From 6b365b5a1b33109bdbcfcc680a9f369233efe75d Mon Sep 17 00:00:00 2001 From: Kyle Moad Date: Mon, 26 Feb 2024 10:23:05 -0500 Subject: [PATCH] using gui example inputs sets assembly to hg38 --- .../websubmit/input-examples/cravat.hg18.txt | 16 ----------- .../websubmit/input-examples/cravat.hg19.txt | 16 ----------- cravat/websubmit/input-examples/vcf.hg18.txt | 28 ------------------- cravat/websubmit/input-examples/vcf.hg19.txt | 28 ------------------- cravat/websubmit/nocache/websubmit.js | 4 +-- 5 files changed, 2 insertions(+), 90 deletions(-) delete mode 100644 cravat/websubmit/input-examples/cravat.hg18.txt delete mode 100644 cravat/websubmit/input-examples/cravat.hg19.txt delete mode 100644 cravat/websubmit/input-examples/vcf.hg18.txt delete mode 100644 cravat/websubmit/input-examples/vcf.hg19.txt diff --git a/cravat/websubmit/input-examples/cravat.hg18.txt b/cravat/websubmit/input-examples/cravat.hg18.txt deleted file mode 100644 index f3d4ef18..00000000 --- a/cravat/websubmit/input-examples/cravat.hg18.txt +++ /dev/null @@ -1,16 +0,0 @@ -chr10 8137625 + A T s3 var001 -chr10 89614207 + A T s4 var002 -chr10 89614223 + A - s0 var003 -chr10 89614223 + AA - s1 var004 -chr10 89643764 + - CG s2 var005 -chr10 89643764 + - CT s3 var006 -chr1 100958005 + A T s4 var007 -chr1 100 + C T s0 var008 -chr1 110684798 + CGGCTTT - s1 var009 -chr11 107603562 + A T s2 var010 -chr11 113165326 + G A s3 var011 -chr1 112106829 + G A s4 var012 -chr11 118582338 + A T s0 var013 -chr1 115058025 + TGGTC - s1 var014 -chr1 115058025 + TGGTCTC - s2 var015 -chr1 115060304 - A T s3 var016 diff --git a/cravat/websubmit/input-examples/cravat.hg19.txt b/cravat/websubmit/input-examples/cravat.hg19.txt deleted file mode 100644 index 26725e03..00000000 --- a/cravat/websubmit/input-examples/cravat.hg19.txt +++ /dev/null @@ -1,16 +0,0 @@ -chr10 8097619 + A T s3 var001 -chr10 89624227 + A T s4 var002 -chr10 89624243 + A - s0 var003 -chr10 89624243 + AA - s1 var004 -chr10 89653784 + - CG s2 var005 -chr10 89653784 + - CT s3 var006 -chr1 101185417 + A T s4 var007 -chr1 10100 + C T s0 var008 -chr1 110883275 + CGGCTTT - s1 var009 -chr11 108098352 + A T s2 var010 -chr11 113660116 + G A s3 var011 -chr1 112305306 + G A s4 var012 -chr11 119077128 + A T s0 var013 -chr1 115256502 + TGGTC - s1 var014 -chr1 115256502 + TGGTCTC - s2 var015 -chr1 115258781 - A T s3 var016 diff --git a/cravat/websubmit/input-examples/vcf.hg18.txt b/cravat/websubmit/input-examples/vcf.hg18.txt deleted file mode 100644 index f4a866c1..00000000 --- a/cravat/websubmit/input-examples/vcf.hg18.txt +++ /dev/null @@ -1,28 +0,0 @@ -##fileformat=VCFv4.1 -##fileDate=20090805 -##source=myImputationProgramV3.1 -##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta -##contig= -##phasing=partial -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FILTER= -##FILTER= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 -22 28751786 TR1 A T 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ:AD 0|0:48:1:51,51:0,1 1|0:48:8:51,51:4,4 1/1:43:4:.,.:1,2 -22 39144446 TR2 T C 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:65,3 -22 39145202 TR3 C G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:18,2 -12 25289521 TR10 T TAGG 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/1:61:2 -12 25289521 TR10 TGTA T,TG 50 PASS NS=3;DP=9;AA=G GT:GQ:DP:AD 0/1:35:4:2,1,1 0/2:17:5:1,1,3 1/1:40:3:0,2,1 -12 25289521 TR10 TGA T 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ:AD 0|0:48:1:51,51:1,0 1|0:48:8:51,51:4,4 1/1:43:5:.,.:0,5 -2 218843010 TR7 GG G 30 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ:AD 0|0:48:3:51,51:3,0 1|0:48:8:51,51:3,5 1/1:43:6:.,.:0,6 -2 218843011 TR8 G GG 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|0:21:6:23,27 0|0:2:0:18,2 1/1:35:4:18,2 diff --git a/cravat/websubmit/input-examples/vcf.hg19.txt b/cravat/websubmit/input-examples/vcf.hg19.txt deleted file mode 100644 index 810c3f4b..00000000 --- a/cravat/websubmit/input-examples/vcf.hg19.txt +++ /dev/null @@ -1,28 +0,0 @@ -##fileformat=VCFv4.1 -##fileDate=20090805 -##source=myImputationProgramV3.1 -##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta -##contig= -##phasing=partial -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FILTER= -##FILTER= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 -22 30421786 TR1 A T 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ:AD 0|0:48:1:51,51:0,1 1|0:48:8:51,51:4,4 1/1:43:4:.,.:1,2 -22 40814500 TR2 T C 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:65,3 -22 40815256 TR3 C G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:18,2 -12 25398254 TR10 T TAGG 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/1:61:2 -12 25398254 TR10 TGTA T,TG 50 PASS NS=3;DP=9;AA=G GT:GQ:DP:AD 0/1:35:4:2,1,1 0/2:17:5:1,1,3 1/1:40:3:0,2,1 -12 25398254 TR10 TGA T 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ:AD 0|0:48:1:51,51:1,0 1|0:48:8:51,51:4,4 1/1:43:5:.,.:0,5 -2 219134766 TR7 GG G 30 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ:AD 0|0:48:3:51,51:3,0 1|0:48:8:51,51:3,5 1/1:43:6:.,.:0,6 -2 219134767 TR8 G GG 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|0:21:6:23,27 0|0:2:0:18,2 1/1:35:4:18,2 diff --git a/cravat/websubmit/nocache/websubmit.js b/cravat/websubmit/nocache/websubmit.js index 7dd26f81..d0e6c620 100644 --- a/cravat/websubmit/nocache/websubmit.js +++ b/cravat/websubmit/nocache/websubmit.js @@ -939,8 +939,7 @@ function deleteJob (jobId) { function inputExampleChangeHandler (event) { var elem = $(event.target); var format = elem.val(); - var assembly = $('#assembly-select').val(); - assembly = assembly === null ? 'hg38' : assembly; + var assembly = 'hg38'; var formatAssembly = format + '.' + assembly; var getExampleText = new Promise((resolve, reject) => { var cachedText = OC.GLOBALS.inputExamples[formatAssembly]; @@ -965,6 +964,7 @@ function inputExampleChangeHandler (event) { var inputArea = $('#input-text'); inputArea.val(text); inputArea.change(); + $('#assembly-select').val(assembly); }) }