1.0.4 - fix in biobambam

Release to fix a problem in BioBamBam bammarkduplicates.

For multiple library files the statistics in the metrics file would be wrong and there could be too many reads which are marked as duplicates (duplicate marking is per library, so if you have two reads/read pairs which map to the same coordinates but which are in different libraries you would not consider those as duplicates. The program however put all the reads in one library, so there is a potential that reads are marked as duplicates which should not be. I guess this does not happen with high probability though).

v1.0.3 - maintenance release

• Corrected issue from dynamic de-reference of hash, issue for pre 5.14 perl and potentially unstable in future.
• Added missing project code to cv terms.
• Bug-fixed upgrade path.
• Cleaned up messaging in Threaded module.

v1.0.2 - maintenance release

Upgrade install to pull biobambam 0.0.138

• fastqtobam option 'pairedfile' for where readnames don't have trailing '/1' or '/2'.
• fastqtobam option to relax qscore validation without turning off... careful

Upgrade install to pull BWA 0.7.8

• performance improvements for short read alignment (100bp)

v1.0.1

SRA.pm - check that rg id is unique within run of code (thanks to Junjun Zhang)

Upgrade install to pull biobambam 0.0.135

• fastqtobam supports Casava v1.8
• bamsort supports NM/MD correction during sam->bam/merge process

Minor enhancement to BAS reader module
Sample name from command line passed through to SM of RG header in bwa_mem.pl
Threads.pm - join interval is now configurable.

v1.0.0 - use with SOP v1.0

For use with PCAP Sequence Submission SOP - v1.0

There is no need to upgrade for GNOS upload purposes unless you are having problems installing under CentOS.

See Changes for full details.

v0.3.0 - use with SOP v1.0

For use with PCAP Sequence Submission SOP - v1.0

Dev-branch beta release

Pre-prelease for initial testing prior to general use. Some documentation (POD) is still pending.

Enhanced with smoother install path

bam_to_sra_xml.pl

• new param to specify the GNOS server
• generates a bash script to automate validation/submission to GNOS.

setup.sh

• Improved to smooth install process.

INSTALL

• Following test on Ubuntu 12.04 VM packages that need to be installed by a package manager prior to running setup.sh are listed.

v0.1.2 - installation consistency

This will only generate submission scripts for the EBI GNOS presence

Fixes incompatibility of MakeMaker with perl #!/usr/bin/env perl which prevents expansion of the #! to the perl used when installing for executable scripts. Also ensured that Makefile.PL is called with pathed perl during installation.

Fixed test case relying on presence of empty folder

Empty folder is not committed to git. Rather than hacking, folder is now generated within test and cleaned up.