[Samtools-announce] Picard release 1.26

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

Release notes for Picard 1.26
21 July 2010

- Bam index building is still pre-release.
- CollectInsertSizeMetrics Added a check that the read being examine must be mapped.
- IoUtil: Added utility method to get the full canonical path for a file, resolving all symbolic links.
- BlockCompressedInputStream, BAMFileReader, SAMFileReader, SAMTextReader, BlockGunzipper: Change to allow users to decide whether or not to compute and validate CRCs when decompressing BAMs and other block compressed GZIP data. Default is to not validate CRCs since it's an expensive operation.
- Modified ValidateSamFile to turn on CRC checking that is off by default since this is probably once place that it should be done.
- Modified MergeBamAlignment to proceed on the assumption that the records being merged are query-name sorted and to only sort if that assumption fails.
- RevertSam: Added ability to overwrite SAMPLE_ALIAS and LIBRARY_NAME when reverting a BAM file.
- SAMRecord: Throw more informative exception if SAMRecord.setReferenceIndex or SAMRecord.setMateReferenceIndex is passed an invalid index.
- AbstractAlignmentMerger: Throw explanatory exception when no sequence dictionary available for reference when merging alignments.



-Alec