Ensure sam-1.77.jar is the JAR of choice.
New versions of sam JAR (e.g. sam-1.85.jar) does not support
SeekableStreams
*Added bounds checking routine when querying for short SC.
*Modified percent identity calculation that subtracts indel count from
NM (edit distance) tag.
little thing...
Added function to ensure BAM index is newer than BAM, otherwise a new
one will be created.
findIndexFile now checks for modified date
double samtools