Mark QC-failing reads instead of skipping them#4
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dawe wants to merge 2 commits into
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…em as QC-failing. I've noticed that bitwise flag for SAM output is only 8-bit long, whereas SAM specs say 10-bits. I've shortened the len of seq in bwa_seq_t struct to 18 (should be sufficientg for many years to come) and increased extra_flag from 8 bits to 10 bits
Author
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Actually the second commit (about barcodes) was not part of the original pull request and it should not be considered... |
Owner
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I will keep the original bwa code. It should not make a big difference. Thank you anyway for contributing the patches. |
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Modified QC behavior for bwa. Instead of skipping lines, just mark them as QC-failing.
I've noticed that bitwise flag for SAM output is only 8-bit long, whereas SAM specs say 10-bits.
I've shortened the len of seq in bwa_seq_t struct to 18 (should be sufficientg for many years to come) and increased extra_flag from 8 bits to 10 bits.