Releases · quinlan-lab/STRling

Major features

Joint genotyping: Add an optional merge subcommand which combines str read information from all sample bins to produce joint bounds that are. These loci are then genotyped in all samples.
Assign reads to bounds based on original cluster distances
provide STR disease loci for hg38
change default: no soft-clipped reads required for reporting loci
count repeats in overlapping reads (not just spanning) and don't report very high depth regions
only count STR loci that pass some size criteria when deciding if unplaced reads should be allocated
update bin file to hold version, frag dist, etc.
update linear models
Force reporting of loci from input files even if they have insufficient supporting reads (useful for comparing individuals across cohorts)

Suppress reporting of several messages and output of read files to debug mode (spanning in particular can be very large for joint calling)
change column order of -bounds.txt to make it valid bed format and add header
add option to manually limit window for bounds
read both bounds and bed files as input at call and merge stage
anchored lm returns NaN when sum_str_counts is 0
set all bam threads to 0. Addresses #32 htslib error
basic end to end test run in CI for a single sample and 2 joint
update simulation to use merge and different insert sizes