[Samtools-help] Picard Release 1.32

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

Picard release 1.32
4 October 2010

- Implementation of BAM index generation.  This is available as a stand-alone program, BuildBamIndex, and Java class, BamIndexer, for indexing existing BAM files.  A BAM index can also be generated on the fly as a BAM is being written, via the CREATE_INDEX command-line option, and through the Java API via new methods on SAMFileWriterFactory.  Note that we have received one bug report about an invalid index being created.  We have not been able to reproduce this problem and continue to investigate.  Our testing has found the code to be working well.

- Allow P CIGAR operator btw pair of Ds.

- In ValidateSAM, allow either 1.0 or 1.3 to be considered valid SAM version in @HD record.

- Make SeekableBufferedStream buffer size configurable.


-Alec