WIP: Added multi-allelic processing for amplicon mode #109
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PolinaBevad
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A test case for amplicon run: https://drive.google.com/open?id=10pRdrqJwN8XisHA3QTHlyIQgAEmzXCXO |
PolinaBevad
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Have to be reviewed by Zhongwu Lai.
Description
This PR adds the same changes for amplicon multi-allelic cases as were added previously in Java version here: AstraZeneca-NGS/VarDictJava#155
For now, Ampbias flag will test all variants on all amplicon, included multi-allelic (so it have to go through all variants in amplicons and not the first one on the position as before). AMPFLAG determining fixed for this criteria.
Also, it will fix part of #55 issue (missed SNV because of multi-allelic skipping, but not Deletion problem which occurs in realignlgdel()),
PR branch was tested on dataset (1,6 Gb BAM file and Gene_Lung_primers.bed).