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cancerit / PCAP-core

NGS reference implementations and helper code for mapping (originally part of ICGC-TCGA-PanCancer)
GNU General Public License v2.0
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Feature/add threadpool #20

Closed ghost closed 6 years ago

ghost commented 6 years ago

@keiranmraine Please review. Then I can make a release candidate from the branch for testing

keiranmraine commented 6 years ago

This looks good, I'm happy to build and test from the branch without a tag.

ghost commented 6 years ago

@keiranmraine Updated to include proper sentinel fixes.

keiranmraine commented 6 years ago

Ran a small mapping flow with updated PCAP-core, runtime reduces and no change to *.bas output.

@drjsanger can you review these few lines: https://github.com/cancerit/PCAP-core/pull/20/commits/9f63d2ba085847fba92d96d72213cd7224372457

keiranmraine commented 6 years ago

@drjsanger FYI it appears for BAM exceeding 2 CPUs for bam_stats has little additional advantage, happily it does halve the runtime of bam_stats.

keiranmraine commented 6 years ago

Discussed with @drjsanger (as his mac with Systems). Good to go