lh3/bwa — pull request #18 by mp15 (2013-06-13 16:02:27+00:00)
Title: Fix bam IO to take account of BAM_FPAIRED when checking BAM_FREAD1/2

This patch fixes bam IO to take account of BAM_FPAIRED when checking BAM_FREAD1/2. According to the spec "If 0x1 is unset, no assumptions can be made about... 0x2, 0x8, 0x20, 0x40 and 0x80".