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Kennedy-Lab-UW / Duplex-Sequencing

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Flag should be 5 for unpaired reads (they are still paired, just this… #37

Closed nh13 closed 8 years ago

nh13 commented 8 years ago

… end of the pair is unmapped)

scottrk commented 8 years ago

I don't think 5 is a valid FLAG value. 0, 4, and 16 are valid for single end sequencing, where as 141, 77, 181, 117, 137, 133, 73, 89, 69, 153, 97, 81, 161, 145, 129, 65, 177, 113, 99, 83, 163, and 147 are valid for paired-end sequences. All other should not be valid...although they occasionally crop up every so often.

nh13 commented 8 years ago

It's a valid flag (see the SAM spec, of which I am an author). You are not producing a single-end read here, but a paired end read with one end all Ns.