Picard release 1.89
8 April 2013
- Add commons-logging to MergeVcfs and SplitVcfs executable jars so that outputting BCF format works.
- IlluminaBasecallsToFastq: For non-demultiplex mode, don't require barcode files.
- CalculateHsMetrics: Adding PCT_TARGET_BASES_40X thru _100X and HS_PENALTY_40X thru _100X metrics
- VCFHeaderLine.java: VCF header lines cannot contain angle brackets in the ID field. Don't allow bad values in VCF keys and IDs.
- Remove redundant SeekableStream class. Add "readFully" method back to SeekableStream class, much in IGV depended on it.
- Add registration and getting of URLHelper to ParsingUtils.