STRling Versions Save

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)

Minor features

• 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

this is a first release of strling. to install, just grab the strling binary below, chmod+x and run

to get more information in case of a problem. run with strling_debug (which will be much slower) but will help as we iron out any issues.