# Change Log
## Unreleased - ReleaseDate
## 0.7.5 - 2023-07-28
* Add `fasr replace`
* Add `fasr pl-p2m`
* Add `fasr xlsx`
* Add --outgroup to `fasr consensus` and `fasr variation`
* Add --required to `fasr subset`
* Add --outgroup, --chop, and --quick to `fasr refine`
* Implementing `--parallel` with `crossbeam`
* for `fasr consensus`
* for `fasr refine`
## 0.7.4 - 2023-07-20
* Add `fasr filter`
* Add `fasr refine`
* Add `fasr variation`
* Add --multi to `fasr create`
## 0.7.3 - 2023-07-18
* New binary `fasr`, ported from `App::Fasops`
* `fasr axt2fas`
* `fasr check`
* `fasr concat`
* `fasr consensus`
* `fasr cover`
* `fasr create`
* `fasr join`
* `fasr link`
* `fasr maf2fas`
* `fasr name`
* `fasr separate`
* `fasr slice`
* `fasr split`
* `fasr stat`
* `fasr subset`
* Add `libs/alignment`
* Add `utils::get_seq_faidx()`
* Add `IntSpan.find_islands_n()` and `IntSpan.find_islands_ints()`
* Use json to replace yaml in `spanr`
* Bump versions of deps
* clap v4
* Use anyhow
## 0.7.1 - 2022-06-14
* Store `IntSpan.edges` in VecDeque
* Switch to `clap` v3.2
## 0.7.0 - 2022-05-23
* Add `rgr sort`
* Add `rgr prop`
* Add --fields to `rgr field`
* Add --header, --sharp, --field to `rgr count` and `rgr runlist`
## 0.6.9 - 2022-05-15
* Add `rgr field`
* Move `spanr range` to `rgr runlist`
* Move `spanr count` to `rgr count`
* Rename .ranges to .rg
## 0.6.8 - 2022-05-14
* New binary `rgr`
* Move `ovlpr replace` to `rgr replace`
* Move `linkr merge` to `rgr merge`
## 0.6.7 - 2022-04-24
* Add `spanr count`
* Add `--detailed` to `spanr coverage`
* Use `Box<dyn std::error::Error>`
## 0.6.5 - 2022-04-22
* Use rust_lapper as an intermediate layer instead of intspan::Coverage
* Greatly improves the speed of `spanr coverage`
## 0.6.4 - 2022-04-21
* Move `far` out
* `spanr stat` use i64 in the `all` lines
* Update Github actions
* Use a container with GLIBC 2.17 to build linux-gnu binary
* Codecov with cargo-tarpaulin
## 0.6.0 - 2022-02-22
* Move `nwr` out
## 0.4.17 - 2022-02-21
* Add `nwr download`
* Add `nwr txdb`
* Add `nwr info`
* Add `nwr lineage`
* Add `nwr restrict`
* Add `nwr member`
* Add `nwr append`
## 0.4.16 - 2022-02-12
* Switch to `clap` v3
* New binary `nwr`
## 0.4.15 - 2021-08-19
* Add `far some`
* Add `slice()` to `IntSpan`
* `ovlpr replace` now processes any .tsv files
## 0.4.14 - 2020-05-15
## 0.4.13 - 2020-05-15
* New binary `far`
## 0.4.12 - 2020-03-05
* Split `spanr cover` into `cover` and `coverage`
## 0.4.11 - 2020-02-15
* Add `--all` to `spanr merge`
## 0.4.10 - 2020-02-15
* Add `--op` to `spanr combine`
## 0.4.9 - 2019-12-09
* Add `ovlpr replace`
* Add `ovlpr restrict`
* Github Actions publish.yml
## 0.4.1 - 2019-09-10
* Add benchmarks.md
* Add `ovlpr paf2ovlp`
* Binary releases by Github Actions
## 0.4.0 - 2019-09-07
* New binary `ovlpr`
* Struct `Overlap`
* Move libraries to libs/
* Passing `&str` when calling methods
* Add `new_len()` and `uniq_tiers()` to `Coverage`
* Add `from_pair()` to `IntSpan`
* Wrap IO functions in utils.rs with Result
* Satisfy clippy
## 0.3.3 - 2019-09-04
* `spanr merge`: take the first part of filename
* `spanr compare`: compare more than two infiles
## 0.3.2 - 2019-09-03
* Add `--suffix` to `spanr split`
## 0.3.1 - 2019-09-03
* Detailed benchmarks on `linkr`
* Make POS_INF, NEG_INF and EMPTY_STRING as lazy_static
* About 10-20% faster
## 0.3.0 - 2019-09-03
* New binary `linkr` for commands ported from `App::Rangeops` and `jrange`
* Illustrations for some concepts
* IntSpans
* Ranges
* Rename binary `intspan` to `spanr`
## 0.2.0 - 2019-08-24
* Ported all commands from `App::RL` and `jrunlist`
* Struct `Range`
* Struct `Coverage`
* Adopt `cargo release`
## 0.1.0 - 2019-08-13
* Struct `IntSpan`
* Examples