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CHANGELOG.md

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Changelog

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

0.3.0 — 10-10-2022

Added

  • Adds reference genome support for GRCh38_no_alt_AnalysisSet, hs37d5, hg38m1x, and T2T-CHM13.
  • ngs index: adds `ngs index command to index common bioinformatics formats.
  • 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 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.

Revised

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

Fixed

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

Important 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 compatability, 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).

0.2.0 — 09-18-2022

Added

  • ngs generate: adds support to generate files resulting from one or more reference FASTAs.
  • 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.

Removed

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

0.1.0 — 05-10-2022

Added

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