Indel revamp #1824
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Indel revamp #1824
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This is just an initial commit so that we can make incremental changes
- proper struct for pileup client data - flesh out the indel type finding routine. This is identical to the original code, the only difference is caching qlen in pileup client data
This version is able to make simple calls, correctly creates up to two reference consensus templates. The code is based on the original indel calling but does not contain the heuristics introduced later by jkb.
It is now possible to call from long reads. To do: consider allowing smaller than 2*110bp window for trimming ref and qry sequences in realignment. Currently it is possible to increase --indel-size but it is not possible to decrease it
Remove the heuristics introduced by e4e1610 which appears unnecessary and even harmful on documented test cases.
…an inheritance but are not novel
…nd check return values when there are no indels types (-1 is returned)
The errors were: - pass correct position to cigar INS matching operator - set the correct offset in the consensus template
…ime when correcting haplotypes
by counting badly matching reads as low quality reference reads. In the original code reads matching badly to any indel type or reference had indelQ set to 0 where thus effectively removed from calling. This leads to problems when there are many soft clipped reads and a few good matching indel reads (see noisy-softclips.bam in mpileup-tests). Only the few good quality indel reads would become visible to the caller and the indel is called with high quality. This commit changes the logic to make the badly matching reads low quality reference reads instead of removing them completely. The threshold was set to make the test case still be called as an indel, but with very low quality.
… only alts were counted
…phred-scaled product of sample genotype likelihoods
…ror in the -std=gnu99 test
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