[Samtools-announce] Picard Release 1.34

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

Picard release 1.34
1 November 2010

- Interval.java: Change validation on to check for end<  start-1 (instead of end<  start) since end = start-1 is used to represent 0-length intervals.

- Enable MarkDuplicates to work in a reasonable amount of RAM even for a reference with many sequences, by using an LRU cache for open file handles in order to avoid exceeding maximum number of open file handles.  MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP option is obsolete.  MAX_FILE_HANDLES_FOR_READ_ENDS_MAP controls the size of the LRU cache of open files.

- AbstractAlignmentMerger.java: Modified so we don't try to calculate UQ tag if QUAL is set to *.

- ValidateSamFile: Store PairEndInfo in file-based data structure so it runs in fixed amount of RAM.  Added check for read marked as paired for which a mate is not found.

- AbstractFastaSequenceFile.java: When trying to find a sequence dictionary corresponding to a reference fasta, try filename.dict if basename.dict isn't found.  Patch from Nils Homer.

- SamToFastq.java: Flush output files before checking for unpaired mates.

- SamToFastq may now output fastq files per read group if OUTPUT_PER_RG (OPRG) is specified.  If OUTPUT_DIR is specified with OUTPUT_PER_RG then a file (two if paired end) will be output in OUTPUT_DIR per read group named after the platform unit for the read group.

- FastqToSam no longer fails on read if trailing /1 or /2 is missing IF the read names are identical AND don't end in /1 or /2.

- CommandLinePrograms no longer display common options unless -H or --stdhelp is used or there was an error with a standard option.

- CollectAlignmentSummaryMetrics no longer fails if there is no reference sequence provided.

- Fix auto-MD5 generation, which wasn't working because of check that output file already exists rather than that it is a normal path.

- Emit warning if MD5 or BAM index creation is requested, but can't be done because output BAM is not a regular file.


-Alec