v0.4.0

0.4.0 — 03-24-2023

Added

• Adds GRCh38FullAnalysisSetWithDecoyHLA (used by 1000 Genomes).
• ngs convert: adds conversion between many common next-generation sequencing
  file formats.
• ngs index: adds CRAM indexing.
• ngs list: adds ngs list plots.
• ngs plot: adds VariantAlleleDistributionPlot.
• ngs qc: adds VAF file output to Edits facet.
• ngs view: adds ngs view.

Revised

• Makes --verbose and --quiet global arguments.
• Updates noodles to 0.34.0.
• ngs list: changes ngs list reference-genomes -> ngs list genomes.
• ngs plot: adds --only flag to ngs plot sample and ngs plot cohort.
• ngs qc: adds --only argument to qc command.
• ngs qc: now preserves struct order of JSON outputs.
• ngs qc: improves logging for qc subcommand.
• ngs qc: adds coverage bins to coverage qc facet.
• ngs qc: updates second-pass qc facets to respect -n records.