[Samtools-devel] Picard release 1.65

[Alec W. <al...@br...>]

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.


-Alec