release: bumps version to v0.4.0

CHANGELOG.md

@@ -1,36 +1,61 @@
 # 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
 
-* `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 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 index`: adds `ngs index command to index common bioinformatics formats.
+* `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
 
-* `ngs qc`: all results are aggregated into a single file now.
+* 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).
-* Unifies command line arguments for number of records (`-n`).
+* `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).
 
 
-### Major Chores
+### 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
@@ -46,12 +71,12 @@
 
 ### 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.
-* `ngs generate`: adds support to generate files resulting from one or more reference FASTAs.
 
 ### Removed
 

Cargo.toml

@@ -1,12 +1,12 @@
 [package]
 authors = ["Clay McLeod <[email protected]>"]
 edition = "2021"
-license = "Apache 2.0 OR MIT"
+license = "Apache-2.0/MIT"
 name = "ngs"
 rust-version = "1.64.0"
 publish = true
 description = "Command line tool for processing next-generation sequencing data."
-version = "0.3.0"
+version = "0.4.0"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html