Per base coverage missing when allele size greater than read length - Githubissues

iqbal-lab-org / gramtools

Genome inference from a population reference graph

MIT License

92 stars 15 forks source link

Per base coverage missing when allele size greater than read length #107

Closed ffranr closed 6 years ago

ffranr commented 6 years ago

This bug was identified by @martinghunt whilst testing minos.

The bug occurs here: https://github.com/iqbal-lab-org/gramtools/blob/7dff14abdb28997dda39691afa3ca38b6ec4911e/libgramtools/src/quasimap/coverage/allele_base.cpp#L64

The end index for writing into the coverage array was erroneously smaller than the start index.

Fix implemented: https://github.com/iqbal-lab-org/gramtools/commit/63c175a20f9477b270f900addd5aa324ac460330#diff-10e132c228c942b89459e7d8e2d86982R64