Bug Fixes

• Template.fixMateInfo() to set primary mate info before supplementary info (#1114) (da4d2966)
• The consensus RX (UMI) should be called from filtered records only (#1116) (cc3b926e)
• Typos in the consensus caller (#1118) (4a8644b5)
• Improve the numeric stability of the consensus caller (#1120) (e2ccac96)
• Preserve input order in filterToMostCommonAlignment (#1119) (d809e1ca)
• Add deterministic tie-breaking to adjacency UMI assigner (#1123) (6696d30b)
• Ensure tools that use Io.assertReadable work on file descriptors too (https://github.com/fulcrumgenomics/fgbio/pull/1113) (ebe3fe0)

Features

• Use an epsilon (2.2204460492503131E-16) when comparing log like… (#1117) (ca4bcde9)
• Add --cram-ref-fasta common argument for CRAM support (#1122) (c8fbd2be)

Miscellaneous Tasks

• Bump to 3.1.1-SNAPSHOT (bba6eaeb)
• Release 3.1.1 (30e22457)