[Samtools-help] Picard release 1.25

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

Picard Release 1.25
6 July 2010

- Speed up SAMFileHeader.hashCode

- In SamFileHeaderMerger, change HashMap to IdentityHashMap to improve 
performance.

- Updated FixMateInformation so that it can handle multiple input files 
and merge them dynamically and fix mate pair information at the same time.

- When closing BlockCompressedOutputStream, do not verify file 
terminator if file is not a regular file.

- Removed version option from command line program  classes as it is not 
currently maintained and so not meaningful. 

- Added method for creating file system safe names to IoUtil.

- Added getComparatorInstance() method to SAMFileHeader.SortOrder

- Ignore SyncFailedException when closing BGZF so that it can write to 
unusual devices.

- Handled skipped region (CIGAR operator N) in 
SequenceUtil.makeReferenceFromAlignment.

- Generate metrics documentation and push up to Sourceforge.

- Reduce memory footprint of IndexedFastaSequenceFile.

- Remove requirement of IndexedFastaSequenceFile that dict file is present.

- Fix error in ClipPairFixer when merging only aligned reads

- Only use CloserUtil on files opened for read.

-Alec