Fix bam IO to take account of BAM_FPAIRED when checking BAM_FREAD1/2 #18
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…out 0x2, 0x8, 0x20, 0x40 and 0x80"
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This has now been tested on UK10K cohort BAMs and in combination with a correction to samtools fixmates has resolved the problem we had with orphaned paired reads (which had run out of sync and were thus mismapping). |
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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".