Detect novel (and reference) STR expansions from short-read data
This release fixes mostly minor bugs and improves scalability by reducing memory and facilitating parallelization.
Full Changelog: https://github.com/quinlan-lab/STRling/compare/v0.5.1...v0.5.2
Updates to documentation only. Created an extra release for the STRling paper.
Code updates: Let outliers script take a glob file pattern (useful when number of input files is extremely large) Merge checks that input file exists
Updates to docs
Fix travis CI
Improved accuracy of STR locus bounds:
More robust statistics in the outlier test
Documentation:
Pipeline fix:
this release is unchanged from 0.4.0 except that it tightens a dependency in nimble which has been updated.
Major:
Minor:
merge
(off by default, use with caution)Major:
merge
subcommand only reports bounds with a minimum number of supporting reads in at least one sample (default: 6)index
subcommand to create an str index of the reference genome. This was previously done per sample, but is more efficient to do once in advance for larger cohortsMinor:
merge
reduced by more than half