtrTrainingSet.pl": 14, + "makeUtrTrainingSet.pl": 15, "makeVariantTaxLookups.pl": 1, "makeWebsite": 2, "make_2d_plots.py": 1, @@ -16126,7 +16128,7 @@ "make_mate_frg.pl": 1, "make_midpoint_matrix": 1, "make_mr_frg.pl": 1, - "make_multi_seq.pl": 46, + "make_multi_seq.pl": 47, "make_ndx": 4, "make_nr_pangenome_matrix.pl": 1, "make_otu_heatmap.py": 1, @@ -16138,7 +16140,7 @@ "make_pp_rst_file.py": 1, "make_prefs_file.py": 1, "make_prg": 2, - "make_pscores.pl": 20, + "make_pscores.pl": 21, "make_qiime_py_file.py": 1, "make_rarefaction_plots.py": 1, "make_rejoin_links.pl": 1, @@ -16155,27 +16157,27 @@ "makeagp2.awk": 1, "makeagp_full.awk": 1, "makeagp_full2.awk": 1, - "makeblastdb": 339, + "makeblastdb": 340, "makecert": 15, - "makechimeras.sh": 30, + "makechimeras.sh": 31, "makeclusterdb": 5, - "makecontaminatedgenomes.sh": 30, - "makeconv": 5862, + "makecontaminatedgenomes.sh": 31, + "makeconv": 5866, "makedtx": 1, "makefasta.awk": 1, "makegeo": 37, "makeglossaries": 1, "makeglossaries-lite": 1, - "makehmmerdb": 181, + "makehmmerdb": 182, "makeidx.pl": 4, - "makemat": 34, - "makembindex": 337, + "makemat": 35, + "makembindex": 338, "makenucseq": 25, "makepBAM_genome.sh": 1, "makepBAM_transcriptome.sh": 1, "makeplot.pl": 3, - "makepolymers.sh": 30, - "makeprofiledb": 337, + "makepolymers.sh": 31, + "makeprofiledb": 338, "makeprotseq": 25, "maker": 1, "maker2chado": 1, @@ -16225,7 +16227,7 @@ "map2bed.pl": 2, "map2gtf": 3, "map2slim": 1, - "mapBed": 274, + "mapBed": 275, "mapCounter": 1, "mapDIA": 1, "mapDamage": 2, @@ -16234,7 +16236,7 @@ "mapGeneNetwork.py": 1, "mapMers": 5, "mapMers-depth": 5, - "mapPacBio.sh": 30, + "mapPacBio.sh": 31, "map_and_profile.py": 1, "map_back": 1, "map_bed.py": 1, @@ -16275,8 +16277,8 @@ "mapula": 1, "mapview": 44, "mapviewToBed.pl": 1, - "maq2sam-long": 517, - "maq2sam-short": 517, + "maq2sam-long": 519, + "maq2sam-short": 519, "mareymaps_untrimmed.smk": 1, "marge": 1, "margin_cons": 2, @@ -16288,7 +16290,7 @@ "mark_partial_genes.py": 2, "mark_productivity": 1, "mark_prophage_features.py": 2, - "markdown-it": 52, + "markdown-it": 53, "markdown_py": 122, "markdups": 1, "markermagu": 1, @@ -16315,9 +16317,9 @@ "mask-ali.pl": 1, "mask-consensus.py": 2, "maskAlignedReads.py": 1, - "maskFastaFromBed": 274, + "maskFastaFromBed": 275, "maskFile.pl": 11, - "maskNregions.pl": 14, + "maskNregions.pl": 15, "mask_and_chain.smk": 1, "mask_gubbins_aln.py": 2, "mask_quality.py": 59, @@ -16373,7 +16375,7 @@ "matrix2meme": 13, "matrix_constructor.py": 1, "matrix_to_fasta.py": 1, - "matrixtocolumns.sh": 30, + "matrixtocolumns.sh": 31, "mauveAligner": 4, "mauveStatic": 4, "mauveToXMFA": 4, @@ -16492,7 +16494,7 @@ "mclcm": 23, "mclpipeline": 23, "mcmc_gtb.py": 1, - "mcmctree": 69, + "mcmctree": 70, "mcomp": 4, "mconfig": 15, "mcookie": 13, @@ -16517,9 +16519,9 @@ "md5cp.2.11.0": 10, "md5cp.3": 2, "md5cp.3.0.0": 2, - "md5fa": 517, + "md5fa": 519, "md5sum": 84, - "md5sum-lite": 517, + "md5sum-lite": 519, "md_coords": 11, "mdasim": 1, "mdassembler": 15, @@ -16607,7 +16609,7 @@ "mega_reads_assemble_cluster2.sh": 1, "mega_reads_assemble_polish.sh": 1, "mega_reads_assemble_ref.sh": 1, - "megablast": 34, + "megablast": 35, "megadepth": 1, "megagta": 1, "megagta.py": 1, @@ -16691,14 +16693,14 @@ "merge.py": 1, "merge2Dbed.pl": 5, "mergeBamWithSameSM.pl": 1, - "mergeBed": 274, + "mergeBed": 275, "mergeBreakpoints.py": 1, "mergeCharges.pl": 2, "mergeCounts": 3, "mergeData.pl": 5, "mergeMerBlasts": 1, "mergeNotCombined": 2, - "mergeOTUs.sh": 30, + "mergeOTUs.sh": 31, "mergeOutputs": 2, "mergePeaks": 5, "mergePolishes": 3, @@ -16731,7 +16733,7 @@ "merge_kallisto.R": 1, "merge_mapping_files.py": 1, "merge_masked_fasta_files.py": 2, - "merge_masking.pl": 11, + "merge_masking.pl": 12, "merge_matches_and_tile_coords_file.pl": 1, "merge_mate_pairs": 4, "merge_matrices.py": 1, @@ -16757,21 +16759,21 @@ "merge_wrapper.py": 1, "mergeabi": 1, "mergeassembly": 1, - "mergebarcodes.sh": 30, + "mergebarcodes.sh": 31, "merged_nodup2pairs.pl": 22, "mergefasta": 1, "mergefastq-p": 1, "mergegfa.py": 1, "mergeit": 2, - "mergepgm.sh": 29, + "mergepgm.sh": 30, "mergeprocess.sh": 1, "mergeqc.pl": 3, "merger": 25, - "mergeribo.sh": 29, - "mergesam.sh": 30, - "mergesketch.sh": 29, + "mergeribo.sh": 30, + "mergesam.sh": 31, + "mergesketch.sh": 30, "mergesolv": 24, - "mergesorted.sh": 29, + "mergesorted.sh": 30, "mergestatetrees": 1, "mergevcf": 1, "mergraphTh_128mer": 1, @@ -16834,7 +16836,7 @@ "metacortex": 1, "metadata_conda_debug.yaml": 31, "metadata_merger.py": 1, - "metaeuk": 4, + "metaeuk": 5, "metaflac": 47, "metagene": 3, "metagenome_pipeline.py": 1, @@ -17015,7 +17017,7 @@ "min_abundance_finder.pl": 1, "min_coverage": 1, "minab": 6, - "minced": 28, + "minced": 29, "mindagap.py": 1, "minesweeper": 2, "mini_align": 9, @@ -17053,7 +17055,7 @@ "minimus2-blat": 2, "minion": 1, "minipolish": 2, - "miniprot": 5, + "miniprot": 6, "minirmd": 1, "miniterm.py": 1, "miniwdl": 2, @@ -17175,7 +17177,7 @@ "mmpbsa_py_energy": 6, "mmpbsa_py_nabnmode": 6, "mmquant": 1, - "mmseqs": 45, + "mmseqs": 46, "mmseqs-server": 1, "mmseqs2.sh": 1, "mmvc": 1, @@ -17290,7 +17292,7 @@ "mount": 13, "mountpoint": 13, "move": 10, - "moveParameters.pl": 14, + "moveParameters.pl": 15, "movescu": 1, "mozroots": 15, "mp3treesim": 1, @@ -17329,7 +17331,7 @@ "mpiswipe": 1, "mpivars": 14, "mpl_utils.py": 1, - "mpmetis": 58, + "mpmetis": 59, "mpost": 1, "mpra-data-access-portal": 1, "mprobability": 1, @@ -17353,10 +17355,10 @@ "ms2rescore-report": 2, "msHOT2glf": 1, "msToGlf": 1, - "msa.sh": 30, + "msa.sh": 31, "msa2bam": 3, "msa2consensus.py": 1, - "msa2prfl.pl": 14, + "msa2prfl.pl": 15, "msa2pssm_unit_test": 5, "msa2vcf.py": 1, "msa_diff": 2, @@ -17378,24 +17380,24 @@ "mseqtools": 1, "msformatter": 1, "msfragger": 2, - "msgattrib": 5297, - "msgcat": 5297, - "msgcmp": 5297, - "msgcomm": 5297, - "msgconv": 5297, - "msgen": 5297, - "msgexec": 5297, + "msgattrib": 5298, + "msgcat": 5298, + "msgcmp": 5298, + "msgcomm": 5298, + "msgconv": 5298, + "msgen": 5298, + "msgexec": 5298, "msgf2pin": 1, "msgf_plus": 3, - "msgfilter": 5297, - "msgfmt": 5297, + "msgfilter": 5298, + "msgfmt": 5298, "msgfplus_search.rb": 1, - "msggrep": 5297, - "msginit": 5297, - "msgmerge": 5297, + "msggrep": 5298, + "msginit": 5298, + "msgmerge": 5298, "msgserv": 1, - "msgunfmt": 5297, - "msguniq": 5297, + "msgunfmt": 5298, + "msguniq": 5298, "msi": 1, "msi_cluster2reads": 1, "msi_clustr2map.pl": 1, @@ -17470,10 +17472,10 @@ "mult-mix-lwt": 1, "multi-bin-packing": 2, "multi-extract": 2, - "multiBamCov": 274, + "multiBamCov": 275, "multiBamSummary": 11, "multiBigwigSummary": 11, - "multiIntersectBed": 274, + "multiIntersectBed": 275, "multiSub": 1, "multi_length_hist.py": 1, "multi_parallel_pick_otus.py": 1, @@ -17518,7 +17520,7 @@ "mupdf-x11": 1, "mupdf-x11-curl": 1, "muraster": 1, - "muscle": 70, + "muscle": 71, "musixflx": 1, "musixtex": 1, "muspinsim": 1, @@ -17530,7 +17532,7 @@ "mutDiff.o": 1, "mut_annotate": 1, "mutate": 2, - "mutate.sh": 30, + "mutate.sh": 31, "mutate_ref": 1, "mutmap": 1, "mutool": 1, @@ -17538,7 +17540,7 @@ "mutscan": 1, "mutselomega": 1, "mutserve.jar": 1, - "muxbyname.sh": 30, + "muxbyname.sh": 31, "mv": 84, "mvicuna": 2, "mvip": 1, @@ -17551,7 +17553,7 @@ "my_imports.py": 1, "my_maker_functional_fasta": 1, "my_maker_functional_gff": 1, - "my_print_defaults": 103, + "my_print_defaults": 104, "mydbfinder.py": 1, "mygene_utils.py": 1, "myisam_ftdump": 10, @@ -17571,7 +17573,7 @@ "mysql.server": 5, "mysql_client_test": 7, "mysql_client_test_embedded": 2, - "mysql_config": 103, + "mysql_config": 104, "mysql_config_editor": 5, "mysql_convert_table_format": 5, "mysql_embedded": 2, @@ -17655,7 +17657,7 @@ "nasm": 1, "nasp": 1, "native2ascii": 112, - "natsort": 152, + "natsort": 153, "nb-classify": 1, "nb-train": 1, "nbmodel_stan2.py": 1, @@ -17663,7 +17665,7 @@ "nc3tonc4": 9, "nc4tonc3": 9, "ncbi-acc-download": 1, - "ncbi-genome-download": 9, + "ncbi-genome-download": 10, "ncbi-gtdb_map.py": 1, "ncbi.py": 1, "ncbiAcc2fa": 2, @@ -17697,12 +17699,12 @@ "ncrf_to_bed": 2, "ncrf_to_bed.py": 2, "ncurses5-config": 565, - "ncurses6-config": 7048, + "ncurses6-config": 7053, "ncursesw5-config": 703, - "ncursesw6-config": 7049, + "ncursesw6-config": 7054, "ndg_httpclient": 2, "ndisasm": 1, - "ndmetis": 58, + "ndmetis": 59, "ndx2resttop": 3, "nearblack": 38, "neato": 199, @@ -17717,6 +17719,7 @@ "neighbor_joining.py": 1, "nemoage": 1, "neo": 1, + "neodisambiguate": 1, "neofox": 1, "neofox-configure": 1, "neofox-epitope": 1, @@ -17758,7 +17761,7 @@ "neural_network_predict": 1, "neurodocker": 1, "newUCSCdb.pl": 1, - "new_species.pl": 14, + "new_species.pl": 15, "newcpgreport": 25, "newcpgseek": 25, "newpreMlocarna.pl": 1, @@ -17788,8 +17791,8 @@ "nf-queue": 13, "nf-test": 1, "nfe-umbrella-slice": 6, - "ngd": 9, - "ngettext": 5297, + "ngd": 10, + "ngettext": 5298, "ngg_barabasi_albert": 2, "ngg_barbell": 2, "ngg_complete": 2, @@ -17799,9 +17802,9 @@ "ngg_newman_watts_strogatz": 2, "ngg_path": 2, "ngg_ring_lattice": 2, - "nghttp": 4497, - "nghttpd": 4497, - "nghttpx": 4497, + "nghttp": 4500, + "nghttpd": 4500, + "nghttpx": 4500, "ngless": 2, "ngless-wrapped": 1, "nglview": 2, @@ -17835,9 +17838,9 @@ "ngsngs": 1, "ngsplotdb.py": 5, "ngsutils": 1, - "nhance.sh": 27, - "nhmmer": 181, - "nhmmscan": 181, + "nhance.sh": 28, + "nhmmer": 182, + "nhmmscan": 182, "nib-conform": 2, "nib-convert": 1, "nib-dicomfs": 3, @@ -17854,7 +17857,7 @@ "nib_intervals_to_fasta.py": 59, "nib_length.py": 59, "nice": 84, - "niceload": 104, + "niceload": 105, "nighthawk": 1, "nii2dcm": 1, "nimblegen2adf.pl": 1, @@ -17942,7 +17945,7 @@ "normalize_multicov.pl": 1, "normalize_oneD.R": 1, "normalize_table.py": 1, - "normalizer": 477, + "normalizer": 478, "normandcorrectwrapper.sh": 1, "nose2": 1, "nose2-2.7": 1, @@ -17960,7 +17963,7 @@ "noveliso.py": 1, "novo2maq": 1, "novo2paf": 2, - "novo2sam.pl": 518, + "novo2sam.pl": 520, "novoBreak": 1, "novoalign": 2, "novoalign-license-register": 2, @@ -17983,7 +17986,7 @@ "nproc": 84, "npth-config": 2, "npx": 16, - "nquire": 303, + "nquire": 304, "nquire.bak": 1, "nrForwardSplicedReads.pl": 1, "nr_ORFs_gff3.pl": 5, @@ -18024,7 +18027,7 @@ "ntsynt_run.py": 1, "ntsynt_run_pipeline.smk": 1, "ntsynt_synteny.py": 1, - "nucBed": 274, + "nucBed": 275, "nucamino": 1, "nucdiff": 1, "nucfreqsfasta": 1, @@ -18043,11 +18046,11 @@ "nullarbor.pl": 1, "nulltype_module.py": 1, "numCI": 4, - "numba": 145, + "numba": 146, "number-lines": 1, "numfmt": 84, "numlines": 1, - "numpy-config": 19, + "numpy-config": 20, "nunit-console": 10, "nunit-console2": 10, "nunit-console4": 10, @@ -18076,8 +18079,8 @@ "nw_topology": 2, "nw_trim": 2, "nwalign3": 1, - "nwns": 105, - "nwnsi": 105, + "nwns": 106, + "nwnsi": 106, "nxtrim": 2, "o-bars-for-each-column.R": 1, "o-boxplots.R": 1, @@ -18330,18 +18333,18 @@ "openslide-quickhash1sum": 2, "openslide-show-properties": 2, "openslide-write-png": 2, - "openssl": 7823, + "openssl": 7828, "opentargets_validator": 1, - "opj_compress": 657, - "opj_decompress": 657, - "opj_dump": 657, + "opj_compress": 658, + "opj_decompress": 658, + "opj_dump": 658, "opl2ofm": 1, "opsin": 1, "opt": 6, - "opt_init_and_term_probs.pl": 14, + "opt_init_and_term_probs.pl": 15, "optimir": 1, "optimize2.pl": 1, - "optimize_augustus.pl": 14, + "optimize_augustus.pl": 15, "optimize_primers.py": 1, "optionshandle_unit_test": 5, "opts-example-required.pl": 2, @@ -18552,8 +18555,8 @@ "painter.py": 20, "pair2tb": 1, "pairDiscordants.py": 1, - "pairToBed": 274, - "pairToPair": 274, + "pairToBed": 275, + "pairToPair": 275, "pair_sequences": 1, "pairalign": 2, "pairaln": 1, @@ -18575,7 +18578,7 @@ "paltohdf": 125, "pam": 1, "pamon": 44, - "pamp": 69, + "pamp": 70, "panISa.py": 1, "panX.py": 1, "pan_genome_assembly_statistics": 7, @@ -18616,10 +18619,10 @@ "panfeed-get-kmers": 1, "panfeed-plot": 1, "pangenome_variants_to_treeWAS.pl": 1, - "pango-list": 4018, + "pango-list": 4019, "pango-querymodules": 10, - "pango-segmentation": 2844, - "pango-view": 4821, + "pango-segmentation": 2845, + "pango-view": 4822, "pangoLEARN": 1, "pango_designation": 1, "pangolearn.smk": 1, @@ -18654,7 +18657,7 @@ "paragone": 1, "paragraph": 1, "paragraph2dot.py": 1, - "parallel": 105, + "parallel": 106, "parallel-fasta": 11, "parallel-fastq": 11, "parallel-fastq-dump": 1, @@ -18695,7 +18698,7 @@ "paraphase": 1, "parascopy": 1, "paraview-config": 1, - "parcat": 104, + "parcat": 105, "parebrick": 1, "parebrick-charts": 1, "parec": 44, @@ -18726,7 +18729,7 @@ "parseGapsNUCmer.pl": 1, "parseMismatch.py": 1, "parseSNP": 3, - "parseSim4Output.pl": 14, + "parseSim4Output.pl": 15, "parseSitePAML.pl": 1, "parse_annotation.py": 1, "parse_blast.pl": 1, @@ -18747,23 +18750,23 @@ "parse_typhi_mykrobe.py": 1, "parsec": 1, "parsecasm": 2, - "parset": 104, + "parset": 105, "parseval": 1, "parsimplify": 1, "parsing_functions.py": 1, "parsing_hmmscan": 1, "parsnp": 2, - "parsort": 88, + "parsort": 89, "partial_least_squares.py": 2, "partition": 7, "partition-graph.py": 7, "partition-smp": 5, - "partition.sh": 30, + "partition.sh": 31, "partitionBank": 2, "partition_fa.pl": 1, - "partition_gtf2gb.pl": 14, + "partition_gtf2gb.pl": 15, "partitions-supported": 1, - "pasapolyA2hints.pl": 14, + "pasapolyA2hints.pl": 15, "pash-3.0lx": 1, "pash2SAM": 1, "pash3.0.rb": 1, @@ -18771,7 +18774,7 @@ "pass": 1, "paste": 84, "pasteseq": 25, - "pasteurize": 240, + "pasteurize": 241, "pastml": 1, "pastrami.py": 1, "pasty": 1, @@ -18849,14 +18852,14 @@ "pbt_plotting_example.py": 38, "pbt_plotting_example.pyc": 1, "pbtools-gather": 1, - "pbunzip2": 82, + "pbunzip2": 83, "pbutgcns": 3, "pbvalidate": 1, "pbvariantcaller": 1, "pbvariantcaller_dir": 1, "pbwt": 1, - "pbzcat": 82, - "pbzip2": 82, + "pbzcat": 83, + "pbzip2": 83, "pca": 1, "pca_anim_mc.pl": 2, "pcatoy": 1, @@ -18865,14 +18868,14 @@ "pcnt_bezier.lua": 1, "pcoaPlot.py": 2, "pcor": 1, - "pcre-config": 4947, - "pcre2-config": 3727, + "pcre-config": 4948, + "pcre2-config": 3729, "pcre2_jit_test": 3681, - "pcre2grep": 3727, + "pcre2grep": 3729, "pcre2posix_test": 113, - "pcre2test": 3727, - "pcregrep": 4947, - "pcretest": 4947, + "pcre2test": 3729, + "pcregrep": 4948, + "pcretest": 4948, "pct2rgb.py": 5, "pctid_ani_sample": 1, "pcz_animate": 1, @@ -19054,8 +19057,8 @@ "pepsum": 1, "peptide-shaker": 2, "peptide_prophet.rb": 1, - "peptides2alternatives.pl": 14, - "peptides2hints.pl": 14, + "peptides2alternatives.pl": 15, + "peptides2hints.pl": 15, "pepwheel": 25, "pepwindow": 25, "pepwindowall": 25, @@ -19070,7 +19073,7 @@ "perf": 1, "perfect-square": 2, "perform_controls.pl": 1, - "perl": 1711, + "perl": 1713, "perl-doc": 2, "perl-reversion": 9, "perl5.22.0": 55, @@ -19078,17 +19081,17 @@ "perl5.26.2": 369, "perl5.30.3": 5, "perl5.32.0": 64, - "perl5.32.1": 1218, - "perlbug": 1711, - "perldoc": 1711, - "perlivp": 1711, + "perl5.32.1": 1220, + "perlbug": 1713, + "perldoc": 1713, + "perlivp": 1713, "perltex": 1, - "perlthanks": 1711, + "perlthanks": 1713, "permuteGPAT++": 31, "permuteSmooth": 31, "permute_structure.pl": 1, "permview": 15, - "perror": 103, + "perror": 104, "petl": 1, "peverify": 15, "pf2afm": 105, @@ -19188,6 +19191,7 @@ "phaser_gene_ae.py": 1, "phasescreen.pl": 1, "phasesubsample.pl": 1, + "phasing": 1, "phasius": 1, "phast": 2, "phastBias": 2, @@ -19195,7 +19199,7 @@ "phastMotif": 2, "phastOdds": 2, "phastaf": 1, - "phastconsDB2hints.pl": 14, + "phastconsDB2hints.pl": 15, "phava": 1, "phcue-ck": 1, "phd2afg": 2, @@ -19216,7 +19220,7 @@ "phist.py": 1, "phizz": 1, "phmm": 5, - "phmmer": 181, + "phmmer": 182, "phold": 1, "phonopy": 1, "phonopy-FHI-aims": 1, @@ -19232,13 +19236,13 @@ "phonopy-vasp-born": 1, "phonopy-vasp-efe": 1, "photo": 2, - "phrase-search": 301, + "phrase-search": 302, "phsolverserver": 3, "phy2nex": 1, "phykit": 1, "phylip": 10, "phylip2ali.pl": 1, - "phylip2fasta.sh": 30, + "phylip2fasta.sh": 31, "phyloBoot": 2, "phyloFit": 2, "phyloFlash.pl": 1, @@ -19426,7 +19430,7 @@ "pickle_cat.py": 1, "pickorientation.awk": 1, "pickout": 1, - "piconv": 1711, + "piconv": 1713, "picopore": 1, "picopore-realtime": 1, "picopore-rename": 1, @@ -19434,13 +19438,13 @@ "picrust2_pipeline.py": 1, "pidof": 1, "pigeon": 1, - "pigz": 124, + "pigz": 125, "pilconvert.py": 23, "pildriver.py": 23, "pilercr": 7, "pileup": 1, "pileup.py": 1, - "pileup.sh": 30, + "pileup.sh": 31, "pileupCaller": 1, "pileup_count_dir": 1, "pileup_count_to_context_dir": 1, @@ -19465,13 +19469,13 @@ "pints_caller": 1, "pints_normalizer": 1, "pints_visualizer": 1, - "pip": 3710, + "pip": 3714, "pip2": 1, "pip2.7": 1, - "pip3": 2635, + "pip3": 2639, "pipdeptree": 1, "pipelign": 1, - "pipeline.py": 2, + "pipeline.py": 3, "pipeline.sh": 1, "pipeline_V30.py": 1, "pipesz": 1, @@ -19621,13 +19625,13 @@ "pkfix-helper": 1, "pkg-config": 76, "pkg-config.bin": 76, - "pkgdata": 5862, + "pkgdata": 5866, "pkginfo": 10, "pkill": 1, "pktogf": 1, "pktype": 1, "pl2bat.pl": 6, - "pl2pm": 1711, + "pl2pm": 1713, "plaScope.sh": 1, "plac_runner.py": 63, "place_orient1.smk": 1, @@ -19662,8 +19666,8 @@ "plip": 1, "plncpro": 1, "plncpro_format_ff.sh": 1, - "plot-ampliconstats": 322, - "plot-bamstats": 517, + "plot-ampliconstats": 324, + "plot-bamstats": 519, "plot-bmprobs": 4, "plot-cnv": 1, "plot-insert-size-distribution": 2, @@ -19673,7 +19677,7 @@ "plot-vcfstats": 168, "plot.R": 1, "plot.pl": 1, - "plot.py": 2, + "plot.py": 3, "plotBfst.R": 17, "plotCorrGram.r": 5, "plotCorrelation": 11, @@ -19698,7 +19702,7 @@ "plotUnknownResults.R": 1, "plotWCfst.R": 17, "plotXPEHH.R": 17, - "plot_2d.pl": 46, + "plot_2d.pl": 47, "plot_3Dpie.R": 3, "plot_RC_vs_GC.R": 1, "plot_aggregate_cut_matrix.R": 1, @@ -19723,7 +19727,7 @@ "plot_histogram.r": 1, "plot_histogram.r.bak": 1, "plot_isoform_usage": 1, - "plot_len1.pl": 46, + "plot_len1.pl": 47, "plot_marey.R": 1, "plot_matrix_heatmap.sh": 1, "plot_orf_density": 2, @@ -19748,8 +19752,8 @@ "plotcircular.py": 1, "plotcon": 25, "plotcritic": 1, - "plotflowcell.sh": 29, - "plotgc.sh": 30, + "plotflowcell.sh": 30, + "plotgc.sh": 31, "plotgen": 13, "plotkmers": 1, "plotorf": 25, @@ -19792,11 +19796,11 @@ "pm4ngs-rnaseq-demo": 1, "pm4ngs-server": 1, "pm_which": 2, - "pma2apa": 27, - "pma2pme": 27, + "pma2apa": 28, + "pma2pme": 28, "pmap": 1, - "pmc2bioc": 27, - "pmc2info": 27, + "pmc2bioc": 28, + "pmc2info": 28, "pmd": 1, "pmdtools": 1, "pmemd_mdrun": 1, @@ -19822,21 +19826,21 @@ "pmxmutate": 1, "pn2pdf": 1, "pneumo-typer": 1, - "png-fix-itxt": 5903, + "png-fix-itxt": 5906, "pngcp": 89, - "pngfix": 5903, + "pngfix": 5906, "pngtogd": 237, "pngtogd2": 237, "pnps-gen": 1, - "poa": 21, + "poa": 22, "pocheck": 1, "poclcc": 3, - "pod2html": 1711, - "pod2man": 1711, - "pod2text": 1711, - "pod2usage": 1711, + "pod2html": 1713, + "pod2man": 1713, + "pod2text": 1713, + "pod2usage": 1713, "pod_cover": 12, - "podchecker": 1711, + "podchecker": 1713, "podselect": 438, "poetry": 6, "pointwise_datasets_concatenator.py": 1, @@ -19845,7 +19849,7 @@ "polish_with_illumina_assembly.sh": 1, "poller.py": 1, "poly.py": 7, - "polyA2hints.pl": 14, + "polyA2hints.pl": 15, "polyQtlseq": 1, "polydNdS": 1, "polydot": 25, @@ -19882,7 +19886,7 @@ "poppunk_sketch": 1, "poppunk_visualise": 1, "popscle": 1, - "popt": 52, + "popt": 53, "populations": 1, "pore_c": 1, "porechop": 12, @@ -19903,7 +19907,7 @@ "post_proc.sh": 1, "post_process.pl": 1, "post_processing.py": 1, - "postfilter.sh": 30, + "postfilter.sh": 31, "postgres": 47, "postmaster": 44, "postprocess-predictions": 2, @@ -19915,7 +19919,7 @@ "pp": 1, "pp-trace": 2, "pp2dot": 4, - "pp_simScore": 9, + "pp_simScore": 10, "ppanggolin": 1, "ppanini": 1, "ppanini_barplot": 1, @@ -19932,7 +19936,7 @@ "ppanini_test": 1, "pphs": 105, "ppi2html": 2, - "pplacer": 21, + "pplacer": 22, "ppltotf": 1, "ppm2tiff": 5296, "pprodigal": 1, @@ -20005,7 +20009,7 @@ "prepare-SV-breakpoints.py": 1, "prepare-rpbp-genome": 2, "prepare-stash": 1, - "prepareAlign": 15, + "prepareAlign": 16, "prepareHistFactory": 1, "prepare_data.smk": 1, "prepare_gene_ref.sh": 1, @@ -20030,6 +20034,7 @@ "preprocesser.py": 1, "preprocessfasta.py": 1, "preprocessing.pl": 1, + "preprocessing.py": 1, "preprocessing.smk": 1, "preprocessor.py": 1, "prequal": 1, @@ -20063,7 +20068,7 @@ "prinseq-graphs-noPCA.pl": 3, "prinseq-graphs.pl": 3, "prinseq-lite.pl": 3, - "print-columns": 215, + "print-columns": 216, "print.pl": 1, "printIcounts": 1, "printScaff": 2, @@ -20080,11 +20085,11 @@ "printenv": 84, "printf": 84, "printimage": 3, - "prints2prfl.pl": 14, + "prints2prfl.pl": 15, "printsextract": 25, "printsplitimage": 3, "printtiff": 3, - "printtime.sh": 30, + "printtime.sh": 31, "priority2meme": 13, "priv-net-run.sh": 1, "prj2make": 2, @@ -20131,11 +20136,11 @@ "process_sff.py": 1, "process_shortreads": 1, "processes.py": 1, - "processfrag.sh": 30, - "processhi-c.sh": 29, - "processspeed.sh": 30, + "processfrag.sh": 31, + "processhi-c.sh": 30, + "processspeed.sh": 31, "proda": 1, - "prodigal": 117, + "prodigal": 118, "prodigal-gv": 4, "prodigal.py": 1, "prodigal_stuff.py": 2, @@ -20158,22 +20163,22 @@ "project.sh.orig": 1, "projectAndStrip": 4, "projectFeatures": 3, - "project_tree_builder": 337, + "project_tree_builder": 338, "projinfo": 40, "projsync": 37, - "prokka": 23, - "prokka-abricate_to_fasta_db": 18, + "prokka": 24, + "prokka-abricate_to_fasta_db": 19, "prokka-annotation-refupdate.py": 1, - "prokka-biocyc_to_fasta_db": 23, - "prokka-build_kingdom_dbs": 23, - "prokka-cdd_to_hmm": 23, - "prokka-clusters_to_hmm": 23, - "prokka-genbank_to_fasta_db": 23, - "prokka-genpept_to_fasta_db": 23, - "prokka-hamap_to_hmm": 23, + "prokka-biocyc_to_fasta_db": 24, + "prokka-build_kingdom_dbs": 24, + "prokka-cdd_to_hmm": 24, + "prokka-clusters_to_hmm": 24, + "prokka-genbank_to_fasta_db": 24, + "prokka-genpept_to_fasta_db": 24, + "prokka-hamap_to_hmm": 24, "prokka-make_tarball": 6, - "prokka-tigrfams_to_hmm": 23, - "prokka-uniprot_to_fasta_db": 23, + "prokka-tigrfams_to_hmm": 24, + "prokka-uniprot_to_fasta_db": 24, "prokka.py": 1, "prokka_annotation.sh": 1, "proksee": 1, @@ -20267,7 +20272,7 @@ "protmapper": 1, "protobuf-net.dll": 2, "protobuf-net.xml": 2, - "protoc": 269, + "protoc": 270, "protoc-23.1.0": 1, "protoc-23.3.0": 4, "protoc-23.4.0": 6, @@ -20303,7 +20308,7 @@ "protxml_to_table.rb": 1, "prov-compare": 9, "prov-convert": 9, - "prove": 1711, + "prove": 1713, "provean": 1, "provean.sh": 1, "provis": 1, @@ -20347,10 +20352,10 @@ "psiCalculator.py": 1, "psiPerGene.py": 1, "psibl2seq_unit_test": 5, - "psiblast": 337, + "psiblast": 338, "psiblast_iteration_unit_test": 5, "psiblast_unit_test": 5, - "psicc": 1007, + "psicc": 1010, "psiclass": 1, "psiphi": 25, "psirc": 1, @@ -20363,7 +20368,7 @@ "psl2bed-float128": 14, "psl2bed-megarow": 14, "psl2bed-typical": 14, - "psl2sam.pl": 517, + "psl2sam.pl": 519, "psl2starch": 14, "psl2starch-float128": 14, "psl2starch-megarow": 14, @@ -20371,7 +20376,7 @@ "pslCDnaFilter": 2, "pslCheck": 1, "pslMap": 1, - "pslMap.pl": 14, + "pslMap.pl": 15, "pslMapPostChain": 1, "pslPosTarget": 1, "pslPretty": 7, @@ -20408,9 +20413,9 @@ "pt2to3": 75, "ptGAUL.sh": 1, "ptangle": 1, - "ptar": 1711, - "ptardiff": 1711, - "ptargrep": 1711, + "ptar": 1713, + "ptardiff": 1713, + "ptargrep": 1713, "ptdump": 75, "ptest": 1, "ptex": 1, @@ -20589,17 +20594,17 @@ "pydemult": 1, "pydicom": 1, "pydna_repeatfinder": 1, - "pydoc": 3709, - "pydoc3": 3378, - "pydoc3.10": 819, - "pydoc3.11": 270, + "pydoc": 3713, + "pydoc3": 3382, + "pydoc3.10": 820, + "pydoc3.11": 271, "pydoc3.12": 226, "pydoc3.4": 6, "pydoc3.5": 103, "pydoc3.6": 342, "pydoc3.7": 383, "pydoc3.8": 577, - "pydoc3.9": 652, + "pydoc3.9": 654, "pydownsampler": 1, "pyega3": 1, "pyemojify": 1, @@ -20614,13 +20619,13 @@ "pyflyte-execute": 1, "pyflyte-fast-execute": 1, "pyflyte-map-execute": 1, - "pyftmerge": 408, - "pyftsubset": 408, + "pyftmerge": 409, + "pyftsubset": 409, "pygal_gen.py": 2, "pygcap": 1, "pygenetic_code": 1, "pygmentex": 1, - "pygmentize": 253, + "pygmentize": 255, "pygmes": 1, "pygrun": 1, "pygtail": 2, @@ -20719,7 +20724,7 @@ "pytest": 146, "pytest-benchmark": 1, "pythia8-config": 1, - "python": 3710, + "python": 3714, "python-argcomplete-check-easy-install-script": 344, "python-argcomplete-tcsh": 191, "python-build": 2, @@ -20730,13 +20735,13 @@ "python2.5-config": 1, "python2.7": 331, "python2.7-config": 314, - "python3": 3379, - "python3-config": 3378, - "python3.1": 1315, - "python3.10": 819, - "python3.10-config": 819, - "python3.11": 270, - "python3.11-config": 270, + "python3": 3383, + "python3-config": 3382, + "python3.1": 1317, + "python3.10": 820, + "python3.10-config": 820, + "python3.11": 271, + "python3.11-config": 271, "python3.12": 226, "python3.12-config": 226, "python3.4": 6, @@ -20757,8 +20762,8 @@ "python3.7m-config": 383, "python3.8": 577, "python3.8-config": 577, - "python3.9": 652, - "python3.9-config": 652, + "python3.9": 654, + "python3.9-config": 654, "pythonsh": 2, "pythontex": 1, "pytleap": 6, @@ -20794,7 +20799,7 @@ "qcli_make_script": 3, "qcollectiongenerator": 250, "qcollectiongenerator-qt4": 3, - "qconvex": 14, + "qconvex": 15, "qcp": 2, "qcreporter.py": 1, "qcs": 2, @@ -20809,7 +20814,7 @@ "qdbusviewer6": 1, "qdbusxml2cpp": 248, "qdbusxml2cpp-qt4": 3, - "qdelaunay": 14, + "qdelaunay": 15, "qdistancefieldgenerator": 134, "qdistancefieldgenerator6": 1, "qdoc": 223, @@ -20820,13 +20825,13 @@ "qfy.py": 1, "qgltf": 182, "qgrs": 1, - "qhalf": 14, + "qhalf": 15, "qhelpconverter": 116, "qhelpconverter-qt4": 3, "qhelpgenerator": 250, "qhelpgenerator-qt4": 3, "qhery": 1, - "qhull": 14, + "qhull": 15, "qiime2lefse.py": 1, "qiimeToMaaslin.py": 1, "qiskit-xyz2pdb": 1, @@ -20909,7 +20914,7 @@ "qual-recalib-stat.3.0.0": 2, "qual_offset.py": 2, "qual_trim.py": 2, - "qualfa2fq.pl": 158, + "qualfa2fq.pl": 159, "qualimap": 3, "qualitativeEvaluation.py": 1, "qualityScores": 5, @@ -20958,7 +20963,7 @@ "quorum": 4, "quorum_create_database": 4, "quorum_error_correct_reads": 4, - "quote-grouped-elements": 27, + "quote-grouped-elements": 28, "qv_to_bqv.py": 59, "qvality": 1, "qvalue": 13, @@ -20967,7 +20972,7 @@ "qvinaw": 1, "qvinaw_split": 1, "qvkgen": 134, - "qvoronoi": 14, + "qvoronoi": 15, "qwebengine_convert_dict": 139, "r-seurat-scripts-post-install-tests.bats": 2, "r-seurat-scripts-post-install-tests.sh": 2, @@ -21023,13 +21028,13 @@ "randRemoveBackground.pl": 5, "rand_sel_reads_from_bam": 1, "randfold": 3, - "randomBed": 274, + "randomBed": 275, "randomFQ": 1, "randomGeneSample": 4, "randomJunctionFilter": 1, "randomList2.pl": 1, "randomRsIds_2.0": 1, - "randomSplit.pl": 14, + "randomSplit.pl": 15, "random_forest.py": 2, "random_forest_classifier": 1, "random_forest_regressor": 1, @@ -21039,13 +21044,13 @@ "random_resampler.py": 1, "random_split": 1, "randomdata": 2, - "randomgenome.sh": 29, + "randomgenome.sh": 30, "randomizeGroupFile.pl": 5, "randomizeMotifs.pl": 5, "randomlinks": 2, "randomly_select_sequences.py": 1, "randomly_subsample_fastq.py": 2, - "randomreads.sh": 30, + "randomreads.sh": 31, "randrep": 1, "randseq": 2, "randtree": 7, @@ -21106,7 +21111,7 @@ "rbhtfinder": 1, "rblist": 2, "rbmoegrid": 2, - "rbox": 14, + "rbox": 15, "rbpbench": 1, "rbrms": 1, "rbs": 9, @@ -21127,8 +21132,8 @@ "rcexplain.3.0.3": 1, "rcexplain.3.1.0": 1, "rcf": 1, - "rchive": 302, - "rchive.Linux": 302, + "rchive": 303, + "rchive.Linux": 303, "rchive.go": 14, "rcl": 1, "rcl-dot-resmap.pl": 1, @@ -21145,7 +21150,7 @@ "rdfgraphisomorphism": 33, "rdfpipe": 33, "rdfs2dot": 33, - "rdjpgcom": 5786, + "rdjpgcom": 5789, "rdkit2fps": 1, "rdma_client": 24, "rdma_server": 24, @@ -21198,13 +21203,13 @@ "reader": 1, "readfq": 1, "readinfo2cam": 2, - "readlength.sh": 30, + "readlength.sh": 31, "readlink": 84, "readme.pdf": 73, "readmutselomega": 1, "readnodemutsel": 1, "readpb_mpi": 1, - "readqc.sh": 29, + "readqc.sh": 30, "readreduce": 1, "reads.py": 1, "reads2graph": 1, @@ -21223,7 +21228,7 @@ "readucks": 1, "reago.py": 1, "real": 1, - "real-tbl2asn": 17, + "real-tbl2asn": 18, "realSFS": 1, "real_time_concatenator.py": 1, "realignPolishes": 3, @@ -21243,7 +21248,7 @@ "recgraph": 1, "reciprocal_blast_local": 1, "reciprocal_blast_local.py": 1, - "recode-sr-latin": 5297, + "recode-sr-latin": 5298, "recode_dir": 1, "recode_dir_legacy": 1, "recoder": 25, @@ -21274,14 +21279,14 @@ "redbuild": 1, "redepth.pl": 4, "redoalignment_unit_test": 5, - "reduce": 6, + "reduce": 7, "reduce-alignment": 13, "reduce-kmers": 1, "reduce-qmers": 1, "reduce_add_hydrogens": 1, "reduce_remove_hydrogens": 1, "reduce_sr": 1, - "reducesilva.sh": 30, + "reducesilva.sh": 31, "redundans.py": 1, "ref-eval": 1, "ref-eval-estimate-true-assembly": 1, @@ -21289,7 +21294,7 @@ "ref-variation.3": 2, "ref-variation.3.0.3": 1, "ref-variation.3.1.0": 1, - "ref2pmid": 27, + "ref2pmid": 28, "refFinder": 1, "ref_map.pl": 1, "ref_seqs_from_bam": 1, @@ -21317,15 +21322,15 @@ "refinemap.sh": 1, "refold": 5, "reformat-seq.sh": 1, - "reformat.sh": 30, + "reformat.sh": 31, "reformat_fasta_residue_lengths.py": 2, "reformat_tables.py": 1, "reformat_transcripts": 3, - "reformatpb.sh": 26, + "reformatpb.sh": 27, "refresh-versioned": 1, "refseq-download": 1, "refseq-extract": 1, - "refseq-nm-cds": 27, + "refseq-nm-cds": 28, "refseq_masher": 1, "refseqget": 25, "refseqsplit.py": 2, @@ -21507,15 +21512,15 @@ "remove_user_specified_row_col.py": 2, "remove_utrs.py": 1, "remove_white_space_in_id.pl": 1, - "removebadbarcodes.sh": 30, - "removecatdogmousehuman.sh": 30, - "removehuman.sh": 30, - "removehuman2.sh": 30, - "removemicrobes.sh": 30, - "removesmartbell.sh": 30, + "removebadbarcodes.sh": 31, + "removecatdogmousehuman.sh": 31, + "removehuman.sh": 31, + "removehuman2.sh": 31, + "removemicrobes.sh": 31, + "removesmartbell.sh": 31, "remuRNA": 1, "rename": 20, - "rename.sh": 30, + "rename.sh": 31, "renameChr.pl": 1, "renamePeaks.pl": 5, "renameReads": 2, @@ -21527,10 +21532,10 @@ "rename_filter_fastq.pl": 1, "rename_from_fasta.sh": 1, "rename_gtf.py": 2, - "rename_species.pl": 4, + "rename_species.pl": 5, "rename_vcf_chrom.py": 3, "renamedat.pl": 2, - "renameimg.sh": 30, + "renameimg.sh": 31, "renano": 1, "renderer": 12, "reneo": 1, @@ -21539,13 +21544,13 @@ "renumberRMFiles.pl": 4, "renumber_structure": 1, "reorder": 1, - "reorder-columns": 303, + "reorder-columns": 304, "reorder-fasta": 3, "reorder.smk": 1, "reorient_sequences_by_id.py": 2, "repack-pubmed": 1, "repair": 5, - "repair.sh": 30, + "repair.sh": 31, "repair_run_summary.rb": 1, "repaq": 1, "reparation.pl": 1, @@ -21563,7 +21568,7 @@ "replace_homopolymeric_repeats_with_Ns.py": 2, "replaceall.pl": 2, "replacecopyright": 3, - "replaceheaders.sh": 30, + "replaceheaders.sh": 31, "replot.r": 5, "repo2solv": 24, "repolish.py": 1, @@ -21590,7 +21595,7 @@ "reporter.pl": 1, "reportfunk": 1, "reports.py": 1, - "representative.sh": 30, + "representative.sh": 31, "repstopdf": 1, "requantAlignedValues.py": 1, "request": 1, @@ -21605,7 +21610,7 @@ "rescue_fusion.py": 1, "reseq": 1, "reseq-prepare-names.py": 1, - "reset": 7755, + "reset": 7760, "resetFragLibrary": 2, "reset_array.pl": 1, "reset_experiment.pl": 1, @@ -21645,7 +21650,7 @@ "retrieveMinRowCol.r": 1, "retrieve_data.py": 1, "retrieve_sequences_from_fasta.pl": 7, - "retroDB2hints.pl": 14, + "retroDB2hints.pl": 15, "retroseq.pl": 1, "rev": 13, "revFasta": 2, @@ -21730,7 +21735,7 @@ "rm": 84, "rmOut2Fasta.pl": 15, "rmOutToGFF3.pl": 15, - "rmRedundantHints.pl": 14, + "rmRedundantHints.pl": 15, "rmToTrackHub.pl": 4, "rmToUCSCTables.pl": 15, "rm_chim": 1, @@ -21749,7 +21754,7 @@ "rmdir": 84, "rmic": 421, "rmid": 421, - "rmiregistry": 542, + "rmiregistry": 544, "rmkdepend": 1, "rmlst-api": 1, "rmsk2bed": 14, @@ -21869,11 +21874,11 @@ "rpkmforgenes.py": 1, "rppr": 17, "rps_unit_test": 5, - "rpsblast": 346, - "rpsbproc": 263, - "rpstblastn": 337, - "rqcfilter.sh": 30, - "rqcfilter2.sh": 29, + "rpsblast": 347, + "rpsbproc": 264, + "rpstblastn": 338, + "rqcfilter.sh": 31, + "rqcfilter2.sh": 30, "rqw": 1, "rrbsreference": 1, "rrmscorer": 1, @@ -21971,12 +21976,12 @@ "run-htseq-workflow": 1, "run-mummer1": 44, "run-mummer3": 44, - "run-ncbi-converter": 302, + "run-ncbi-converter": 303, "run-ncbi-converter.bak": 1, "run-ntedit": 1, "run-roh.pl": 157, "run-rpbp-pipeline": 2, - "run-sepp.sh": 4, + "run-sepp.sh": 5, "run-signalp": 3, "run-singularity": 4, "run-t1k": 1, @@ -21986,7 +21991,7 @@ "run-unittest.py": 10, "run-vadr-local-tests.sh": 1, "runAdt": 1, - "runAllSim4.pl": 14, + "runAllSim4.pl": 15, "runAmos": 2, "runAssembly-MPI.sh": 1, "runAssembly.sh": 1, @@ -22067,7 +22072,7 @@ "run_Trinity_edgeR_pipeline.pl": 1, "run_Trinity_from_samples_file.pl": 2, "run_TrinotateWebserver.pl": 1, - "run_abundance.py": 3, + "run_abundance.py": 4, "run_and_plot_chromeister.sh": 1, "run_anything.pl": 1, "run_arriba.sh": 1, @@ -22156,7 +22161,7 @@ "run_resfinder.py": 1, "run_segalign": 2, "run_segalign_repeat_masker": 2, - "run_sepp.py": 4, + "run_sepp.py": 5, "run_seqtools.py": 7, "run_snp_pipeline.py": 1, "run_snp_pipeline.sh": 1, @@ -22167,17 +22172,17 @@ "run_syny.pl": 1, "run_tasmanian": 1, "run_tests": 1, - "run_tipp.py": 3, - "run_tipp_tool.py": 3, + "run_tipp.py": 4, + "run_tipp_tool.py": 4, "run_treeshrink": 2, "run_treeshrink.py": 2, "run_type_CP.sh": 2, "run_unicycler.py": 1, - "run_upp.py": 4, + "run_upp.py": 5, "run_vote.py": 1, "run_voteSpecies.py": 1, "run_vsclust_app.R": 1, - "run_with_lock": 327, + "run_with_lock": 328, "run_workflows.py": 1, "run_x_platform_fuzz_corpus": 38, "runabyss.py": 1, @@ -22190,7 +22195,7 @@ "runef": 3, "runerrcor.py": 1, "rungs": 1, - "runhmm.sh": 24, + "runhmm.sh": 25, "runidba.py": 1, "runjob": 2, "runmitos.py": 2, @@ -22307,10 +22312,10 @@ "sam2starch-float128": 14, "sam2starch-megarow": 14, "sam2starch-typical": 14, - "sam2vcf.pl": 517, + "sam2vcf.pl": 519, "samFLAGinfo.pl": 1, "samFilter": 1, - "samMap.pl": 14, + "samMap.pl": 15, "samPileupConsensus": 2, "samToDelta": 1, "sam_add_rg.pl": 16, @@ -22367,11 +22372,11 @@ "samtoh5": 1, "samtom4": 1, "samtom5_dir": 1, - "samtools": 542, - "samtools.pl": 517, + "samtools": 544, + "samtools.pl": 519, "samtools_0.1.18": 3, "samtools_mpileup_to_var": 1, - "samtoroc.sh": 30, + "samtoroc.sh": 31, "samview": 2, "samview-util": 2, "samview-util.3": 2, @@ -22490,7 +22495,7 @@ "scancel-range": 1, "scancel_range.py": 1, "scandeps.pl": 2, - "scanpy": 45, + "scanpy": 46, "scanpy-cli": 1, "scanpy-filter-cells": 1, "scanpy-filter-genes": 1, @@ -22556,13 +22561,13 @@ "scip_utils.py": 1, "sciphi": 1, "sciphin": 1, - "scipiogff2gff.pl": 14, + "scipiogff2gff.pl": 15, "scitokens-create": 1, "scitokens-list-access": 1, "scitokens-test": 1, "scitokens-test-access": 1, "scitokens-verify": 1, - "sclient": 5833, + "sclient": 5837, "sclust_summary.sh": 1, "scluster": 3, "scmap-cli-post-install-tests.bats": 1, @@ -22581,7 +22586,7 @@ "scn-post-install-tests.sh": 1, "scn-predict.R": 1, "scn-train-model.R": 1, - "scn2xml": 27, + "scn2xml": 28, "scoary": 3, "scoary_GUI": 3, "scompare": 6, @@ -22672,7 +22677,7 @@ "sdust": 153, "sea": 2, "seagen": 3, - "seal.sh": 30, + "seal.sh": 31, "sealer-gr": 1, "searchSVbyGene": 1, "search_fusion_gene": 1, @@ -22688,12 +22693,12 @@ "secondary2split.py": 1, "sectosupp": 1, "secutil": 15, - "sed": 3944, + "sed": 3945, "seealso": 25, "seedRand.py": 1, "seedme": 1, "seedme.py": 1, - "seedtop": 84, + "seedtop": 85, "seeker.pl": 1, "seer": 1, "segToGc": 1, @@ -22701,7 +22706,7 @@ "segalign": 2, "segalign_repeat_masker": 2, "segemehl.x": 1, - "segmasker": 337, + "segmasker": 338, "segment-cnv": 1, "segment.py": 1, "segmentFst": 31, @@ -22761,9 +22766,9 @@ "selene_sdk": 1, "selenium-manager": 1, "selscan": 1, - "sem": 104, + "sem": 105, "send2trash": 21, - "sendsketch.sh": 30, + "sendsketch.sh": 31, "senergy": 6, "sensv": 1, "sentieon": 1, @@ -22773,7 +22778,7 @@ "sepdRangerfusion": 1, "seperatePFMs.py": 1, "seperatePFMsAndCheckActivity.py": 1, - "seppJsonMerger.jar": 4, + "seppJsonMerger.jar": 5, "seq": 84, "seq-gen": 3, "seq-seq-pan": 1, @@ -22786,7 +22791,7 @@ "seq2onehot": 1, "seq2profile.pl": 5, "seq2science": 2, - "seq_cache_populate.pl": 517, + "seq_cache_populate.pl": 519, "seq_count": 2, "seq_diff": 1, "seq_download.py": 2, @@ -22810,7 +22815,7 @@ "seqidtype": 1, "seqinfosrc_unit_test": 5, "seqio.py": 1, - "seqkit": 31, + "seqkit": 32, "seqmagick": 2, "seqmap": 2, "seqmatchall": 25, @@ -22859,12 +22864,12 @@ "seqxref": 25, "seqxrefget": 25, "seqyclean": 1, - "serialver": 542, + "serialver": 544, "seroba": 1, "serotypefinder": 1, "servertell": 25, "servertool": 117, - "setStopCodonFreqs.pl": 12, + "setStopCodonFreqs.pl": 13, "setTableDefaults.py": 5, "set_finder": 1, "set_haploid_region": 1, @@ -22987,12 +22992,12 @@ "sharq.3": 2, "sharq.3.0.0": 2, "shasta": 1, - "shasum": 1711, + "shasum": 1713, "shed-tools": 2, "shell_utils.py": 1, "shiboken2": 2, "shiboken_tool.py": 2, - "shiftBed": 261, + "shiftBed": 262, "shigatyper": 1, "shigeifinder": 1, "shims.py": 1, @@ -23039,16 +23044,16 @@ "showserver": 25, "showtable": 3, "shred": 84, - "shred.sh": 30, + "shred.sh": 31, "shrink_bedgraph": 1, "shrink_db.pl": 1, - "shrinkaccession.sh": 30, + "shrinkaccession.sh": 31, "shuf": 84, "shuffle": 4, - "shuffle.sh": 30, - "shuffle2.sh": 29, + "shuffle.sh": 31, + "shuffle2.sh": 30, "shuffleBank": 2, - "shuffleBed": 274, + "shuffleBed": 275, "shuffleCodons.rb": 2, "shuffleCodonsAddMotifs.rb": 2, "shuffleSequences_fasta.pl": 1, @@ -23082,7 +23087,7 @@ "sim-cover2": 2, "sim-shotgun": 2, "sim4db": 3, - "sim_client": 5833, + "sim_client": 5837, "sim_reads": 10, "sim_reads.o": 10, "sim_reads_tran": 10, @@ -23105,7 +23110,7 @@ "simple": 5, "simple-overlap": 2, "simpleContigLoader": 2, - "simpleFastaHeaders.pl": 14, + "simpleFastaHeaders.pl": 15, "simple_numeric_bow_union.py": 1, "simple_sv_annotation.py": 1, "simple_unzip.py": 1, @@ -23113,7 +23118,7 @@ "simplepbsa": 6, "simplepp": 1, "simplify-fasta": 1, - "simplifyFastaHeaders.pl": 14, + "simplifyFastaHeaders.pl": 15, "simplifyLibraries": 2, "simqual": 6, "simread": 6, @@ -23190,14 +23195,14 @@ "skc": 1, "skera": 1, "skesa": 10, - "sketch.sh": 30, - "sketchblacklist.sh": 30, - "sketchblacklist2.sh": 27, + "sketch.sh": 31, + "sketchblacklist.sh": 31, + "sketchblacklist2.sh": 28, "sketchlib": 1, "sketchy": 1, "skewer": 1, "skg_convert.py": 2, - "skip-if-file-exists": 272, + "skip-if-file-exists": 273, "skip_psl_self.awk": 2, "skip_psl_self_ss.awk": 2, "skip_selfmatches.py": 1, @@ -23229,7 +23234,7 @@ "slivar": 1, "slncky": 2, "slncky.v1.0": 2, - "slopBed": 274, + "slopBed": 275, "slow5curl": 1, "slow5tools": 1, "slsh": 2, @@ -23347,8 +23352,8 @@ "snp-pileup": 2, "snp-pileup-quickbam": 1, "snp-sites": 13, - "snp2hgvs": 215, - "snp2tbl": 215, + "snp2hgvs": 216, + "snp2tbl": 216, "snpEff": 23, "snpEffAnnotate.py": 3, "snp_diversity.py": 1, @@ -23373,7 +23378,7 @@ "snver-pool": 1, "soap": 2, "soap.coverage": 2, - "soap2sam.pl": 517, + "soap2sam.pl": 519, "soapcpp2": 1, "soapsplice": 1, "soapsuds": 15, @@ -23421,11 +23426,11 @@ "sort-last-maf": 1, "sort-snos": 2, "sort-snos.pl": 2, - "sort-table": 215, - "sort-uniq-count": 303, - "sort-uniq-count-rank": 303, + "sort-table": 216, + "sort-uniq-count": 304, + "sort-uniq-count-rank": 304, "sort2": 2, - "sortBed": 274, + "sortBed": 275, "sortByRefAndCor.pl": 1, "sortGeneMark.py": 2, "sortHits": 4, @@ -23442,7 +23447,7 @@ "sort_psl.o": 10, "sort_reads": 10, "sort_reads.o": 10, - "sortbyname.sh": 30, + "sortbyname.sh": 31, "sorted_merge": 1, "sortgrcd": 4, "sortmerna": 6, @@ -23500,7 +23505,7 @@ "sparsetable_unittest": 1, "spatypes.txt": 1, "spdi2prod": 12, - "spdi2tbl": 215, + "spdi2tbl": 216, "specialk": 1, "spectra-cluster-cli": 1, "spectral_clustering": 1, @@ -23522,7 +23527,7 @@ "sphinx-quickstart": 40, "spine.pl": 1, "spinner.py": 1, - "splain": 1711, + "splain": 1713, "splash": 1, "splice_site_summary.pl": 1, "spliceai": 1, @@ -23531,7 +23536,7 @@ "splinter.pl": 1, "splinter_scaffolds.pl": 1, "split": 84, - "split-at-intron": 215, + "split-at-intron": 216, "split-bed12-blocks": 3, "split-coverages.py": 1, "split-fasta": 1, @@ -23552,7 +23557,7 @@ "splitLongKUnitigs.pl": 1, "splitMEM": 1, "splitMSE.py": 1, - "splitMfasta.pl": 14, + "splitMfasta.pl": 15, "splitReads": 6, "splitScaffoldsAtNs.pl": 1, "splitScaffoldsAtNs.sh": 1, @@ -23609,10 +23614,10 @@ "split_scaffolds_to_subcontigs.pl": 1, "split_sequence_data.py": 1, "split_sequence_file_on_sample_ids.py": 1, - "split_sequences.py": 4, + "split_sequences.py": 5, "split_wide_dataset.py": 1, - "split_wiggle.pl": 14, - "splitbytaxa.sh": 30, + "split_wiggle.pl": 15, + "splitbytaxa.sh": 31, "splitcode": 1, "splitfa": 1, "splitfa.c": 1, @@ -23622,14 +23627,14 @@ "splitindex": 1, "splitmaf.pl": 1, "splitmates": 6, - "splitnextera.sh": 30, + "splitnextera.sh": 31, "splitp": 1, "splitreads": 6, - "splitribo.sh": 27, + "splitribo.sh": 28, "splitrim": 1, - "splitsam.sh": 30, - "splitsam4way.sh": 30, - "splitsam6way.sh": 30, + "splitsam.sh": 31, + "splitsam4way.sh": 31, + "splitsam6way.sh": 31, "splitsource": 25, "splitter": 25, "splitubam": 1, @@ -23657,11 +23662,11 @@ "sqStoreDumpMetaData": 6, "sqfscat": 2, "sqfstar": 2, - "sql": 104, + "sql": 105, "sqlformat": 9, "sqlite.pl": 1, - "sqlite3": 2714, - "sqlite3_analyzer": 7155, + "sqlite3": 2716, + "sqlite3_analyzer": 7159, "sqlitebrowser": 1, "sqlmetal": 15, "sqlsharp": 15, @@ -23941,14 +23946,14 @@ "stats-cat": 1, "stats-merge": 1, "stats-select": 1, - "stats.sh": 30, + "stats.sh": 31, "stats2plot.pl": 1, "statsGenerator": 3, "statsPlot.Rmd": 1, "stats_alignment.py": 1, "stats_from_bam": 1, "stats_utils.py": 1, - "statswrapper.sh": 30, + "statswrapper.sh": 31, "stdbuf": 84, "stecfinder": 1, "steel-mill": 2, @@ -23989,16 +23994,17 @@ "strainscan": 1, "strainscan_build": 1, "stranger": 1, + "strawk": 1, "stream": 76, - "stream-local": 27, - "stream-pubmed": 301, + "stream-local": 28, + "stream-pubmed": 302, "stream_atac": 1, "stream_run_test": 1, "streamer_1d": 22, "streamlit": 6, "streamlit.cmd": 6, - "streamsam.sh": 30, - "streamzip": 1282, + "streamsam.sh": 31, + "streamzip": 1284, "streme": 6, "streme_xml_to_html": 6, "stress-ng": 1, @@ -24012,7 +24018,7 @@ "stringmeup": 2, "strings": 8, "stringtie": 7, - "stringtie2fa.py": 4, + "stringtie2fa.py": 5, "strip": 9, "strip-it": 1, "strip-seq-from-bam.py": 1, @@ -24025,6 +24031,7 @@ "strling": 1, "strling-outliers.py": 1, "strobealign": 4, + "strpg": 1, "strucVis": 1, "structConnect": 1, "structure": 1, @@ -24065,13 +24072,14 @@ "subseq": 1, "subseq.py": 2, "subset": 2, + "subset-bam": 1, "subset.py": 1, "subset_alignments.pl": 1, "subset_data.py": 2, "subsetdb": 2, - "subsketch.sh": 29, + "subsketch.sh": 30, "subtract-bed": 3, - "subtractBed": 274, + "subtractBed": 275, "subtractBedGraphs.pl": 5, "subtractBedGraphsDirectory.pl": 5, "sucos": 1, @@ -24084,7 +24092,7 @@ "sumaclust": 3, "sumatra": 1, "sumlabels": 1, - "sumlabels.py": 66, + "sumlabels.py": 67, "summ_domain_ident.pl": 7, "summarize": 1, "summarize-ancestors": 1, @@ -24093,7 +24101,7 @@ "summarize-rpbp-predictions": 2, "summarize-rpbp-profile-construction": 2, "summarize-tin.py": 1, - "summarizeACGTcontent.pl": 14, + "summarizeACGTcontent.pl": 15, "summarizeConsensus": 1, "summarizeMultiTest": 2, "summarizePolishes": 3, @@ -24106,15 +24114,15 @@ "summarize_sample_GFF_junctions.py": 1, "summarize_taxa.py": 1, "summarize_taxa_through_plots.py": 1, - "summarizecontam.sh": 29, - "summarizecoverage.sh": 26, - "summarizecrossblock.sh": 30, + "summarizecontam.sh": 30, + "summarizecoverage.sh": 27, + "summarizecrossblock.sh": 31, "summarized_coverage_profiles.R": 1, - "summarizemerge.sh": 30, - "summarizequast.sh": 30, - "summarizescafstats.sh": 30, - "summarizeseal.sh": 30, - "summarizesketch.sh": 30, + "summarizemerge.sh": 31, + "summarizequast.sh": 31, + "summarizescafstats.sh": 31, + "summarizeseal.sh": 31, + "summarizesketch.sh": 31, "summary.py": 1, "summary_from_stats": 1, "summary_get_organelle_output.py": 1, @@ -24125,7 +24133,7 @@ "summation.pl": 2, "summits.py": 1, "sumtrees": 1, - "sumtrees.py": 68, + "sumtrees.py": 69, "superScaffoldGenerator.pl": 1, "super_distance": 1, "superfocus": 1, @@ -24236,11 +24244,11 @@ "synctex": 1, "syngap": 1, "synteny_block.py": 1, - "synthmda.sh": 30, + "synthmda.sh": 31, "syri": 1, "syrupy.py": 1, "sysc": 1, - "systematic-mutations": 7, + "systematic-mutations": 8, "t1k-build.pl": 1, "t1k-merge.py": 1, "t1k-smartseq.pl": 1, @@ -24250,7 +24258,7 @@ "tRNAscan-SE": 14, "tRNAscan-SE.conf": 14, "tRNAscanChecker.py": 1, - "t_coffee": 70, + "t_coffee": 71, "t_coffee_run.py": 2, "ta2ace": 2, "tab-to-vcf": 10, @@ -24260,7 +24268,7 @@ "tab2krona.py": 1, "tab2mapper.pl": 1, "tab2ovls": 2, - "tabix": 714, + "tabix": 716, "tabix++": 23, "table2asn": 3, "table_add_column.py": 59, @@ -24269,7 +24277,7 @@ "tableproxy64": 1, "tableschema": 1, "tablet": 1, - "tabs": 7755, + "tabs": 7760, "tabulate": 132, "tabulate.py": 1, "tabulator": 1, @@ -24282,17 +24290,17 @@ "tadaridaC.r": 1, "tadaridaD": 1, "tadbit": 1, - "tadpipe.sh": 30, - "tadpole.sh": 30, + "tadpipe.sh": 31, + "tadpole.sh": 31, "tadrep": 1, "tadtool": 1, - "tadwrapper.sh": 30, + "tadwrapper.sh": 31, "taeper": 1, "tag": 1, "tag2bed.pl": 5, "tag2pos.pl": 5, "tag2sort": 1, - "tagBam": 274, + "tagBam": 275, "tagDir2HiCsummary.pl": 5, "tagDir2bed.pl": 5, "tagDir2hicFile.pl": 5, @@ -24362,7 +24370,7 @@ "tantan": 1, "tap": 1, "tap2": 1, - "tar": 57, + "tar": 58, "taranis.py": 1, "taranis_configuration.py": 1, "tarchive2amos": 2, @@ -24409,7 +24417,7 @@ "taxonlist.tsv": 2, "taxonomy-reader": 1, "taxonomy.py": 1, - "taxonomy.sh": 30, + "taxonomy.sh": 31, "taxonomy2tree": 1, "taxonomy_filter_fastq": 1, "taxonomy_filter_refseq": 1, @@ -24418,24 +24426,24 @@ "taxpasta": 1, "taxprof": 1, "taxsbp": 2, - "taxserver.sh": 30, - "taxsize.sh": 30, + "taxserver.sh": 31, + "taxsize.sh": 31, "taxsummary2krona": 2, "taxtree.py": 2, - "taxtree.sh": 30, + "taxtree.sh": 31, "tb-ml": 1, "tb-profiler": 1, "tb_bed_to_region_list": 1, "tb_region_list_to_bed": 1, "tb_variant_filter": 1, "tba": 1, - "tbl2asn": 29, - "tbl2asn-test": 12, - "tbl2prod": 203, - "tbl2xml": 215, - "tblastn": 337, - "tblastn_vdb": 50, - "tblastx": 337, + "tbl2asn": 30, + "tbl2asn-test": 13, + "tbl2prod": 204, + "tbl2xml": 216, + "tblastn": 338, + "tblastn_vdb": 51, + "tblastx": 338, "tblite": 1, "tbox-scan": 1, "tbpore": 1, @@ -24443,9 +24451,9 @@ "tbvcfreport": 1, "tcdemux": 1, "tcfinder": 1, - "tclsh": 7392, + "tclsh": 7396, "tclsh8.5": 473, - "tclsh8.6": 7155, + "tclsh8.6": 7159, "tcode": 25, "tcsh": 3, "td_bignet": 2, @@ -24484,12 +24492,12 @@ "test-download": 2, "test-download.3": 2, "test-download.3.0.0": 2, - "test-edirect": 272, - "test-eutils": 301, + "test-edirect": 273, + "test-eutils": 302, "test-gzip": 1, "test-merStream": 5, - "test-pmc-index": 27, - "test-pubmed-index": 301, + "test-pmc-index": 28, + "test-pubmed-index": 302, "test-read-write-cursor": 2, "test-read-write-cursor.3": 2, "test-read-write-cursor.3.0.0": 2, @@ -24541,7 +24549,7 @@ "test_install.bak": 1, "test_miso": 1, "test_musicc.py": 2, - "test_pcre": 98, + "test_pcre": 99, "test_proton.bam": 1, "test_proton.bam.bai": 1, "test_regexp": 1, @@ -24554,9 +24562,9 @@ "testepsg": 15, "tester": 2, "tester.py": 1, - "testfilesystem.sh": 30, - "testformat.sh": 30, - "testformat2.sh": 30, + "testfilesystem.sh": 31, + "testformat.sh": 31, + "testformat2.sh": 31, "testld": 2, "testld.3": 2, "testld.3.0.0": 2, @@ -24567,7 +24575,7 @@ "testsomatic.R": 2, "teststrandbias.R": 2, "testval": 1, - "tetramerfreq.sh": 30, + "tetramerfreq.sh": 31, "tex": 1, "tex4ebook": 1, "texconfig": 1, @@ -24588,7 +24596,7 @@ "texosquery": 1, "texosquery-jre5": 1, "texosquery-jre8": 1, - "textfile.sh": 30, + "textfile.sh": 31, "textget": 25, "textsearch": 25, "tf_intersect": 1, @@ -24644,7 +24652,7 @@ "thumbpdf": 1, "tiara": 2, "tiara-test": 2, - "tic": 7755, + "tic": 7760, "tiddit": 1, "tides": 1, "tidk": 1, @@ -24659,16 +24667,16 @@ "tiff2rgba": 5296, "tiffcmp": 5296, "tiffcomment": 20, - "tiffcp": 5536, + "tiffcp": 5539, "tiffcrop": 5296, "tiffdither": 5296, - "tiffdump": 5536, + "tiffdump": 5539, "tifffile": 23, - "tiffinfo": 5536, + "tiffinfo": 5539, "tiffmedian": 5296, - "tiffset": 5536, - "tiffsplit": 5536, - 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"xz": 7811, + "xzcat": 7586, + "xzcmp": 7586, + "xzdec": 7586, + "xzdiff": 7586, + "xzegrep": 7586, + "xzfgrep": 7586, + "xzgrep": 7586, + "xzless": 7586, + "xzmore": 7586, "y2racc": 7, "yacc": 4, "yacht": 1, @@ -26351,9 +26359,9 @@ "yaha": 2, "yahs": 1, "yak": 2, - "yaml2gff.1.4.pl": 14, + "yaml2gff.1.4.pl": 15, "yaml2obj": 4, - "yaml2xml": 27, + "yaml2xml": 28, "yamllint": 1, "yamlpp5-events": 4, "yamlpp5-highlight": 4, @@ -26373,7 +26381,7 @@ "yass": 1, "yat2m": 34, "yes": 84, - "yn00": 69, + "yn00": 70, "yoyo": 3, "yoyo-migrate": 3, "yplan": 1, @@ -26404,7 +26412,7 @@ "zipHomerResults.pl": 5, "zipcloak": 2, "zipcmp": 93, - "zipdetails": 1711, + "zipdetails": 1713, "zipgrep": 25, "zipinfo": 25, "zipmerge": 93, @@ -26419,7 +26427,7 @@ "znew": 18, "zol": 1, "zoom": 1, - "zoom2sam.pl": 517, + "zoom2sam.pl": 519, "zopfli": 23, "zopflipng": 23, "zorro": 1, @@ -26429,10 +26437,10 @@ "zrun": 3, "zsh": 3, "zsh-5.8": 3, - "zstd": 5241, - "zstdcat": 5241, - "zstdgrep": 5039, - "zstdless": 5039, - "zstdmt": 5241, + "zstd": 5245, + "zstdcat": 5245, + "zstdgrep": 5043, + "zstdless": 5043, + "zstdmt": 5245, "ztr_dump": 2 } \ No newline at end of file diff --git a/quay.io/biocontainers/d/diphase:1.0.0--h739ee2d_0.json b/quay.io/biocontainers/d/diphase:1.0.0--h739ee2d_0.json new file mode 100644 index 0000000..ecdb7bb --- /dev/null +++ b/quay.io/biocontainers/d/diphase:1.0.0--h739ee2d_0.json @@ -0,0 +1,164 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.9": "/usr/local/bin/2to3-3.9", + "ace2sam": "/usr/local/bin/ace2sam", + "adig": "/usr/local/bin/adig", + "ahost": "/usr/local/bin/ahost", + "bgzip": "/usr/local/bin/bgzip", + "blast2sam.pl": "/usr/local/bin/blast2sam.pl", + "bowtie2sam.pl": "/usr/local/bin/bowtie2sam.pl", + "bunzip2": "/usr/local/bin/bunzip2", + "bwa": "/usr/local/bin/bwa", + "bzcat": "/usr/local/bin/bzcat", + "bzcmp": "/usr/local/bin/bzcmp", + "bzdiff": "/usr/local/bin/bzdiff", + "bzegrep": "/usr/local/bin/bzegrep", + "bzfgrep": "/usr/local/bin/bzfgrep", + "bzgrep": "/usr/local/bin/bzgrep", + "bzip2": "/usr/local/bin/bzip2", + "bzip2recover": "/usr/local/bin/bzip2recover", + "bzless": "/usr/local/bin/bzless", + "bzmore": "/usr/local/bin/bzmore", + "c_rehash": "/usr/local/bin/c_rehash", + "captoinfo": "/usr/local/bin/captoinfo", + "clear": "/usr/local/bin/clear", + "compile_et": "/usr/local/bin/compile_et", + "corelist": "/usr/local/bin/corelist", + "cpan": "/usr/local/bin/cpan", + "curl-config": "/usr/local/bin/curl-config", + "enc2xs": "/usr/local/bin/enc2xs", + "encguess": "/usr/local/bin/encguess", + "eval.py": "/usr/local/bin/eval.py", + "export2sam.pl": "/usr/local/bin/export2sam.pl", + "fasta-sanitize.pl": "/usr/local/bin/fasta-sanitize.pl", + "gss-client": "/usr/local/bin/gss-client", + "h2ph": "/usr/local/bin/h2ph", + "h2xs": "/usr/local/bin/h2xs", + "htsfile": "/usr/local/bin/htsfile", + "idle3": "/usr/local/bin/idle3", + "idle3.9": "/usr/local/bin/idle3.9", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "instmodsh": "/usr/local/bin/instmodsh", + "interpolate_sam.pl": "/usr/local/bin/interpolate_sam.pl", + "json_pp": "/usr/local/bin/json_pp", + "k5srvutil": "/usr/local/bin/k5srvutil", + "kadmin": "/usr/local/bin/kadmin", + "kdestroy": "/usr/local/bin/kdestroy", + "keyctl": "/usr/local/bin/keyctl", + "kinit": "/usr/local/bin/kinit", + "klist": "/usr/local/bin/klist", + "kpasswd": "/usr/local/bin/kpasswd", + "krb5-config": "/usr/local/bin/krb5-config", + "ksu": "/usr/local/bin/ksu", + "kswitch": "/usr/local/bin/kswitch", + "ktutil": "/usr/local/bin/ktutil", + "kvno": "/usr/local/bin/kvno", + "libdeflate-gunzip": "/usr/local/bin/libdeflate-gunzip", + "libdeflate-gzip": "/usr/local/bin/libdeflate-gzip", + "libnetcfg": "/usr/local/bin/libnetcfg", + "lzcat": "/usr/local/bin/lzcat", + "lzcmp": "/usr/local/bin/lzcmp", + "lzdiff": "/usr/local/bin/lzdiff", + "lzegrep": "/usr/local/bin/lzegrep", + "lzfgrep": "/usr/local/bin/lzfgrep", + "lzgrep": "/usr/local/bin/lzgrep", + "lzless": "/usr/local/bin/lzless", + "lzma": "/usr/local/bin/lzma", + "lzmadec": "/usr/local/bin/lzmadec", + "lzmainfo": "/usr/local/bin/lzmainfo", + "lzmore": "/usr/local/bin/lzmore", + "maq2sam-long": "/usr/local/bin/maq2sam-long", + "maq2sam-short": "/usr/local/bin/maq2sam-short", + "md5fa": "/usr/local/bin/md5fa", + "md5sum-lite": "/usr/local/bin/md5sum-lite", + "ncurses6-config": "/usr/local/bin/ncurses6-config", + "ncursesw6-config": "/usr/local/bin/ncursesw6-config", + "nghttp": "/usr/local/bin/nghttp", + "nghttpd": "/usr/local/bin/nghttpd", + "nghttpx": "/usr/local/bin/nghttpx", + "novo2sam.pl": "/usr/local/bin/novo2sam.pl", + "openssl": "/usr/local/bin/openssl", + "perl": "/usr/local/bin/perl", + "perl5.32.1": "/usr/local/bin/perl5.32.1", + "perlbug": "/usr/local/bin/perlbug", + "perldoc": "/usr/local/bin/perldoc", + "perlivp": "/usr/local/bin/perlivp", + "perlthanks": "/usr/local/bin/perlthanks", + "phasing": "/usr/local/bin/phasing", + "piconv": "/usr/local/bin/piconv", + "pip": "/usr/local/bin/pip", + "pip3": "/usr/local/bin/pip3", + "pipeline.py": "/usr/local/bin/pipeline.py", + "pl2pm": "/usr/local/bin/pl2pm", + "plot-ampliconstats": "/usr/local/bin/plot-ampliconstats", + "plot-bamstats": "/usr/local/bin/plot-bamstats", + "plot.py": "/usr/local/bin/plot.py", + "pod2html": "/usr/local/bin/pod2html", + "pod2man": "/usr/local/bin/pod2man", + "pod2text": "/usr/local/bin/pod2text", + "pod2usage": "/usr/local/bin/pod2usage", + "podchecker": "/usr/local/bin/podchecker", + "preprocessing.py": "/usr/local/bin/preprocessing.py", + "prove": "/usr/local/bin/prove", + "psl2sam.pl": "/usr/local/bin/psl2sam.pl", + "ptar": "/usr/local/bin/ptar", + "ptardiff": "/usr/local/bin/ptardiff", + "ptargrep": "/usr/local/bin/ptargrep", + "pydoc": "/usr/local/bin/pydoc", + "pydoc3": "/usr/local/bin/pydoc3", + "pydoc3.9": "/usr/local/bin/pydoc3.9", + "python": "/usr/local/bin/python", + "python3": "/usr/local/bin/python3", + "python3-config": "/usr/local/bin/python3-config", + "python3.9": "/usr/local/bin/python3.9", + "python3.9-config": "/usr/local/bin/python3.9-config", + "qualfa2fq.pl": "/usr/local/bin/qualfa2fq.pl", + "reset": "/usr/local/bin/reset", + "sam2vcf.pl": "/usr/local/bin/sam2vcf.pl", + "samtools": "/usr/local/bin/samtools", + "samtools.pl": "/usr/local/bin/samtools.pl", + "sclient": "/usr/local/bin/sclient", + "seq_cache_populate.pl": "/usr/local/bin/seq_cache_populate.pl", + "shasum": "/usr/local/bin/shasum", + "sim_client": "/usr/local/bin/sim_client", + "soap2sam.pl": "/usr/local/bin/soap2sam.pl", + "splain": "/usr/local/bin/splain", + "sqlite3": "/usr/local/bin/sqlite3", + "sqlite3_analyzer": "/usr/local/bin/sqlite3_analyzer", + "streamzip": "/usr/local/bin/streamzip", + "tabix": "/usr/local/bin/tabix", + "tabs": "/usr/local/bin/tabs", + "tclsh": "/usr/local/bin/tclsh", + "tclsh8.6": "/usr/local/bin/tclsh8.6", + "tic": "/usr/local/bin/tic", + "toe": "/usr/local/bin/toe", + "tools.py": "/usr/local/bin/tools.py", + "tput": "/usr/local/bin/tput", + "tset": "/usr/local/bin/tset", + "unlzma": "/usr/local/bin/unlzma", + "unxz": "/usr/local/bin/unxz", + "util.py": "/usr/local/bin/util.py", + "uuclient": "/usr/local/bin/uuclient", + "wgsim": "/usr/local/bin/wgsim", + "wgsim_eval.pl": "/usr/local/bin/wgsim_eval.pl", + "wheel": "/usr/local/bin/wheel", + "wish": "/usr/local/bin/wish", + "wish8.6": "/usr/local/bin/wish8.6", + "x86_64-conda-linux-gnu-ld": "/usr/local/bin/x86_64-conda-linux-gnu-ld", + "x86_64-conda_cos6-linux-gnu-ld": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld", + "xa2multi.pl": "/usr/local/bin/xa2multi.pl", + "xsubpp": "/usr/local/bin/xsubpp", + "xz": "/usr/local/bin/xz", + "xzcat": "/usr/local/bin/xzcat", + "xzcmp": "/usr/local/bin/xzcmp", + "xzdec": "/usr/local/bin/xzdec", + "xzdiff": "/usr/local/bin/xzdiff", + "xzegrep": "/usr/local/bin/xzegrep", + "xzfgrep": "/usr/local/bin/xzfgrep", + "xzgrep": "/usr/local/bin/xzgrep", + "xzless": "/usr/local/bin/xzless", + "xzmore": "/usr/local/bin/xzmore", + "zipdetails": "/usr/local/bin/zipdetails", + "zoom2sam.pl": "/usr/local/bin/zoom2sam.pl" +} \ No newline at end of file diff --git a/quay.io/biocontainers/g/gempipe:1.33.4--pyhdfd78af_0.json b/quay.io/biocontainers/g/gempipe:1.33.4--pyhdfd78af_0.json new file mode 100644 index 0000000..cfbe19f --- /dev/null +++ b/quay.io/biocontainers/g/gempipe:1.33.4--pyhdfd78af_0.json @@ -0,0 +1,1232 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.9": "/usr/local/bin/2to3-3.9", + "AnalyseDists": "/usr/local/bin/AnalyseDists", + "AnalyseSeqs": "/usr/local/bin/AnalyseSeqs", + "FET.pl": "/usr/local/bin/FET.pl", + "Kinfold": "/usr/local/bin/Kinfold", + "PF00225_full.blocks.txt": "/usr/local/bin/PF00225_full.blocks.txt", + "PF00225_seed.blocks.txt": "/usr/local/bin/PF00225_seed.blocks.txt", + "R": "/usr/local/bin/R", + "RNA2Dfold": "/usr/local/bin/RNA2Dfold", + "RNALalifold": "/usr/local/bin/RNALalifold", + "RNALfold": "/usr/local/bin/RNALfold", + "RNAPKplex": "/usr/local/bin/RNAPKplex", + "RNAaliduplex": "/usr/local/bin/RNAaliduplex", + "RNAalifold": "/usr/local/bin/RNAalifold", + "RNAcofold": "/usr/local/bin/RNAcofold", + "RNAdistance": "/usr/local/bin/RNAdistance", + "RNAdos": "/usr/local/bin/RNAdos", + "RNAduplex": "/usr/local/bin/RNAduplex", + "RNAeval": "/usr/local/bin/RNAeval", + "RNAfold": "/usr/local/bin/RNAfold", + "RNAforester": "/usr/local/bin/RNAforester", + "RNAheat": "/usr/local/bin/RNAheat", + "RNAinverse": "/usr/local/bin/RNAinverse", + "RNAlocmin": "/usr/local/bin/RNAlocmin", + "RNAmultifold": "/usr/local/bin/RNAmultifold", + "RNApaln": "/usr/local/bin/RNApaln", + "RNAparconv": "/usr/local/bin/RNAparconv", + "RNApdist": "/usr/local/bin/RNApdist", + "RNAplex": "/usr/local/bin/RNAplex", + "RNAplfold": "/usr/local/bin/RNAplfold", + "RNAplot": "/usr/local/bin/RNAplot", + "RNApvmin": "/usr/local/bin/RNApvmin", + "RNAsnoop": "/usr/local/bin/RNAsnoop", + "RNAsubopt": "/usr/local/bin/RNAsubopt", + "RNAup": "/usr/local/bin/RNAup", + "Rscript": "/usr/local/bin/Rscript", + "SplicedAlignment.pm": "/usr/local/bin/SplicedAlignment.pm", + "TMalign": "/usr/local/bin/TMalign", + "Xcalcmem.sh": "/usr/local/bin/Xcalcmem.sh", + "a_sample_mt.sh": "/usr/local/bin/a_sample_mt.sh", + "aa2nonred.pl": "/usr/local/bin/aa2nonred.pl", + "accn-at-a-time": "/usr/local/bin/accn-at-a-time", + "ace2sam": "/usr/local/bin/ace2sam", + "add_name_to_gff3.pl": "/usr/local/bin/add_name_to_gff3.pl", + "addadapters.sh": "/usr/local/bin/addadapters.sh", + "addssu.sh": "/usr/local/bin/addssu.sh", + "adig": "/usr/local/bin/adig", + "adjusthomopolymers.sh": "/usr/local/bin/adjusthomopolymers.sh", + "ahost": "/usr/local/bin/ahost", + "align-columns": "/usr/local/bin/align-columns", + "alimask": "/usr/local/bin/alimask", + "alltoall.sh": "/usr/local/bin/alltoall.sh", + "aln2wig": "/usr/local/bin/aln2wig", + "amino-acid-composition": "/usr/local/bin/amino-acid-composition", + "analyzeaccession.sh": "/usr/local/bin/analyzeaccession.sh", + "analyzegenes.sh": "/usr/local/bin/analyzegenes.sh", + "analyzesketchresults.sh": "/usr/local/bin/analyzesketchresults.sh", + "annotateBed": "/usr/local/bin/annotateBed", + "applyvariants.sh": "/usr/local/bin/applyvariants.sh", + "aragorn": "/usr/local/bin/aragorn", + "archive-ncbinlp": "/usr/local/bin/archive-ncbinlp", + "archive-nihocc": "/usr/local/bin/archive-nihocc", + "archive-nmcds": "/usr/local/bin/archive-nmcds", + "archive-pmc": "/usr/local/bin/archive-pmc", + "archive-pubmed": "/usr/local/bin/archive-pubmed", + "archive-taxonomy": "/usr/local/bin/archive-taxonomy", + "args2slice": "/usr/local/bin/args2slice", + "aria2c": "/usr/local/bin/aria2c", + "aserver": "/usr/local/bin/aserver", + "asn2ref": "/usr/local/bin/asn2ref", + "asn2xml": "/usr/local/bin/asn2xml", + "augustify.py": "/usr/local/bin/augustify.py", + "augustus": "/usr/local/bin/augustus", + "augustus2browser.pl": "/usr/local/bin/augustus2browser.pl", + "augustus2gbrowse.pl": "/usr/local/bin/augustus2gbrowse.pl", + "autoAug.pl": "/usr/local/bin/autoAug.pl", + "autoAugPred.pl": "/usr/local/bin/autoAugPred.pl", + "autoAugTrain.pl": "/usr/local/bin/autoAugTrain.pl", + "autopoint": "/usr/local/bin/autopoint", + "awk": "/usr/local/bin/awk", + "b2ct": "/usr/local/bin/b2ct", + "bam2hints": "/usr/local/bin/bam2hints", + "bam2wig": "/usr/local/bin/bam2wig", + "bamToBed": "/usr/local/bin/bamToBed", + "bamToFastq": "/usr/local/bin/bamToFastq", + "bamToGBrowse.pl": "/usr/local/bin/bamToGBrowse.pl", + "bamToWig.py": "/usr/local/bin/bamToWig.py", + "bamtools": "/usr/local/bin/bamtools", + "barrnap": "/usr/local/bin/barrnap", + "baseml": "/usr/local/bin/baseml", + "basemlg": "/usr/local/bin/basemlg", + "bbcms.sh": "/usr/local/bin/bbcms.sh", + "bbcountunique.sh": "/usr/local/bin/bbcountunique.sh", + "bbduk.sh": "/usr/local/bin/bbduk.sh", + "bbest.sh": "/usr/local/bin/bbest.sh", + "bbfakereads.sh": "/usr/local/bin/bbfakereads.sh", + "bbmap.sh": "/usr/local/bin/bbmap.sh", + "bbmapskimmer.sh": "/usr/local/bin/bbmapskimmer.sh", + "bbmask.sh": "/usr/local/bin/bbmask.sh", + "bbmerge-auto.sh": "/usr/local/bin/bbmerge-auto.sh", + "bbmerge.sh": "/usr/local/bin/bbmerge.sh", + "bbnorm.sh": "/usr/local/bin/bbnorm.sh", + "bbrealign.sh": "/usr/local/bin/bbrealign.sh", + "bbrename.sh": "/usr/local/bin/bbrename.sh", + "bbsketch.sh": "/usr/local/bin/bbsketch.sh", + "bbsplit.sh": "/usr/local/bin/bbsplit.sh", + "bbsplitpairs.sh": "/usr/local/bin/bbsplitpairs.sh", + "bbstats.sh": "/usr/local/bin/bbstats.sh", + "bbversion.sh": "/usr/local/bin/bbversion.sh", + "bbwrap.sh": "/usr/local/bin/bbwrap.sh", + "bed12ToBed6": "/usr/local/bin/bed12ToBed6", + "bedToBam": "/usr/local/bin/bedToBam", + "bedToIgv": "/usr/local/bin/bedToIgv", + "bedgraph2wig.pl": "/usr/local/bin/bedgraph2wig.pl", + "bedpeToBam": "/usr/local/bin/bedpeToBam", + "bedtools": "/usr/local/bin/bedtools", + "between-two-genes": "/usr/local/bin/between-two-genes", + "bgzip": 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"/usr/local/bin/zstdmt" +} \ No newline at end of file diff --git a/quay.io/biocontainers/n/neodisambiguate:1.1.0--hdfd78af_0.json b/quay.io/biocontainers/n/neodisambiguate:1.1.0--hdfd78af_0.json new file mode 100644 index 0000000..2581f43 --- /dev/null +++ b/quay.io/biocontainers/n/neodisambiguate:1.1.0--hdfd78af_0.json @@ -0,0 +1,166 @@ +{ + "aserver": "/usr/local/bin/aserver", + "bunzip2": "/usr/local/bin/bunzip2", + "bzcat": "/usr/local/bin/bzcat", + "bzcmp": "/usr/local/bin/bzcmp", + "bzdiff": "/usr/local/bin/bzdiff", + "bzegrep": "/usr/local/bin/bzegrep", + "bzfgrep": "/usr/local/bin/bzfgrep", + "bzgrep": "/usr/local/bin/bzgrep", + "bzip2": "/usr/local/bin/bzip2", + "bzip2recover": "/usr/local/bin/bzip2recover", + "bzless": "/usr/local/bin/bzless", + "bzmore": "/usr/local/bin/bzmore", + "c_rehash": "/usr/local/bin/c_rehash", + "cairo-trace": "/usr/local/bin/cairo-trace", + "captoinfo": "/usr/local/bin/captoinfo", + "cjpeg": "/usr/local/bin/cjpeg", + "clear": 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a/quay.io/biocontainers/r/reduce:4.14--py310hb119401_1.json b/quay.io/biocontainers/r/reduce:4.14--py310hb119401_1.json new file mode 100644 index 0000000..d4e0faa --- /dev/null +++ b/quay.io/biocontainers/r/reduce:4.14--py310hb119401_1.json @@ -0,0 +1,91 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.10": "/usr/local/bin/2to3-3.10", + "bunzip2": "/usr/local/bin/bunzip2", + "bzcat": "/usr/local/bin/bzcat", + "bzcmp": "/usr/local/bin/bzcmp", + "bzdiff": "/usr/local/bin/bzdiff", + "bzegrep": "/usr/local/bin/bzegrep", + "bzfgrep": "/usr/local/bin/bzfgrep", + "bzgrep": "/usr/local/bin/bzgrep", + "bzip2": "/usr/local/bin/bzip2", + "bzip2recover": "/usr/local/bin/bzip2recover", + "bzless": "/usr/local/bin/bzless", + "bzmore": "/usr/local/bin/bzmore", + "c_rehash": "/usr/local/bin/c_rehash", + "captoinfo": "/usr/local/bin/captoinfo", + "clear": "/usr/local/bin/clear", + "derb": "/usr/local/bin/derb", + "f2py": "/usr/local/bin/f2py", + "genbrk": "/usr/local/bin/genbrk", + "gencfu": 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"/usr/local/bin/unzstd", + "wish": "/usr/local/bin/wish", + "wish8.6": "/usr/local/bin/wish8.6", + "x86_64-conda-linux-gnu-ld": "/usr/local/bin/x86_64-conda-linux-gnu-ld", + "x86_64-conda_cos6-linux-gnu-ld": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld", + "xz": "/usr/local/bin/xz", + "xzcat": "/usr/local/bin/xzcat", + "xzcmp": "/usr/local/bin/xzcmp", + "xzdec": "/usr/local/bin/xzdec", + "xzdiff": "/usr/local/bin/xzdiff", + "xzegrep": "/usr/local/bin/xzegrep", + "xzfgrep": "/usr/local/bin/xzfgrep", + "xzgrep": "/usr/local/bin/xzgrep", + "xzless": "/usr/local/bin/xzless", + "xzmore": "/usr/local/bin/xzmore", + "zstd": "/usr/local/bin/zstd", + "zstdcat": "/usr/local/bin/zstdcat", + "zstdgrep": "/usr/local/bin/zstdgrep", + "zstdless": "/usr/local/bin/zstdless", + "zstdmt": "/usr/local/bin/zstdmt" +} \ No newline at end of file diff --git a/quay.io/biocontainers/s/scspectra:0.2.0--pyhdfd78af_0.json b/quay.io/biocontainers/s/scspectra:0.2.0--pyhdfd78af_0.json new file mode 100644 index 0000000..0066351 --- /dev/null +++ b/quay.io/biocontainers/s/scspectra:0.2.0--pyhdfd78af_0.json @@ -0,0 +1,204 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.11": "/usr/local/bin/2to3-3.11", + "adig": "/usr/local/bin/adig", + "ahost": "/usr/local/bin/ahost", + "brotli": "/usr/local/bin/brotli", + "bunzip2": "/usr/local/bin/bunzip2", + "bzcat": "/usr/local/bin/bzcat", + "bzcmp": "/usr/local/bin/bzcmp", + "bzdiff": "/usr/local/bin/bzdiff", + "bzegrep": "/usr/local/bin/bzegrep", + "bzfgrep": "/usr/local/bin/bzfgrep", + "bzgrep": "/usr/local/bin/bzgrep", + "bzip2": "/usr/local/bin/bzip2", + "bzip2recover": "/usr/local/bin/bzip2recover", + "bzless": "/usr/local/bin/bzless", + "bzmore": "/usr/local/bin/bzmore", + "c_rehash": "/usr/local/bin/c_rehash", + "captoinfo": "/usr/local/bin/captoinfo", + "cjpeg": "/usr/local/bin/cjpeg", + "clear": "/usr/local/bin/clear", + "compile_et": "/usr/local/bin/compile_et", + "convert-caffe2-to-onnx": "/usr/local/bin/convert-caffe2-to-onnx", + "convert-onnx-to-caffe2": "/usr/local/bin/convert-onnx-to-caffe2", + "curl-config": "/usr/local/bin/curl-config", + "derb": "/usr/local/bin/derb", + "djpeg": "/usr/local/bin/djpeg", + "f2py": "/usr/local/bin/f2py", + "fonttools": "/usr/local/bin/fonttools", + "freetype-config": "/usr/local/bin/freetype-config", + "genbrk": "/usr/local/bin/genbrk", + "gencfu": "/usr/local/bin/gencfu", + "gencnval": "/usr/local/bin/gencnval", + "gendict": "/usr/local/bin/gendict", + "genrb": "/usr/local/bin/genrb", + "gif2h5": "/usr/local/bin/gif2h5", + "gss-client": "/usr/local/bin/gss-client", + "h52gif": "/usr/local/bin/h52gif", + "h5c++": "/usr/local/bin/h5c++", + "h5cc": "/usr/local/bin/h5cc", + "h5clear": "/usr/local/bin/h5clear", + "h5copy": "/usr/local/bin/h5copy", + "h5debug": "/usr/local/bin/h5debug", + "h5delete": "/usr/local/bin/h5delete", + "h5diff": "/usr/local/bin/h5diff", + "h5dump": "/usr/local/bin/h5dump", + "h5fc": "/usr/local/bin/h5fc", + "h5format_convert": "/usr/local/bin/h5format_convert", + "h5fuse.sh": "/usr/local/bin/h5fuse.sh", + "h5import": "/usr/local/bin/h5import", + "h5jam": "/usr/local/bin/h5jam", + "h5ls": "/usr/local/bin/h5ls", + "h5mkgrp": "/usr/local/bin/h5mkgrp", + "h5perf_serial": "/usr/local/bin/h5perf_serial", + "h5redeploy": "/usr/local/bin/h5redeploy", + "h5repack": "/usr/local/bin/h5repack", + "h5repart": "/usr/local/bin/h5repart", + "h5stat": "/usr/local/bin/h5stat", + "h5tools_test_utils": "/usr/local/bin/h5tools_test_utils", + "h5unjam": "/usr/local/bin/h5unjam", + "h5watch": "/usr/local/bin/h5watch", + "hwloc-annotate": "/usr/local/bin/hwloc-annotate", + "hwloc-bind": "/usr/local/bin/hwloc-bind", + "hwloc-calc": "/usr/local/bin/hwloc-calc", + "hwloc-compress-dir": "/usr/local/bin/hwloc-compress-dir", + "hwloc-diff": "/usr/local/bin/hwloc-diff", + "hwloc-distrib": "/usr/local/bin/hwloc-distrib", + "hwloc-gather-cpuid": "/usr/local/bin/hwloc-gather-cpuid", + "hwloc-gather-topology": "/usr/local/bin/hwloc-gather-topology", + "hwloc-info": "/usr/local/bin/hwloc-info", + "hwloc-ls": "/usr/local/bin/hwloc-ls", + "hwloc-patch": "/usr/local/bin/hwloc-patch", + "hwloc-ps": "/usr/local/bin/hwloc-ps", + "icu-config": "/usr/local/bin/icu-config", + "icuexportdata": "/usr/local/bin/icuexportdata", + "icuinfo": "/usr/local/bin/icuinfo", + "idle3": "/usr/local/bin/idle3", + "idle3.11": "/usr/local/bin/idle3.11", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "ipython": "/usr/local/bin/ipython", + "ipython3": "/usr/local/bin/ipython3", + "jpegtran": "/usr/local/bin/jpegtran", + "jpgicc": "/usr/local/bin/jpgicc", + "k5srvutil": "/usr/local/bin/k5srvutil", + "kadmin": "/usr/local/bin/kadmin", + "kdestroy": "/usr/local/bin/kdestroy", + "keyctl": "/usr/local/bin/keyctl", + "kinit": "/usr/local/bin/kinit", + "klist": "/usr/local/bin/klist", + "kpasswd": "/usr/local/bin/kpasswd", + "krb5-config": "/usr/local/bin/krb5-config", + "ksu": "/usr/local/bin/ksu", + "kswitch": "/usr/local/bin/kswitch", + "ktutil": "/usr/local/bin/ktutil", + "kvno": "/usr/local/bin/kvno", + "libdeflate-gunzip": "/usr/local/bin/libdeflate-gunzip", + "libdeflate-gzip": "/usr/local/bin/libdeflate-gzip", + "libpng-config": "/usr/local/bin/libpng-config", + "libpng16-config": "/usr/local/bin/libpng16-config", + "linkicc": "/usr/local/bin/linkicc", + "lstopo": "/usr/local/bin/lstopo", + "lstopo-no-graphics": "/usr/local/bin/lstopo-no-graphics", + "lzcat": "/usr/local/bin/lzcat", + "lzcmp": "/usr/local/bin/lzcmp", + "lzdiff": "/usr/local/bin/lzdiff", + "lzegrep": "/usr/local/bin/lzegrep", + "lzfgrep": "/usr/local/bin/lzfgrep", + "lzgrep": "/usr/local/bin/lzgrep", + "lzless": "/usr/local/bin/lzless", + "lzma": "/usr/local/bin/lzma", + "lzmadec": "/usr/local/bin/lzmadec", + "lzmainfo": "/usr/local/bin/lzmainfo", + "lzmore": "/usr/local/bin/lzmore", + "makeconv": "/usr/local/bin/makeconv", + "natsort": "/usr/local/bin/natsort", + "ncurses6-config": "/usr/local/bin/ncurses6-config", + "ncursesw6-config": "/usr/local/bin/ncursesw6-config", + "nghttp": "/usr/local/bin/nghttp", + "nghttpd": "/usr/local/bin/nghttpd", + "nghttpx": "/usr/local/bin/nghttpx", + "numba": "/usr/local/bin/numba", + "openssl": "/usr/local/bin/openssl", + "opj_compress": "/usr/local/bin/opj_compress", + "opj_decompress": "/usr/local/bin/opj_decompress", + "opj_dump": "/usr/local/bin/opj_dump", + "pip": "/usr/local/bin/pip", + "pip3": "/usr/local/bin/pip3", + "pkgdata": "/usr/local/bin/pkgdata", + "png-fix-itxt": "/usr/local/bin/png-fix-itxt", + "pngfix": "/usr/local/bin/pngfix", + "protoc": "/usr/local/bin/protoc", + "psicc": "/usr/local/bin/psicc", + "pydoc": "/usr/local/bin/pydoc", + "pydoc3": "/usr/local/bin/pydoc3", + "pydoc3.11": "/usr/local/bin/pydoc3.11", + "pyftmerge": "/usr/local/bin/pyftmerge", + "pyftsubset": "/usr/local/bin/pyftsubset", + "pygmentize": "/usr/local/bin/pygmentize", + "python": "/usr/local/bin/python", + "python3": "/usr/local/bin/python3", + "python3-config": "/usr/local/bin/python3-config", + "python3.1": "/usr/local/bin/python3.1", + "python3.11": "/usr/local/bin/python3.11", + "python3.11-config": "/usr/local/bin/python3.11-config", + "qconvex": "/usr/local/bin/qconvex", + "qdelaunay": "/usr/local/bin/qdelaunay", + "qhalf": "/usr/local/bin/qhalf", + "qhull": "/usr/local/bin/qhull", + "qvoronoi": "/usr/local/bin/qvoronoi", + "rbox": "/usr/local/bin/rbox", + "rdjpgcom": "/usr/local/bin/rdjpgcom", + "reset": "/usr/local/bin/reset", + "scanpy": "/usr/local/bin/scanpy", + "sclient": "/usr/local/bin/sclient", + "sim_client": "/usr/local/bin/sim_client", + "sqlite3_analyzer": "/usr/local/bin/sqlite3_analyzer", + "tabs": "/usr/local/bin/tabs", + "tclsh": "/usr/local/bin/tclsh", + "tclsh8.6": "/usr/local/bin/tclsh8.6", + "tic": "/usr/local/bin/tic", + "tiffcp": "/usr/local/bin/tiffcp", + "tiffdump": "/usr/local/bin/tiffdump", + "tiffinfo": "/usr/local/bin/tiffinfo", + "tiffset": "/usr/local/bin/tiffset", + "tiffsplit": "/usr/local/bin/tiffsplit", + "tificc": "/usr/local/bin/tificc", + "tjbench": "/usr/local/bin/tjbench", + "toe": "/usr/local/bin/toe", + "torchrun": "/usr/local/bin/torchrun", + "tput": "/usr/local/bin/tput", + "tqdm": "/usr/local/bin/tqdm", + "transicc": "/usr/local/bin/transicc", + "tset": "/usr/local/bin/tset", + "ttx": "/usr/local/bin/ttx", + "unlzma": "/usr/local/bin/unlzma", + "unxz": "/usr/local/bin/unxz", + "unzstd": "/usr/local/bin/unzstd", + "uuclient": "/usr/local/bin/uuclient", + "wheel": "/usr/local/bin/wheel", + "wish": "/usr/local/bin/wish", + "wish8.6": "/usr/local/bin/wish8.6", + "wrjpgcom": "/usr/local/bin/wrjpgcom", + "x86_64-conda-linux-gnu-ld": "/usr/local/bin/x86_64-conda-linux-gnu-ld", + "x86_64-conda_cos6-linux-gnu-ld": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld", + "xml2-config": "/usr/local/bin/xml2-config", + "xmlcatalog": "/usr/local/bin/xmlcatalog", + "xmllint": "/usr/local/bin/xmllint", + "xz": "/usr/local/bin/xz", + "xzcat": "/usr/local/bin/xzcat", + "xzcmp": "/usr/local/bin/xzcmp", + "xzdec": "/usr/local/bin/xzdec", + "xzdiff": "/usr/local/bin/xzdiff", + "xzegrep": "/usr/local/bin/xzegrep", + "xzfgrep": "/usr/local/bin/xzfgrep", + "xzgrep": "/usr/local/bin/xzgrep", + "xzless": "/usr/local/bin/xzless", + "xzmore": "/usr/local/bin/xzmore", + "zstd": "/usr/local/bin/zstd", + "zstdcat": "/usr/local/bin/zstdcat", + "zstdgrep": "/usr/local/bin/zstdgrep", + "zstdless": "/usr/local/bin/zstdless", + "zstdmt": "/usr/local/bin/zstdmt" +} \ No newline at end of file diff --git a/quay.io/biocontainers/s/strangepg:0.8.0--h9a53f25_0.json b/quay.io/biocontainers/s/strangepg:0.8.0--h9a53f25_0.json new file mode 100644 index 0000000..00a1e3f --- /dev/null +++ b/quay.io/biocontainers/s/strangepg:0.8.0--h9a53f25_0.json @@ -0,0 +1,4 @@ +{ + "strawk": "/usr/local/bin/strawk", + "strpg": "/usr/local/bin/strpg" +} \ No newline at end of file diff --git a/quay.io/biocontainers/s/subset-bam:1.1.0--h4349ce8_0.json b/quay.io/biocontainers/s/subset-bam:1.1.0--h4349ce8_0.json new file mode 100644 index 0000000..2ac8456 --- /dev/null +++ b/quay.io/biocontainers/s/subset-bam:1.1.0--h4349ce8_0.json @@ -0,0 +1,3 @@ +{ + "subset-bam": "/usr/local/bin/subset-bam" +} \ No newline at end of file