v3.5.0

• Adds RNA downloads to PanCancer download tool gnos_pull.pl
• Hardening of external process handling in PCAP::Threaded
• Adds C version of diff_bams

v3.3.4 - Efficiency

bwa_mem.pl

• Reduces temp data overhead (BAM/CRAM inputs)
• Improve throughput via slightly unintuitive use of additional pipes

(couple of intermediate tags to get to stable version)

v3.3.0 - threading and malloc control

• adds map_threads|mt option to bwa_mem.pl to allow more control of parallel processing in one shot submission.
• adds bwa_pl|l option to bwa_mem.pl to allow preload of different malloc libraries.

v3.2.0 - migrate to cgpBigWig

Now uses cgpBigWig now used for BigWig file generation.

v3.1.0 - Milestone 3.1.0

Please see the milestone details:

https://github.com/ICGC-TCGA-PanCancer/PCAP-core/milestone/5?closed=1

v2.5.0 - New tools and reduced dependancies

Added detectExtremeDepth.pl, see wiki page Hi seq depth regions.

Bugfix/optional functionality in bam_stats.pl

• Fixes long standing bug in bam_stats.pl -plots option which failed when it encountered
  empty default readgroup '.', used when a read has no RG_ID attached.
• Allows PCAP-core to be installed without support for the bam_stats.pl -plots option.
  Removes dependancy on GD::Image and Math::Gradient. Functionallity preserved provided
  if modules found in PERL5LIB, otherwise warnings.

v2.4.1 - reheadSQ more robust

• Making reheadSQ more robust

v2.4.0 - More representative BigWig output

Previous versions of the bamToBw.pl script included all reads in the input BAM/CRAM in the counts. Historically all of the common tools for generating these files have done this. With the introduction of several new flags for BWA-mem the data becomes skewed (particularly by supplimentary reads).

This release filters reads where the flags overlap with 3844

• 4 - read unmapped
• 256 - Not primary alignment
• 512 - read fails platform/vendor quality checks
• 1024 - read is PCR or optical duplicate
• 2048 - supplementary alignment

See: explain-flags

We plan to expose the parameter in the future so please add support to the issue #121 if you want to be able to control this value.

v2.1.3 - Upgrades of dependancies

Dependancies updated:

• htslib 1.3.1
• samtools 1.3.1
• biobambam 2.0.40

v2.1.2 - bugfix

Resolves some bugs in bam_stats[.pl] which primarily affected RNA data.