Picard release 1.65
26 March 2012
- Major refactoring of ClippingUtil underlying IlluminaBasecallsToSam. All existing adapterTrim... methods are deprecated and no longer return any warning strings. ClippingUtliity.AdapterPair has been removed and now their is an AdapterPair interface (in the util package) that is implemented by IlluminaAdapterPair. In IlluminaBasecallsToSam the MARK_ADAPTER paramter has been removed and replaced with ADAPTERS_TO_CHECK, which is a list of IlluminaAdapterPairs. If any adapter pairs are provided, adapter marking is done. New adapter pairs have been added and the defaults in use have changed.
- IlluminaBasecallsToSam.java:Support multiple barcode reads
- Remove validation that complains about CIGAR starting with P operator.
- MergeSamFiles.java: Fix hang when USE_THREADING=true and exception reading input.
- BAMFileReader.java: Print file name when error in BAMFileReader when possible.
- Pass filename through to BAMRecordCodec to improve error messages.
- Accept VN:1.4 in SAM header.