v2.1.0

What's Changed

• Support input BAMs without basemods. Reads without basemods will not contribute to basemod pileups.
• Support input BAMs without rq tags. rq will not be calculated for these reads, but the reads will be aligned for downstream processes.

• Updated to TRGT v1.4.1. by @williamrowell in #173
  • Increased memory for trgt task to better support larger catalogs with lower complexity motifs.
  • Added the max_depth parameter and limited to 50 to reduce memory usage for high depth low complexity loci.
  • Reduced the number of samtools sort threads to lower total memory used for sort.
• Update to pbmm2 v1.16.99 prerelease. by @williamrowell in #177 Fixes behavior where SA tags were not stripped from aligned input.

• Remove StarPhase outputs that are not allowed as PharmCAT input (PharmGKB/PharmCAT/issues/204)
  • NO_READS is used in StarPhase output to indicate no-calls.
  • NO_MATCH is used when StarPhase can't match the variants to a known allele.
  • This workaround removes NO_READS/NO_MATCH outputs.

• Gracefully handle low depth samples with StarPhase/PharmCAT by @williamrowell in #176

Full Changelog: v2.0.7...v2.1.0