# Changelog
All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
## [Unreleased]
## [0.7.0](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.6.9...v0.7.0) - 2026-09-03
### Added
- output alignment statistics to a csv file
### Fixed
- *(vcf)* align on the edited cluster region
- *(vcf)* strip the entire shared allele prefix
- clippy
## [0.6.9](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.6.8...v0.6.9) - 2026-09-03
### Added
- *(vcf)* log failed alignments with OOM or timeout (need at least -vv)
### Fixed
- align VCF and BAM coordinates
- *(tsalign)* disable range extension
- clippy
- clippy continued, refactoring
- bunch of clippy warnings
- clustering algorithm now handles length-changing MNVs
- change default min-density to 0, effectively deprecating the setting
### Other
- *(vcf)* cover undeclared and mismatched FORMAT fields
- *(vcf)* split input and output record types
- update minimum rust version to 1.96
## [0.6.8](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.6.7...v0.6.8) - 2026-08-17
### Fixed
- don't abort on overlapping equal-cost-ranges (although they are not sound)
## [0.6.7](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.6.6...v0.6.7) - 2026-08-14
### Added
- *(vcf)* add `allele_count` to csv output
### Fixed
- handle off-path cluster offsets
- do not abort on missing contig
## [0.6.6](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.6.5...v0.6.6) - 2026-08-11
### Added
- *(phasing)* add `-f` and `-F` to filter reads for phasing
## [0.6.5](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.6.4...v0.6.5) - 2026-08-10
### Added
- *(viz)* upgrade lib_ts*, migrating `-e` for more equal cost rendering modes
- upgrade `--output-unresolvable` to show the reason and more information
- assert that VCF version is between 4.2 and 4.5
### Fixed
- *(vcf)* do not stumble on a star allele (overlapping deletion)
- use generic `tsalign` API instead of configurable to reduce binary size and compile times
## [0.6.4](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.6.3...v0.6.4) - 2026-08-05
### Fixed
- *(vcf)* Add missing PS header if not already present
- *(tests)* Change test data so that tsalign v4 does not hallucinate forward template switches
## [0.6.3](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.6.2...v0.6.3) - 2026-08-03
### Added
- upgrade upstream tsalign to v4
### Fixed
- *(cluster)* make VCF and BAM clustering consistent
- wording of settings warning
## [0.6.2](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.6.1...v0.6.2) - 2026-07-30
### Added
- add warnings for non-sensical or likely unintended settings
- *(csv)* add ts_2_3_min and ..._max fields to csv output
### Fixed
- *(csv)* on invalid equal-cost ranges, output null string
## [0.6.1](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.6.0...v0.6.1) - 2026-07-27
### Added
- *(vcf)* flag records with rewritten GT/PS
## [0.6.0](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.5.0...v0.6.0) - 2026-06-26
### Added
- *(fpa)* charge first_offset offset cost
- *(fpa)* add forward template switch matrices to fpa
- early-return with -t/-T: done if no contigs left
- *(clustering)* gate edit-mass behind --cluster-strategy
- *(clustering)* [**breaking**] Add --min-mass which makes it easier to target indels. Change default min_records to 1
### Fixed
- *(fpa)* correct forward TS first_offset
- *(fpa)* correct first_offset
- *(vcf)* ignore missing / no alt records
- *(vcf)* in single-unphased-het clusters, validate haplotype clusters before emitting
- add newline to stats output
- *(costs)* disable rr and qq and penalize secondary forward edits higher
### Other
- *(fpa)* deduplicate code for the four TS matrices
- *(fpa)* replace jump enum variants with cell back-pointer
- *(fpa)* add some more strict tests to fpa
## [0.5.0](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.4.0...v0.5.0) - 2026-06-15
### Added
- *(vcf)* resolve singleton unphased het with hom-alt
### Fixed
- *(vcf)* update tests for new phasing fn signatures
- *(vcf)* don't treat empty subclusters as error after phasing
### Other
- [**breaking**] update to tsalign v3
- This includes renames "primary" -> "descendant" and "secondary" -> "ancestor"
- Existing cost files will need to be updated: `sed -i 's/AntiPrimary/AntiDescendant/g' <cost-file>`
## [0.4.0](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.3.4...v0.4.0) - 2026-06-08
### Added
- *(vcf)* add --output-unresolvable
- *(vcf)* unify and refactor counters
- *(vcf)* MAPQ and base-quality gates for phasing
- *(vcf)* granular phasing resolution counters
- *(vcf)* reconstruct per-haplotype records on passthrough
- *(vcf)* thread allele number through phasing downstream
- *(vcf)* refactor phasing to allow for 1/2 records
- *(vcf)* implement local read-based phasing
- *(vcf)* haplotype-aware cluster splitting
### Fixed
- *(vcf)* ignore ref/ref reads in local phasing
- *(vcf)* add hom-alt into phased haplotype groups
- *(vcf)* remove unneccessary debug info
- *(vcf)* clippy
- *(vcf)* add reference to phasing bam reader to allow cram files
- *(vcf)* clippy + cargo-fmt
- *(vcf)* some more phasing fixes
### Other
- *(vcf)* add phasing trace logging, fix stats separator
- *(vcf)* add documentation on phasing
- *(vcf)* assert slot-to-haplotype phasing orientation
- *(vcf)* tests for local read-phasing
- *(vcf)* verify split-haplotype cluster correlation
- *(vcf)* remove phasing to re-implement from scratch
## [0.3.4](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.3.3...v0.3.4) - 2026-06-01
### Added
- *(viz)* accept float-formatted integers (42.0) in input CSV
## [0.3.3](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.3.2...v0.3.3) - 2026-05-26
### Added
- add --range-extension parameter to expand AlignmentRange
### Fixed
- *(vcf)* remove dead clear_cache() call; reads clears on tid change
- *(align)* release cache lock before DB write; close in_progress/finished gap
- *(vcf)* record first write error and return it after draining all messages
- *(vcf)* propagate Clusterizer init errors instead of silently producing empty output
- *(vcf)* flush SortingWriter explicitly before drop to propagate tail errors
- *(vcf)* track rid in FilteredOutputWriter to prevent cross-contig window bleed
- *(reads)* propagate CSV flush error from writer task
- *(vcf)* propagate BAM open error instead of panicking
- *(vcf)* warn on multi-allelic records in apply_mutations
### Other
- *(reads)* rename find_clusters -> find_cigar_clusters
- *(vcf)* replace bcf::Read impl with inherent methods
- *(reads)* replace htslib::Read impl with inherent methods
- *(vcf)* rename ClusterSettings -> ClusterizerSettings
- *(vcf)* document why alt_context_region equals ref_context_region
- *(reads)* remove obsolete channel from ClusterFinder
- *(reads)* cache hot counters outside read/cluster loops
- remove commented-out dbg! blocks
## [0.3.2](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.3.1...v0.3.2) - 2026-05-21
### Added
- *(viz)* only require the necessary fields in the input csv
- *(vcf)* warn if the input vcf has more than one sample
- remove -s flag to avoid confusion with -s from bcftools. --soft-mask still works as before.
### Fixed
- *(align)* re-enable extension of alignment ranges in tsalign
## [0.3.1](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.3.0...v0.3.1) - 2026-05-19
### Added
- *(vcf)* write cluster hash as VCF info field TSID
- *(vcf)* report TSCOST, TSINNERLEN, TSJUMP in output records
- *(align)* option to output failed alignment regions to file
### Fixed
- *(vcf)* compute AN from called genotype alleles, not ALT count
- clippy
### Other
- *(vcf)* verify variant ID written to VCF records
## [0.3.0](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.2.2...v0.3.0) - 2026-05-19
### Added
- *(db)* store constraints, retry OOM/timeout on larger limits
### Fixed
- *(docs)* small fixes in the cli help options ([#59](https://version.helsinki.fi/kraujasp/twitcher/pulls/59))
### Other
- *(reads)* add DB retry integration test for OOM with larger memory
## [0.2.2](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.2.1...v0.2.2) - 2026-05-13
### Added
- *(build)* update caching mechanism for gitlab runner
### Fixed
- *(vcf)* fix potential NPE
- *(build)* simplify CI build with stages
### Other
- *(vcf)* add crash regression from #58 as test
- add --fpa flag tests to vcf_tests and reads_tests
- add reads/viz integration tests, restructure test modules
- add meaningful integration tests with real WGS data
## [0.2.1](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.2.0...v0.2.1) - 2026-05-12
### Other
- update Cargo.toml dependencies
## [0.2.0](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.1.13...v0.2.0) - 2026-05-12
### Added
- *(align)* update default costs to something slightly more sensible
- include a default `.tsa` cost file in our repo
- *(align)* Allow to restrict that all TSMs have the same descendant
- *(viz)* align the cli interface more with `tsalign`
- *(viz)* add flags for eq range visualisation and context
- *(viz)* use id instead of cluster number for output files
### Fixed
- *(align)* flip default, `--only-equal-descendants` becomes `--allow-mixed-descendants`
- rename variable
- temporatily disable assertion
### Other
- update deps
## [0.1.13](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.1.12...v0.1.13) - 2026-05-07
### Added
- *(fpa)* add RQR template switch support
- add id to csv output that is a unique hash
## [0.1.12](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.1.11...v0.1.12) - 2026-04-30
### Fixed
- *(vcf)* repair progress bar
- *(clippy)* some pedantic / nursery lints
## [0.1.11](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.1.10...v0.1.11) - 2026-04-29
### Other
- update Cargo.lock dependencies
## [0.1.10](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.1.9...v0.1.10) - 2026-04-27
### Fixed
- *(fpa)* correct first_offset coordinate system
- *(reads)* exclude soft-clipped bases from window
- *(reads)* fix alignment indexing error
## [0.1.9](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.1.8...v0.1.9) - 2026-04-23
### Added
- *(viz)* Add id selector
- *(vcf)* enable csv output, some small buxfixes to make that happen
- *(viz)* add svg visualization subcommand
- *(csv)* output MI-string and alignment details
### Fixed
- clippy
- *(build)* update rust to 1.88 (needed by lib_tsshow)
- *(deps)* use crates.io version of tsalign libs
### Other
- update reads and vcf pipelines to use new alignment types
- extract alignment operations into dedicated module
## [0.1.8](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.1.7...v0.1.8) - 2026-03-25
### Added
- use new cluster density also in \'reads\' mode
- *(vcf)* expose clustering settings, add density parameter
### Fixed
- apply custom costs to tsalign (lost during refactor)
### Other
- write up some basic functionality
## [0.1.7](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.1.6...v0.1.7) - 2026-03-19
### Fixed
- test (again...)
- use characters M and X in vcf output cigar strings
- fix a test failure that expected M instead of = in cigar string
### Other
- update lib_tsalign to version 1
## [0.1.6](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.1.5...v0.1.6) - 2026-03-10
### Added
- add cram support
- add database feature to store known alignment cases
- in-memory deduplication of alignments
- show running alignments in progress bar
### Fixed
- buffer db writes, refactor counters
- Handle matches (eq or diff) properly in reads mode
- simplify dependencies
- some test coverage
- reduce tokio features
## [0.1.5](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.1.4...v0.1.5) - 2026-02-27
### Added
- parameter for buffer size, smaller tweaks
- rewrite many methods to async
- basic setup for tokio
- implement timeout for worker
- properly limit memory usage per alignment
- more info in log messages
- describe subcommands
- update to latest lib_tsalign with serde support
### Fixed
- lots of clippy fixes about number conversions, some of which have caused issues crashed
- differentiate between non-zero exit and signal termination
- Use subprocesses for the aligner to fail gracefully
## [0.1.4](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.1.3...v0.1.4) - 2026-02-18
### Added
- Refactor plumbing code to allow a selection of the aligner
- implement DP-based Four-Point-Aligner
- add --min-quality to require minimum quality for cluster bases
- *(vcf)* add command to output header
- some progress bars and less memory usage
### Fixed
- indexing bug in record creation, allow for full-range TSes in FPA
- clippy
- small changes to --help
- update test method to use new `augment_header` method
- make memory limit arg global so that it can be used at any point
- don't exclude reference parts with lowercase, even with --soft-mask
- use capped allocator for memory limit
## [0.1.3](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.1.2...v0.1.3) - 2026-02-02
### Added
- Add counters for alignments to reads mode
- add counters and runtime to reads mode (and refactor)
### Fixed
- use bounded channels to avoid uncontrolled memory growth
## [0.1.2](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.1.1...v0.1.2) - 2026-01-30
### Added
- unify the alignment tpool stuff, report alignment cost without TS for reads mode
### Fixed
- coordinate fix in soft mask feature
- update readme to use published twitcher version
## [0.1.1](https://version.helsinki.fi/kraujasp/twitcher/compare/v0.1.0...v0.1.1) - 2026-01-30
### Other
- Add some metadata to Cargo.toml