[Samtools-help] Picard Release 1.36

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

Picard Release 1.36 6 December 2010

- BAMIndexMetaData.java: Make public getAlignedRecordCount, 
getUnalignedRecordCount, getNoCoordinateCount. Improve interface to bam 
index metaData - public getMetaData in AbstractBamFileIndex.

- Support bgzipped SAM files in SAMFileReader.

- AbstractAlignmentMerger.java: Allow Sam or Bam output.

- FixMateInformation.java; When merging the input files, if they are all 
sorted then take advantage of that to produce a sorted input iterator.

- Soft-clip CIGAR operator inside of hard-clip operator is now 
considered valid.

- Non-standard SAM header tag values are no longer typed. They are all 
stored as strings. Any existing files that have a non-standard header 
tag value with a value type encoded in it will need to be repaired. 
These header tags will parse, but may not yield the expected results. 
AbstractSAMHeaderRecord.setAttribute(String, Object) has been 
deprecated. Use AbstractSAMHeaderRecord(String, String) instead. 
AbstractSAMHeaderRecord.getAttribute and .getAttributes have been 
changed to return String and Map<String, String>, respectively. Existing 
code that called these methods may need to be changed, in the cases 
where other than a String return value was expected.

-Alec