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Broken CIGAR string #2

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ocxtal opened this issue Nov 28, 2016 · 0 comments
Open

Broken CIGAR string #2

ocxtal opened this issue Nov 28, 2016 · 0 comments

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@ocxtal
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ocxtal commented Nov 28, 2016

This is a self issue report.

Setting relatively large mismatch penalty respect to gap open penalty, such as -a1 -b3 -p1 -q1, sometimes results in broken CIGAR strings in the output SAM file. This is probably due to a bug in the alignment routine but the exact reason is not identified yet.

Please use the default (-a1 -b2 -p2 -q1) or some -a1 -b1 -p1 -q1 values to avoid this bug.

Hajime Suzuki
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