Add flanks to gather #64
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@fnothaft This looks good - do you have to rebase before it can be merged? Looks the other commits are still showing in the diff? |
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Thanks @arahuja! I've just rebased, which should fix the diff. |
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| @@ -38,7 +38,7 @@ class TransitionMatrix(val LOG_GAP_OPEN: Double = -4.0, | |||
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| // P( indel -> match) = 1 - P(indel -> indel) = 1 - P( gap-continue) | |||
| // in log-space | |||
| val LOG_GAP_CLOSE = log10(1 - pow(10, LOG_GAP_CONTINUE)) | |||
| val LOG_GAP_CLOSE = -log10(1 - pow(10, LOG_GAP_CONTINUE)) | |||
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This seems to have snuck back
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Sorry about that! I think that was an artifact of the squash/rebase?
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@fnothaft This looks good to merge - but a negative sign on the gap_close probability seems to have returned - this should be removed correct? |
…calling variants with assembly.
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Thanks! |
Adds code to gather flanking sequence to gather/groupBy phase of assembly. Updates all variant calling algorithms to provide PartitionSet, and also adds configuration hooks to assembler. Depends on #63.