New alignment wf 3 #7
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Fix added to mtVariantCaller.py to overcome the problem of cases where bam.cov file contains more positions than those expected from the mt fasta file.
This is actually a trick, which iterates through all positions of the mt ref file instead of all positions of the cov file. I am aware that's not the way to solve this, because we have to understand first why samtools depth generates such a file. @domenico-simone would be good to discuss this soon.
best,
C