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

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merged 1 commit into from
Jun 20, 2023

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brentp
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@brentp brentp commented May 24, 2023

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.

@brentp brentp force-pushed the read_filter_alignment branch 2 times, most recently from f20fa89 to 8f8e4bc Compare May 24, 2023 20:23
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sstadick commented Jun 8, 2023

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.

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brentp commented Jun 15, 2023

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 sstadick merged commit cbc7a95 into sstadick:master Jun 20, 2023
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See release v0.9.0 which should land on crates.io shortly.

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And thanks for the PR!

@brentp brentp deleted the read_filter_alignment branch June 21, 2023 00:00
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brentp commented Jun 21, 2023

Thanks Seth!

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2 participants