non-static to avoid problems when multiple references are used within the same
thread (eg., during integration tests). This should kill the intermittent
IndelRealignerIntegrationTest failures.
a) Modified the way clipped bases are dealt with in ReadPosRankSumTest when annotating indels. Cigar string cannot be trusted because BWA can clip good high quality bases and some sites get incorrect ReadPos annotations if BWA systematically clips at an indel breakpoint.
b) PL header needs to specify "." as length. Otherwise we fail VCF validation if multiallelic sites are present.
describe" as an absolute version number (if the repository has at least one
tag), using the raw SHA-1 hash value as a fallback version number in the case
where there are no tags.
Ryan Poplin
Guillermo del Angel
Eric Banks
Khalid Shakir
David Roazen