CRAM support

• Adds support for CRAM
• Upgrades to verifyBamId 1.1.3

v1.4.2 - Hotfix release

Validate sample metadata: strict column name match

v1.4.1 - Hotfix Release

Improved sample metadata validation:

• require is_normal_for_donor column in input
• checks for each donor if there is normal/tumour/matched_normal
• tests are mainly on tsv files instead of xlsx files

v1.4.0 - Feature Release

Added module and executable to validate sample meta data and bam headers. It's mainly for the use of Pan Prostate project.

Migrates to Bio::DB::HTS

Some of the underlying tools don't support CRAM so only removed legacy perl bindings at present

v1.1.0 - Dependancy updates and fixes

Fixes execution of alleleCounter since update to htslib.
Updates VerifyBamID to 1.1.2.

v1.0.2 - improved gender determination

Revises gender determination to be based on normal sample, comparison to tumour is still included.
Gender is now considered XY on presence of any of the gender (male) specific loci.

v1.0.1 - patch to summary output

gender data was not being dumped to output summary correctly, plus corrected cut-off to >= 0.5, as result not output before no effect on result.

v1.0.0 - First stable release

Merge pull request #2 from cancerit/develop

Roll 1.0.0

v0.0.1-dev: preliminary release for testing externally

forgot to update dist name in modules