Bug fix 2.1.5

This fixes a bug in vcf output.

New release to reflect -somatic

New release to reflect -somatic.

Bug fix from 2.1.1

This release fixes a show-stopper of a bug for processing phased reads. The haplotype tag was not being correctly set from the bam.

Additional changes include adding a --max_coverage flag for allowing more reads to be used to call a TR value, and --somatic to output calls for all reads in a tabular file.

Version 2.1.1

This is a release that tracks updates to the locus/motif list. The new version has 1,243,954 loci in GRCh38, and 1,175,953 loci for CHM13. The majority of new loci relative to v2.0 are in mobile elements.

Extended-locus release

This update references 1243954 loci on GRCh38 and 1175953 loci on CHM13.

Version 1.3.8

Not changing version since this just updates the makefile.

Bug fix for first region in each file.

This fixes a bug where the first tandem repeat on each chromosome was output as a deletion.

Fixed printing help

Now prints help with empty command line, and exits with success.

Fixing errors from 1.3

Fixes:

• Memory leak
• Incorrect read assignment for het strs
• conda build.

Bug fix release for 1.3

This fixes some memory leaks and data flow errors introduced in the first version that supported STR annotations.

This fix annotates full deletions of tandem repeat loci as DEL in the output.