v4.0.0

Features

• v4 release (711ad95)

BREAKING CHANGES

• all TSV result headers are now PascalCase.
  --split-by-rg is now the default for strandedness and endedness.
  Percentages are now returned when 'Pct' is used in the header.
  strandedness now adds an overall entry when --split-by-rg.
  Read Groups are compared in the header definition and those found while
  sampling sequences. Discrepancies between the two are logged as an
  error. Header RGs without sequences are added as ZERO results to the
  output.
  endedness no longer exits with an ERROR on Unknown cases.

v3.3.2

Bug Fixes

• endedness: missing key for dictionary (b077893)

v3.3.1

Bug Fixes

• strandedness: pass in required max_tries arg to main() (#136) (544be1a)

v3.3.0

Features

• endedness subcommand (#124) (d61e82d)

v3.2.1

Bug Fixes

• -1 n-reads default for encoding. don't falsely imply random sampling (#119) (c83275a)

v3.2.0

Features

• handle case of BAM without RG tag (#100) (4436abf)

v3.1.1

Bug Fixes

• Revert "feat: junction-saturation (#16)" (#110) (9262af0)

v3.1.0

Features

• junction-saturation (#16) (e4811e7)

v3.0.0

Features

• junction-annotation: by default discard unannotated contigs (#96) (d2f2e18)
• adds Dockerfile (#97) (26242b2)

BREAKING CHANGES

• junction-annotation: Always annotate as unannotated_reference in the junctions file.
  By default, exclude from the summary report.
  With flag, call them "novel" in the summary

• style: whitespace

• docs: fix bad hyperlink

• docs: add new -c param to documentation

• chore: changes requested by @claymcleod

• chore: add default=False for explicitness (per @claymcleod suggestion)

• chore: make defaults match

v2.4.0

Features

• adds Dockerfile (2a663ff)