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1.5

  • Python 3 support

1.4.4

  • Created bioconda package
  • Add script to build Venn diagram for a set of BED files:
bed_venn.py *.bed -o res_dir

1.4.1

  • Support custom genomes. Provide a path to indexed fasta file with -g:
targqc *.bam --bed target.bed -o results -g /path/to/some_genome.fa

When running from BAMs, only the .fai index is used, and the fasta file itself can be non-existent. When running from fastq, bwa indexes are also required.

1.4

  • Update BED file annotation package.

1.3

  • BED annotation: --seq2c mode.

1.2

  • Downsampling to 5% by default instead of 500k read pairs.

1.1

  • Moved code from AZ Reporting Suite
  • Decoupled from SGE using iPython-cluster-helper (https://github.com/roryk/ipython-cluster-helper)
  • New BED annotation, using Ensembl
  • New region coverage reports
  • Support FastQ processing with downsampling
  • Add nosetests
  • Add Travis CI support
  • Dockerized
  • Added MultiQC module
  • Much less dependencies, easier to install
  • Setup.py and uploaded PyPI (available via pip)