• Bugfix: Update default platform for IlluminaBasecallsToSam (#1351)
• Recover from side effects introduced in CollectIndependentReplicatesMetric tests. (#1341)
• Adding in some enum constants that are used in existing/old extended manifest files. (#1347)
• Yf provide arbtrary inputs to cmm (#1337)
• GtcToVcf a tool to convert Illumina GTC files to VCF format Responded to a lot (but not all) comments dont recompute tan Refactored some math Enable support for zeroed-out SNPs Generalize AA/AB/BB related fields in VCF Headers Reove zcall from GtcToVcf Added test for GtcToVcf.getGenotypes Use BidiMap Error out / inform user if reference is not HG19 Use IlluminaStrand for Illumina-strand specific fields. Update test to cover all chromosomes used.
• Added whitepaper describing fingerprinting Math (#1247)
• Fixes bug that prevented liftover of spanning deletions. (#1339)
• Removed boilerplate "main" function from picard CLPs. (#1311)
• Trim descriptions to shorten --list display width. (#1259)
• Handle edge cases with no evidence in CrosscheckFingerprints consistently (#1323)