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.

v0.3.0

0.3.0 — 10-10-2022

Added

• ngs qc: adds coverage and edits quality check in a second pass.
• ngs qc: adds mate mismatched sequence id and CIGAR accumulation to the
  General quality control facet.
• Adds reference genome support for GRCh38_no_alt_AnalysisSet, hs37d5,
  hg38m1x, and T2T-CHM13.
• ngs list: adds ngs list command to list out particular subjects that are
  supported by the ngs command line tool.
• ngs plot: adds ngs plot command to visualize the output of data from ngs qc. In the initial sample-level implementation, we support graphs for GC
  Content Distribution & Quality Score Distribution. In the initial cohort-level
  implementation, we just support GC Content Distribution.
• ngs index: adds `ngs index command to index common bioinformatics formats.

Revised

• ngs qc: all results are aggregated into a single file now.
• ngs generate: now supports better read names (the location where read one
  originated from is now in the read name).
• Unifies command line arguments for number of records (-n).

Fixed

• ngs generate: fixed off by one error when generating records (one too many
  records was being generated).

Major Chores

• Minimum supported Rust version is now 1.64.0.
• Updates license to be either MIT or Apache 2.0 licensed (at the user's
  discretion).
• Updates dependencies as of 09/29/2022.
• Adds lint groups for documentation, Rust 2021 compatibility, and Rust 2018
  idioms. This caused a few changes in the code, as well as a massive
  improvement in documentation.
• The code was reorganized by subcommand (in terms of file system structure).

v0.2.0

0.2.0 — 09-18-2022

Added

• ngs qc: adds ngs qc command with the initial four modules:
  • General metrics reports general statistics about the records contained within the file.
  • GC content reports statistics regarding the GC content for records within the file.
  • Genomic features reports statistics regarding genomic features contained within a GFF file.
  • Template length reports statistics regarding the template lengths contained within the file.
• ngs generate: adds support to generate files resulting from one or more reference FASTAs.

Removed

• ngs flagstat: ngs flagstat has been removed in favor of the general metrics module in ngs qc.

v0.1.0

0.1.0 — 05-10-2022

Added

• ngs derive: added experimental support for ngs derive instrument.
• ngs flagstat: added experimental support for ngs flagstat.