Speed up mapping by not running samtools view
Speed up mapping by not running samtools view

Recent `samtools sort` versions support reading SAM from stdin (they still write BAM output). In my tests, leaving out this line gives a binary identical BAM file in the end, but is roughly 10% faster. The speedup comes from getting rid of one compression/decompression round (`samtools view` compresses its output, which is then immediately decompressed by `samtools sort`).
szilvajuhos/CAW,szilvajuhos/CAW,marcelm/CAW,szilvajuhos/CAW,marcelm/CAW,marcelm/CAW