v2.0.4 - Missing check on manual inputs

Fixes failure to check manual assembly/species was defined before assigning as override

v2.0.1 - legacy software cleanup

• Removed use of legacy Tabix codebase and switches to samtools 1.2+
• Removed use of legacy vcftools codebase, now using GitHub version
• Several bugfixes to test cases

v1.3.1 - adds extended copynumber reporting to VCF

Now possible to include a secondary copynumber change (and fraction for primary).

Bugfix release - v1.2.6

• cgpVCFSplit.pl deployed to bin

Bugfix release - v1.2.5

• Correcting version number, prerelease run.

v1.2.4: Now warns when platform passed doesn't match bam, header. Overrides b…

*Now warn instead of die when platform passed doesn't match bam, header.

• Overrides bam header to passed value. Fixes #13

v1.2.2 - Bugfix CN conversion module

See #11 for details.

v1.2.1 - Minor fix to setup.sh

Some missing dependencies.

v1.2.0 - new generic ID script

Merge pull request #7 from cancerit/dev

merge in cgpAppendIdsToVcf.pl

cgpVcf-v1.1

Now supports simple segmented copynumber to VCF.