v2.1.0 - xam_coverage_bins.pl

• Adds xam_coverage_bins.pl which calculates fraction of targets covered at various depths (BAM/CRAM), using BED/GFF3 as target bait file.

warning please ensure all of your downstream tools will function without legacy samtools.

v2.0.1 - CRAM, samtools 1.3+, htslib

• bwa_mem.pl
  • allow user to specify BWA mapping parameters
  • now accepts CRAM as input
• bamToBw.pl - now accepts CRAM as input.
• bam_stats - Adds 2 new stats:
  • #_mapped_pairs
  • #_inter_chr_pairs
• Dependancy changes
  • WARNING: ensure all related tools handle these updates
  • samtools, now only uses htslib based versions (1.3+, handling deprecated use of sort)
  • Bio::DB::HTS htslib bindings replacing Bio::DB::Sam

v1.14.0 - Adds ability to disable duplicate marking

bwa_mem.pl:

• new option -nomarkdup allows generation of BAMs without running duplicate removal
  • For some types of quantitive targeted/amplicon analysis this is necessary.
• deprecated option -charts - has been non funtional since switch to bam_stats from bam_stats.pl
  • Still possible to generate with bam_stats.pl (if this is imperative to your use case please let us know)

Upgrade

• biobambam2 - 2.0.31

bam_stats unit tests

• unit tests added for bam_stats c
• bugfix to median inset size calculation

Additional features in perl modules and improved bam_stats

Improved bam_stats memory handling.
bam_stats now exits when '-v' requested rather than waiting for stdin.
bam_stats version is now dependant on perl module version to prevent mis-match due to having it in multiple places.
Added additional options to sample_name parsing from BAM.

v1.11.0 - Minor changes to functionallity (all backwards compat)

1.11.0

• bam_stats - new rna switch to give more appropriate insert size stats
• bam_stats - more robust handling of optional RG header entries
• bam_stats - allows streaming IO (thanks to @jenniferliddle)
• bwa_mem.pl - Handle ' in RG header line/IDs
• Generally improved version handling and updated versions of some tools.

v1.10.0 - Additional download features

Adds DKFZ, Broad to results downloads
Slightly more robust GNOS handling
Minor fix to BWA-mem wrapper to work better with links

v1.9.4 - bwa_mem.pl handles single end sequencing appropriately

This means relevant data is skipped and for filed containing only single ended sequencing an error is thrown.

Also updates cpanm location.

v1.9.1 - change log locations

Changed final location of logs generated by bwa_mem.pl and bwa_aln.pl so that multiple analysis in same output location is safe.

v1.9.0 - enhanced BWA-mem mapping

Now possible to start from merged BAM files with multiple read-groups.

Also fixes #52 and #53.