- Fix deprecated tool CrosscheckReadGroupFingerprints for compatibility with
picard-privaterepository (#868). Cross-checking by read-group gives results as a metrics file, and cross-checking by samples or libraries gives results as a matrix. Bug had reversed this application.
- Fix bug in LiftoverVcf pertaining to indels that straddle two links in the chain file (#864, addresses #859). Error appears as, e.g.
Exception in thread "main" java.lang.IllegalStateException: BUG: GenomeLoc 1:1634405-1634409 has a size == 5 but the variation reference allele has length 2 this = [VC Unknown @ 1:1634405-1634409 Q. of type=INDEL. Now, instead of a tool error, the tool shunts these variants to the