Eric Banks 53a7d5cbae Fixing a bug in the GVCF writer. ... The writer was never resetting the pointer to the end of the last non-ref VariantContext that it saw. This was fine except when it jumped to a new contig - and a lower position on that contig - where it thought that it was still part of that previous non-ref VariantContext so wouldn't emit a reference block. Therefore, ref blocks were missing from the beginnings of all chromosomes (except chr1). Added unit test to cover this case.		2014-02-20 02:33:43 -05:00
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gatk-protected	Fixing a bug in the GVCF writer.	2014-02-20 02:33:43 -05:00
scala/test/org/broadinstitute/sting/queue/pipeline/examples	Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest	2013-02-27 04:45:53 -05:00
pom.xml	Bumped version to 2.8-SNAPSHOT, using new update_pom_versions.sh script.	2014-02-03 13:50:46 -05:00