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.