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).