Re: [Samtools-announce] Picard release 1.27

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

Picard release 1.27
2 August 2010


- In BlockCompressedOutputStream, when compressed block is too big, downshift to NO_COMPRESSION mode instead of pushing some input into the next block.  Reduce max uncompressed bytes per GZIP block so that in NO_COMPRESSION mode these will always fit in the GZIP block.

- Modified SamFileHeaderMerger to work with SAMFileHeaders (as its name implies) instead of SAMFileReaders.  All constructors and methods that involved the use of readers have been deprecated and replaced with ones using SAMFileHeaders.  This also involved changes to MergingSamRecordIterator, whose old constructor has been deprecated and replaced with one that requires that the readers be handed in separately.

- Added the option to add comment(s) to the header when merging SAM files.

- Added a toString() to SamLocusIterator.LocusInfo

- Minor improvements to help text.

- BAM indexing code still under construction.

-Alec