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sstadick / perbase

Per-base per-nucleotide depth analysis
MIT License
115 stars 13 forks source link

enh: filter_read also takes Option<&Alignment> #61

Closed brentp closed 1 year ago

brentp commented 1 year ago

see #60

This seems to be the smallest change and makes it possible for only_depth to work with minimal changes since that doesn't actually use the htslib pileup stuff.

sstadick commented 1 year ago

Any chance you have the benchmarks you ran on the PR are available to check on this one? I don't see any reason to suspect that this would slow things down, just being cautious since I haven't touched this code in a long time.

brentp commented 1 year ago

Sorry for the delay. I just built a release for main and my branch and ran a few times

time ./perbase-main base-depth $bam | md5sum
time ./perbase-bsp base-depth $bam | md5sum

and the times are nearly identical.

sstadick commented 1 year ago

See release v0.9.0 which should land on crates.io shortly.

sstadick commented 1 year ago

And thanks for the PR!

brentp commented 1 year ago

Thanks Seth!