I'm writing code to remove insertions/deletions (indels) and also reference skips from pileup lines. I found an online discussion that suggests that " The qualities for insertions don't appear anywhere as there is not +/- markup in the quality field." (https://sourceforge.net/p/samtools/mailman/samtools-help/thread/CADSMrEZmPztQfEXabWKJzKd%3DjqRyRpQmaDV_qAWaWfc7YpDerQ%40mail.gmail.com/#msg36245398).
It's unclear to me if I need to remove anything from the quality string field (of a certain pileup line) when removing deletions from it (from the field of the bases in the pileup line), and the same question when removing ref. skips. Regarding deletions, the post I found (link above) says that "The quality for the deletion is fake as it doesn't actually exist in the called sequence. However the format requires a base & quality, so it uses base * and quality for the next base instead." - I don't completely understand the meaning of this answer and what should practically be done in my code.
I'd appreciate any help in understanding what needs to be done in order to make my code work accordingly to the pileup format in these cases :)
