samtools/htsjdk — pull request #130 by BeatWolf (2014-10-29 12:58:03+00:00)
Title: Speedup SAMUtils.compressedBasesToBytes for faster BAM file parsing

In my simple testcase (iterating through all sequences in one bam file) i saw that a large portion of the time was spent in SAMUtils.compressedBasesToBytes. Optimizing this function to use a Lookuptable made it about 50% faster, giving a speedup of 20% on the complete testcase.