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twolinin / longphase

GNU General Public License v3.0
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LongPhase Phase out-of-range issue #16

Closed zhengzhenxian closed 6 months ago

zhengzhenxian commented 2 years ago

Thanks for the great tool!

We would like to report an error that happened in Clair3 with LongPhase phase but not with whatshap. The error was reported at HKU-BAL/Clair3#112. Much appreciated if any suggestion or comment on it, and pls let me know if you need more details, thanks!

twolinin commented 2 years ago

Hi @zhengzhenxian

Thank you for the issue. This issue is caused by the following alignment in the bam file. This alignment has CIGAR for column 6 but no information for column 10. I have pushed a new version to handle this situation. If you have any questions, welcome to ask.

cca98b9e-206c-4a36-af9e-fc7e0ec79e75    2064    chr16   3203484 60      5634H436M1I249M1I32M1D5M1D45M1D19M2I154M3I3M3I17M1D293M1I55M2D161M1I34M1I177M1D3M1D5M1I146M1D194M1D17M1I76M1I326M2D1M1I101M1I12M1I49M1D109M1I60M2D188M1D92M1D78M1D144M2I3M2I3M1D56M1D220M1D16M27H       *       0       9264    *       *       AS:i:6754       MD:Z:448C77A1T50T137^G0C2T1^C45^G20T172^T294C51C1^CT158C0C212^G0G2^T104C46^T194^G0C17C400^AA73T0A0A1T0G0G0A27T54^G46T122^TC156T1A0C28^T92^C78^G50A99^G56^A220^G8C7      NM:i:74 SA:Z:chr3,160832957,+,3628S4296M32D1340S,60,77;chr11,40335868,+,7924S1340M6D,60,28;     cm:i:475        de:f:0.0177     ms:i:6763       nn:i:0  s1:i:2863       s2:i:336        tp:A:P
zhengzhenxian commented 2 years ago

Hi @twolinin

Thanks so much for the prompt response and quick fix! It worked perfectly using the updated binary, thanks!

Zhenxian