search

BenLangmead / qtip

Qtip: a tandem simulation approach for accurately predicting read alignment mapping qualities
MIT License
25 stars 7 forks source link

Use BAM instead of SAM. #8

Open johanneskoester opened 6 years ago

johanneskoester commented 6 years ago

This PR uses samtools pipes to store all alignments in BAM instead of SAM. On real data this avoids massive storage issues and should also speed up IO.

This adds two dependencies to qtip:

  1. samtools
  2. bash

The latter should not be a problem, because it should be available on any current linux and macOS. Samtools will be available for almost everybody who uses qtip. Any samtools and bash version will work.

johanneskoester commented 6 years ago

@BenLangmead this is ready for review.