[Samtools-announce] Picard release 1.28

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

Picard Release 1.28
18 August 2010

- In various programs, write messages to stderr rather than stdout, so that BAM output can be sent to stdout.

- BlockCompressedFilePointerUtil: encapsulate code for manipulating BGZF virtual file pointers.  Make sure it works for virtual file pointer that is so large as to be negative as signed long.

- BamToBfq: Added option to write only the first N bases of the read to the bfq file.

- CigarUtil: Added method to add soft-clipped bases to either end of a cigar (used when reads have been trimmed before alignment and the cigar needs to be adjusted to reflect this).

- AlignmentMerger: Added option to specify reserved tags from alignment bam to bring over when merging.

- SamRecord: Change mAttributes from ArrayList to custom linked list to reduce memory footprint.

- SamFileValidator: Added some progress logging.

- DuplicationMetrics: Change to allow calculation of estimated library size in heavily duplicated (as in 99%+ duplicaiton) data.

- MergeBamAlignment: Clarified documentation to make clear that a sequence dictionary is expected in the same directory as the reference fasta and that its extension should be .dict.



-Alec