use coarser loci-ranges in TakeLociIterator - Githubissues

hammerlab / guacamole

Spark-based variant calling, with experimental support for multi-sample somatic calling (including RNA) and local assembly

Apache License 2.0

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use coarser loci-ranges in TakeLociIterator #593

Closed ryan-williams closed 7 years ago

ryan-williams commented 7 years ago

improves performance of capped-regions partitioner in cases where coverage is sparse; pathological cases would end up generating LociSets with many 1000s of ranges comprising them.

coveralls commented 7 years ago

Coverage increased (+0.2%) to 78.843% when pulling 9a8d4d2f57cf559614c5ccb6c4d0540bc1ef6e87 on ryan-williams:pra into 738996d8cfcc4bbcabf2138cf269b965dff5b190 on hammerlab:master.

coveralls commented 7 years ago

Coverage increased (+0.1%) to 79.087% when pulling 8ef23747b7074ed910b96f035f1ef53d07ee1f62 on ryan-williams:pra into 4afd15011eb01576ca3789ce77ea03a526515ebe on hammerlab:master.

coveralls commented 7 years ago

Coverage increased (+0.1%) to 78.633% when pulling dfae6063d8c7a17a2ba13ea2e35ccfee0d6c2ff1 on ryan-williams:pra into 5f87847d5b069e9b3bd6c88b80b291b9d712838d on hammerlab:master.

ryan-williams commented 7 years ago

trimRanges is added by never set to true other than the tests - is that expected?

weird, I thought I'd added a cmdline-flag for it, but can't find it any of my branches, maybe I hadn't at all; anyway, I added it now, thanks for catching!

coveralls commented 7 years ago

Changes Unknown when pulling bdae61c456907b57733dff6575172a4a6788afbc on ryan-williams:pra into \ on hammerlab:master**.

coveralls commented 7 years ago

Changes Unknown when pulling bdae61c456907b57733dff6575172a4a6788afbc on ryan-williams:pra into \ on hammerlab:master**.