v1.5.1 - bam_stats c now has CRAM support.

Also dropped need for samtools v1.x api as can be handled by htslib on it's own.

v1.5.0 - bamToBw.pl and new biobambam dep

No changes to old tools, just additions and prep for handling CRAM input.

v1.4.0 - bam_stats in C

Takes less than 2 hours to generate stats on a sample level BAM file of ~120GB.

v1.3.0 - multi-threaded bam_stats.pl

bam_stats.pl is now multi-threaded, can get ~50% runtime reduction with 3-4 threads, memory still <500MB.

Upgrades biobambam to 0.0.185 (and dependencies).

v1.2.3 - more robust xml_to_bas.pl

See #54

v1.2.2 - Bugfix for bwa_mem.pl

Fixed bug in bwa_mem.pl when using '-f' option on paired fastq.

This issue has no impact on pancancer related tools.

v1.2.1 - bugfix

Makes xml_to_bas.pl more robust on AWS. Retrieved XML was being truncated on some network configurations.

Symptom:
unclosed token at line 90, column 12, byte 8117 at /usr/lib/perl5/XML/Parser.pm line 187.
(or similar line/column/byte)

There are no other changes in this release that affect functionality.

v1.2.0 - parallel processing bwa_mem.pl

Modifications made to the bwa_mem.pl code to split a lane of data into fragments to reduce failure recovery time. Primarily added to handle X10 data better.

Also updated samtools to 0.1.20, last version that is currently compatible with Bio::DB::Sam.

v1.1.1 - maintenance release

Fix missing dependancy and build a relocatable version of biobambam suitable for use in artifactory.

v1.1.0

• Minor enhancement to bwa_mem.pl to automatically generate the *.bas file.
• Added xml_to_bas.pl for pancancer users, see the wiki for details.
• Fixed a few minor issues
  • #36
  • #37
  • #39