Merge dip_polish branch to mainstream

[mp15]

Hi,

I've been using hapdup (https://github.com/KolmogorovLab/hapdup) and was looking at how it was put together (I'm interested in using it with chromothriptic genomes and I want to modify it for CN=1 regions) and noticed it is based on your dip_polish branch rather than main. I was wondering what the reasoning in abandoning dip_polish was? Do you recommend just flat filtering reads to HP=[1|2] instead with samtools view -d HP=1 or something else? Also I notice there was INDEL cluster code that didn't make it to main? I assume it didn't perform well?

[mikolmogorov]

Hello,

dip_polish is indeed currently used in Hapup - so it is not abandoned.

[mp15]

Thanks for getting back so quick. That's awesome, any plans to merge it to master or is there a compromise in using the INDEL cluster method? Developing against a special purpose branch always kinda makes me nervous. I'm happy to do the work on a pull request to get it resynced if time is an issue.

[mikolmogorov]

Sorry for the late response - we do plan to merge eventually. But this is not the priority currently, so I can't tell you exactly when this would happen..