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collaborativebioinformatics / STRdust

MIT License
13 stars 3 forks source link

Code avdeev #32

Closed PavelAvdeyev closed 3 years ago

PavelAvdeyev commented 3 years ago

This pull request combines some progress from @Fu-Yilei and @AvdeevPavel and @lfpaulin .

Added functionality:

  1. vcf output
  2. baby logging (need to check permission for writing files)
  3. mreps functionality
  4. bug fixing merge merge_overlapping_insertions function
  5. implementing weird hack for having cut-off on seq lengths before running poa.

Overall changes made it possible to process whole human bam file (without memory issues).

The existence of such long insertion sequences is worrisome.

wdecoster commented 3 years ago

I am going to merge all of this, but I haven't tested the mreps and vcfy code. It all looks reasonable... and we can debug it from here.