Provide more informative error message when countMismatches has an ArrayIndexOutOfBoundsException.
Release 1.35
Initial versions of 454 tools
Changes needed by 454 - accidentally left off last commit
Changes needed by 454 - accidentally left off last commit
Add some more assertions.
Make public getAlignedRecordCount, getUnalignedRecordCount, getNoCoordinateCount
Support bgzipped SAM files in SAMFileReader.
Improve interface to bam index metaData - public getMetaData in AbstractBamFileIndex.
Allow Sam or Bam output
When merging the input files, if they are all sorted then use that to produce a sorted input iterator.
Soft-clip CIGAR operator inside of hard-clip operator is now considered valid.
Non-standard 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.
Fixed most of the problems running unit tests on windows
Optimized getMetaData to avoid query PIC-465
Fixed the check that the BamIndexFile lastModifiedDate >= BamFile.lastModifiedDate
Validate that cigar's readLength matches record's readLenth
Undid last commit - awaiting unit tests
Prepare for Sourceforge release 1.36.
Pass -lib lib/ant to ant commands