# 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).
## v0.3.2 (2023-10-09)
### Chore
- <csr-id-9b7ceba1f664fe6cdb553b5de43ff856a2cf94c2/> improve progress bar
- <csr-id-c07f66b37f3e4e8d267578b7fc873c44e3df5d29/> improve progress bar
### Commit Statistics
<csr-read-only-do-not-edit/>
- 5 commits contributed to the release.
- 2 commits were understood as [conventional](https://www.conventionalcommits.org).
- 0 issues like '(#ID)' were seen in commit messages
### Commit Details
<csr-read-only-do-not-edit/>
<details><summary>view details</summary>
* **Uncategorized**
- Improve progress bar ([`9b7ceba`](https://github.com/fiberseq/fibertools-rs/commit/9b7ceba1f664fe6cdb553b5de43ff856a2cf94c2))
- Improve progress bar ([`c07f66b`](https://github.com/fiberseq/fibertools-rs/commit/c07f66b37f3e4e8d267578b7fc873c44e3df5d29))
- Add notes ([`ff061a1`](https://github.com/fiberseq/fibertools-rs/commit/ff061a17a67ee8fa99e274613e4b2c4c1baa88a4))
- Add notes ([`9fa61a0`](https://github.com/fiberseq/fibertools-rs/commit/9fa61a055952d16bd4b76010d5d3b44bf44d917b))
- Release fibertools-rs v0.3.4 ([`8731ecb`](https://github.com/fiberseq/fibertools-rs/commit/8731ecb18abb4d1bcbcd4d95047c9f16785301f4))
</details>
## v0.3.1 (2023-10-08)
<csr-id-12186d106224f211ac39844b6a8c82a54825ffcf/>
<csr-id-e216e7d184ddcd235e0e22dd1da3e99382d78277/>
### Chore
- <csr-id-12186d106224f211ac39844b6a8c82a54825ffcf/> update deps
### Other
- <csr-id-958e330daa4c51f7d69d9f7763333d78a92fb843/> add docs.
- <csr-id-f60e8fa97ae89b8b19a52b5f9a0e62931262b622/> add docs.
- <csr-id-d54dba8523a49eb9eac5d1b4743bcf9922094f8e/> add docs.
- <csr-id-35d498ab1be9efa670d08c8191e639ebdbecbd5a/> add docs.
- <csr-id-415cc7f2d151b18164e7cb2a8484e1369e61c2ca/> add docs.
- <csr-id-e6ac4d3a7c63554a65511a15d4c7aca144203797/> add docs.
- <csr-id-cef74228e5933e7b911db53b65352cfde5246b29/> add docs.
- <csr-id-b1b148a865cbc0223d55ad2dc11b826f51210b54/> add docs.
- <csr-id-8c818835c2c6f58103b3a8bfb0bbdd8e24379016/> add docs.
- <csr-id-4ca7269d0851c70ea25c466bf2d8092075658e52/> add docs.
- <csr-id-737fb50d4f311612f5f9aa5d1c342ed0d049b575/> add docs.
- <csr-id-c6fec85f40be60b5b101ab7ed1ade439e07d4052/> add docs.
- <csr-id-f2311eda7b3a400c39d93b8e95b7966b7ecba4da/> add docs.
- <csr-id-5ffa686bc22216a497abfa48c5adf318a743a815/> add docs.
- <csr-id-d166b29fdf08e24873afee8c37523293e288b762/> add docs.
- <csr-id-30645d382bfc0a02f4ffa516044995a87acfea7c/> add docs.
- <csr-id-897eca5bd467fc5ae7f888be1696af88bd3f4d9f/> add docs.
- <csr-id-893f5f9e4dfca97b459281b5d667f7449a54364e/> add docs.
- <csr-id-fe3aa9a2511944b4078b3b7ed9dbb2ca756f9b81/> fix warning msg
### Chore
- <csr-id-619081fa421d6658149f28b3a0458e83c4e16af2/> fix typo in cli message
### Other
- <csr-id-e216e7d184ddcd235e0e22dd1da3e99382d78277/> add docs.
### Bug Fixes
- <csr-id-6eb0527acb082d87eeb2dda2d898fe3642910dce/> progress bar display issues.
- <csr-id-ea456be994b9209e32332bf5b46c183eba45ca3d/> extra comma in ft center wide format. fixes 21
### Commit Statistics
<csr-read-only-do-not-edit/>
- 33 commits contributed to the release over the course of 55 calendar days.
- 55 days passed between releases.
- 24 commits were understood as [conventional](https://www.conventionalcommits.org).
- 0 issues like '(#ID)' were seen in commit messages
### Commit Details
<csr-read-only-do-not-edit/>
<details><summary>view details</summary>
* **Uncategorized**
- Release bio-io v0.3.1 ([`efc9b3f`](https://github.com/fiberseq/fibertools-rs/commit/efc9b3f569490dac5b10462d359a834e324d62ef))
- Release fibertools-rs v0.3.4, bio-io v0.3.1 ([`0697d8d`](https://github.com/fiberseq/fibertools-rs/commit/0697d8db1797a1a46bd276269be8687ebbd102df))
- Add docs. ([`e216e7d`](https://github.com/fiberseq/fibertools-rs/commit/e216e7d184ddcd235e0e22dd1da3e99382d78277))
- Release bio-io v0.3.1 ([`2d57bc1`](https://github.com/fiberseq/fibertools-rs/commit/2d57bc138cc952b466ac9b377169ba5994b31737))
- Release fibertools-rs v0.3.3 ([`85ee32a`](https://github.com/fiberseq/fibertools-rs/commit/85ee32aea21eccdfccc699ae1e2c4222e16855f7))
- Add docs. ([`958e330`](https://github.com/fiberseq/fibertools-rs/commit/958e330daa4c51f7d69d9f7763333d78a92fb843))
- Add docs. ([`f60e8fa`](https://github.com/fiberseq/fibertools-rs/commit/f60e8fa97ae89b8b19a52b5f9a0e62931262b622))
- Add docs. ([`d54dba8`](https://github.com/fiberseq/fibertools-rs/commit/d54dba8523a49eb9eac5d1b4743bcf9922094f8e))
- Add docs. ([`35d498a`](https://github.com/fiberseq/fibertools-rs/commit/35d498ab1be9efa670d08c8191e639ebdbecbd5a))
- Add docs. ([`415cc7f`](https://github.com/fiberseq/fibertools-rs/commit/415cc7f2d151b18164e7cb2a8484e1369e61c2ca))
- Add docs. ([`e6ac4d3`](https://github.com/fiberseq/fibertools-rs/commit/e6ac4d3a7c63554a65511a15d4c7aca144203797))
- Add docs. ([`cef7422`](https://github.com/fiberseq/fibertools-rs/commit/cef74228e5933e7b911db53b65352cfde5246b29))
- Add docs. ([`b1b148a`](https://github.com/fiberseq/fibertools-rs/commit/b1b148a865cbc0223d55ad2dc11b826f51210b54))
- Add docs. ([`8c81883`](https://github.com/fiberseq/fibertools-rs/commit/8c818835c2c6f58103b3a8bfb0bbdd8e24379016))
- Add docs. ([`4ca7269`](https://github.com/fiberseq/fibertools-rs/commit/4ca7269d0851c70ea25c466bf2d8092075658e52))
- Add docs. ([`737fb50`](https://github.com/fiberseq/fibertools-rs/commit/737fb50d4f311612f5f9aa5d1c342ed0d049b575))
- Add docs. ([`c6fec85`](https://github.com/fiberseq/fibertools-rs/commit/c6fec85f40be60b5b101ab7ed1ade439e07d4052))
- Add docs. ([`f2311ed`](https://github.com/fiberseq/fibertools-rs/commit/f2311eda7b3a400c39d93b8e95b7966b7ecba4da))
- Add docs. ([`5ffa686`](https://github.com/fiberseq/fibertools-rs/commit/5ffa686bc22216a497abfa48c5adf318a743a815))
- Add docs. ([`d166b29`](https://github.com/fiberseq/fibertools-rs/commit/d166b29fdf08e24873afee8c37523293e288b762))
- Add docs. ([`30645d3`](https://github.com/fiberseq/fibertools-rs/commit/30645d382bfc0a02f4ffa516044995a87acfea7c))
- Add docs. ([`897eca5`](https://github.com/fiberseq/fibertools-rs/commit/897eca5bd467fc5ae7f888be1696af88bd3f4d9f))
- Add docs. ([`893f5f9`](https://github.com/fiberseq/fibertools-rs/commit/893f5f9e4dfca97b459281b5d667f7449a54364e))
- Progress bar display issues. ([`6eb0527`](https://github.com/fiberseq/fibertools-rs/commit/6eb0527acb082d87eeb2dda2d898fe3642910dce))
- Release fibertools-rs v0.3.2 ([`f39c11b`](https://github.com/fiberseq/fibertools-rs/commit/f39c11b54046af24684a8726ee7e6d54f52a6595))
- Chore clippy ([`9c80dcb`](https://github.com/fiberseq/fibertools-rs/commit/9c80dcb2053ce42f2a33007954fc4506d50ce8a4))
- Fix centered_query_start and centered_query_end values in ft center ([`a43c082`](https://github.com/fiberseq/fibertools-rs/commit/a43c0826c8a454e9ebb142e1fe4636a537883b6d))
- Extra comma in ft center wide format. fixes 21 ([`ea456be`](https://github.com/fiberseq/fibertools-rs/commit/ea456be994b9209e32332bf5b46c183eba45ca3d))
- Fix warning msg ([`fe3aa9a`](https://github.com/fiberseq/fibertools-rs/commit/fe3aa9a2511944b4078b3b7ed9dbb2ca756f9b81))
- Update deps ([`12186d1`](https://github.com/fiberseq/fibertools-rs/commit/12186d106224f211ac39844b6a8c82a54825ffcf))
- Fix typo in cli message ([`619081f`](https://github.com/fiberseq/fibertools-rs/commit/619081fa421d6658149f28b3a0458e83c4e16af2))
- Add to cli message ([`7bf04d2`](https://github.com/fiberseq/fibertools-rs/commit/7bf04d280cef747391739896719b6fb0f84f6931))
- Release fibertools-rs v0.3.1 ([`6c5adf4`](https://github.com/fiberseq/fibertools-rs/commit/6c5adf4a88f04420e4024378cbed2bfdee73fe79))
</details>
## v0.3.0 (2023-08-13)
### New Features
- <csr-id-02070669179e6b6ff3383ade356d0a307e903905/> move progress bar into bamchunk iterator, unify progress bar.
- <csr-id-d0a80ace111bb5e2477502ac264dd44fd988007e/> move progress bar into bamchunk iterator, unify progress bar.
- <csr-id-678db90a111c54e33fed654031fe679b940d2d5a/> move progress bar into bamchunk iterator, unify progress bar.
- <csr-id-c4c4b027dc400aeaf30b378270d073582e859a7e/> move progress bar into bamchunk iterator, unify progress bar.
- <csr-id-b37eb2c6fcbe2b8e7c80e9ce380a24a951332887/> better progress bar for extract.
### Commit Statistics
<csr-read-only-do-not-edit/>
- 29 commits contributed to the release over the course of 15 calendar days.
- 15 days passed between releases.
- 5 commits were understood as [conventional](https://www.conventionalcommits.org).
- 0 issues like '(#ID)' were seen in commit messages
### Commit Details
<csr-read-only-do-not-edit/>
<details><summary>view details</summary>
* **Uncategorized**
- Release fibertools-rs v0.3.1 ([`f5cc324`](https://github.com/fiberseq/fibertools-rs/commit/f5cc32460016b0a4ee9ea0804f236fc0aa73b803))
- Update ([`9d870a9`](https://github.com/fiberseq/fibertools-rs/commit/9d870a928615c04cffe21b296970c9c6403d97de))
- Release fibertools-rs v0.3.1 ([`0de730e`](https://github.com/fiberseq/fibertools-rs/commit/0de730e4949d61fff32fa06ff42c2d2f3bb16c29))
- Update ([`1e7a6c1`](https://github.com/fiberseq/fibertools-rs/commit/1e7a6c1dfbb7805646a7d1e193b79e5699797269))
- Release fibertools-rs v0.3.0 ([`b6cc95c`](https://github.com/fiberseq/fibertools-rs/commit/b6cc95c9b25b5da24fa522e2dd658f3a65d53bfe))
- Release fibertools-rs v0.3.0 ([`3d3d534`](https://github.com/fiberseq/fibertools-rs/commit/3d3d534b7d214ae13a5b1e3f313007bbe21f385e))
- Release fibertools-rs v0.3.0 ([`8262358`](https://github.com/fiberseq/fibertools-rs/commit/8262358293c29863d5eb44c6fe98df2c361659e2))
- Update center.rs ([`90b1917`](https://github.com/fiberseq/fibertools-rs/commit/90b1917b38852a7bf3b3761cc08fa628a64e5a61))
- Move progress bar into bamchunk iterator, unify progress bar. ([`0207066`](https://github.com/fiberseq/fibertools-rs/commit/02070669179e6b6ff3383ade356d0a307e903905))
- Move progress bar into bamchunk iterator, unify progress bar. ([`d0a80ac`](https://github.com/fiberseq/fibertools-rs/commit/d0a80ace111bb5e2477502ac264dd44fd988007e))
- Move progress bar into bamchunk iterator, unify progress bar. ([`678db90`](https://github.com/fiberseq/fibertools-rs/commit/678db90a111c54e33fed654031fe679b940d2d5a))
- Move progress bar into bamchunk iterator, unify progress bar. ([`c4c4b02`](https://github.com/fiberseq/fibertools-rs/commit/c4c4b027dc400aeaf30b378270d073582e859a7e))
- Better progress bar for extract. ([`b37eb2c`](https://github.com/fiberseq/fibertools-rs/commit/b37eb2c6fcbe2b8e7c80e9ce380a24a951332887))
- Fmt ([`e50243a`](https://github.com/fiberseq/fibertools-rs/commit/e50243aa6f0857d188f9899203eda551bbdca6db))
- Fmt ([`eccd328`](https://github.com/fiberseq/fibertools-rs/commit/eccd328d71a2b99bed146defe25ac2b0e1839d6c))
- Fmt ([`250f080`](https://github.com/fiberseq/fibertools-rs/commit/250f080b65db4e4fd78f9edad6acf425a3ecdd78))
- Fmt ([`9c10eff`](https://github.com/fiberseq/fibertools-rs/commit/9c10eff61ff5904ffcc85e214618b46b032ae616))
- Release fibertools-rs v0.3.0 ([`740a4bc`](https://github.com/fiberseq/fibertools-rs/commit/740a4bce224e6345458450ea589c521c60fc998a))
- Readme ([`d11301f`](https://github.com/fiberseq/fibertools-rs/commit/d11301fa6826563d397cb4ba7000810aae8f09c4))
- Readme ([`b356b22`](https://github.com/fiberseq/fibertools-rs/commit/b356b22fa0596e2735c05cbf4004516e2899e411))
- Readme ([`fe9dd43`](https://github.com/fiberseq/fibertools-rs/commit/fe9dd43268d0c5bc023146b14081346288d5d9be))
- Readme ([`b532eb0`](https://github.com/fiberseq/fibertools-rs/commit/b532eb0d814cb965df7958f652279ecc8dd6f4fa))
- Readme ([`2c4b6ef`](https://github.com/fiberseq/fibertools-rs/commit/2c4b6ef2eb7bb2d935e94be0f41ec727acf64c77))
- Readme ([`ae12da9`](https://github.com/fiberseq/fibertools-rs/commit/ae12da9d5c7df82cfce89ed4e56d73200a7514e7))
- Readme ([`9ca181d`](https://github.com/fiberseq/fibertools-rs/commit/9ca181de2ed1afb86e594b68a81118a50acd5b48))
- Readme ([`5c2d004`](https://github.com/fiberseq/fibertools-rs/commit/5c2d004b326ae5a0164398d4bd436a1f2c6ad812))
- Readme ([`f27c56d`](https://github.com/fiberseq/fibertools-rs/commit/f27c56d742a8eb8be2dd8d5271e5fa8568b56313))
- Readme ([`67fc6eb`](https://github.com/fiberseq/fibertools-rs/commit/67fc6eb1d2eaa45d4e4fbd0fe750b1d4a22dd85e))
- Release fibertools-rs v0.3.0 ([`668ff64`](https://github.com/fiberseq/fibertools-rs/commit/668ff648e125609e92d9c3b81d4f4b3481b8d152))
</details>
## v0.2.0 (2023-07-29)
<csr-id-6bb4c5c8b041c24743d2f89283c005f011084452/>
<csr-id-f73a36a716023835e16da50838752d74a2768843/>
### Chore
- <csr-id-6bb4c5c8b041c24743d2f89283c005f011084452/> Release bio-io version 0.2.0
- <csr-id-f73a36a716023835e16da50838752d74a2768843/> regex update
### New Features
- <csr-id-9d07122e49b817f531b4a412ae77dced2e936f3a/> change the result of liftovers to be an Option<i64>.
- <csr-id-b9f4950f2839c5d8df61593ec58997e439fc5c6a/> add qual to ft cetner, and clean the ft center code more
- <csr-id-96f251b7f370f68e729357f52d3f2b6400d1af33/> adding ft center to the python module!
- <csr-id-9da4fa3b27e991250185463de48ba0ebea866bce/> Reorganize pyft api and docs
- <csr-id-248bf4e56c5b10c2dd4613888818a995e6f75529/> adding liftover to pyft
- <csr-id-6a695ec7a71e5002709d5496c8aade541e737514/> very large improvment in speed of lifting over ranges, some liftover results differ from before by 1bp but it is rare.
- <csr-id-3ea32b01fda3e12f0cacae90d5a52495cec0b6bd/> add cpg to python modele and make easier access in the rust basemod api
- <csr-id-1f6fea3cf07e1e798649df45d944a5396bf82902/> I have a minimal working python package yay!
### Chore
- <csr-id-36a975a57afd5be38e4eb66429fc5b7f84ebe32d/> Release bamlift version 0.2.0
- <csr-id-6fe2beb91b2552292563fdae391c5ce026eded1d/> simplifed center with new api.
- <csr-id-df3ffba3aafa8403cdc95b6e0c31de07ac0a8114/> refactor a large part of the code base to reduce redudance. TODO simplify center and basemods with this new api.
- <csr-id-96b4fc0638e991ec6c29dffbb1678b99ffc00b1d/> improve docs
- <csr-id-1436dbfb05c542aa1f4c862d46113e43d0b396d8/> drop darkmode
- <csr-id-04b1e9b02059718fea91b0aef71efc0d9d86f744/> fix docs and fetch
- <csr-id-8bf2168969acf67fa5069fb578f94941bd01e3f4/> readme
- <csr-id-15d535ae7dc90f86bec99a18015a22376c195788/> readme
- <csr-id-aba1d7572a6109bb2e7d2acffea5f5e5c4f1ced6/> readme
- <csr-id-9ea0b5f04f21cf74ab40a0ff1097eac996cc5b8b/> readme
- <csr-id-69d87ea41febf0bd88380708cacea4232ae57f24/> readme
- <csr-id-970c41f9ba4a8c26bf980f0ce87f635dd4f68bd3/> readme
- <csr-id-49180bccd2dffdc49313e0b259dcdd0e80682bba/> readme
- <csr-id-c8a2ab45cbff913c41bde48903c129b6e4d2f70a/> readme
- <csr-id-168c9517b5137dbd58950f341d96a420c7d50935/> readme
- <csr-id-f5a65a612b8978f9742dab6990a8d52c6df7645a/> readme
- <csr-id-9f711585d39c66ff45598d85dbf3783aca6ee44c/> clippy
- <csr-id-b4278e4599a6634f37f05874a7e2e860c0b6a45a/> clippy
- <csr-id-a80fe514ff3d4bf860dedbf7130a21d97b9537ab/> hide more deps under features for pyft
- <csr-id-c55fcc59749216e0f65c3d9c07efc14f32fb5fdf/> example py-ft
- <csr-id-66b98f9f3c2644e79bf72de2ed070fba75b2ba38/> rename iterator
- <csr-id-9e8cda2fb47eff101eb3d458cf4599543e7d05a2/> rename iterator
- <csr-id-23e6b12a7601afb4aa21454048a53d803ca1bcdf/> rename iterator
- <csr-id-b03df77d99a8f28ecd6d43509a43ff92fb300329/> rename iterator
- <csr-id-6e8cd6f9f25dcabc15ef2a25595b3a3ee86de241/> docs
- <csr-id-79ca845b0e72e832cdc57b1e1b58090a09417936/> docs
- <csr-id-41bcd27e9de8654fd46bfb50d3c7efabad59a17e/> docs
- <csr-id-66338fd576a66ee230aa4234d072a93b3a3b21d5/> docs
- <csr-id-6f910c53a4e0cb7be411b724385e540517f21306/> docs
- <csr-id-85d471df45a0c88567857427725852c491c041ff/> docs
- <csr-id-c5eb60a8d42616eacfafb871cf4f46fb2fa924c8/> docs
- <csr-id-5bd6803c346a409150daea7713878af46995e836/> docs
- <csr-id-a59f41d0b2d4b97b277b738f04b23010be8d6449/> docs
- <csr-id-7a633d71272a9425ae276d9b846fcda38f6526e5/> docs
- <csr-id-8d16055edc4bf9bc5f94d5be42b86b2a2df712c8/> docs
- <csr-id-467072ae6419b3ece8329f587467d0d0bf316911/> docs
- <csr-id-09994bdbdd3949186d44ecef36199a8d228ea280/> docs
- <csr-id-8ea9fb1efc4897e191468ee10aa66500456fa0fc/> docs
- <csr-id-82399e6e702033acbb455ef6aea3a9935338d77f/> docs
- <csr-id-fd115b7fdb6754d6f6885e901bc34d7364bfc7df/> docs
- <csr-id-1d25caf7e8c19f97d39dec8eb69de7219e85621b/> docs
- <csr-id-e73e00c849726e4577344ec8e964b3eda93ddbc6/> docs
- <csr-id-a3f29cd798fcbeb071fce7ea7041c4e71a98f8f6/> docs
- <csr-id-e85afd963f513fe578b2d0f3e368a7ae56b59d84/> docs
- <csr-id-580968a9da3c2a66740d01dfcc0d8c574bfd46c8/> docs
- <csr-id-6b1e714ccda049aef3199563c03d6f5ec1df9dfa/> docs
- <csr-id-c8502ac7cf87d375a5aa9fcf3494a3cf8f43105c/> docs
- <csr-id-b9274c2a7064cd615b079b3cc0b44d9e2f4b5e50/> docs
- <csr-id-eb44bdaf8280689eb06e536266b64802f509a7b3/> docs
- <csr-id-b98edf9f855ae24f81389a5ea481bf0b16dcd794/> python docs
- <csr-id-32f01826bbf06ac726464d59eee2769dfe80b138/> python docs
- <csr-id-94dfd521a3f637df47c996fd046d1de3cde85776/> python docs
- <csr-id-b3fa1c3b218379a3290fbed2382572b5e1c3e091/> python docs
- <csr-id-d4b75b1a569d694495bc1e87de651c1bb4e63778/> python docs
- <csr-id-73c918f9344fe362f602fa5356b11c9574c5ffec/> python docs
- <csr-id-5f635e04085c012d39d8afa362416ca3642fc7c5/> python docs
- <csr-id-c86cc585993506c55bd0243936767afe4a5f671c/> python docs
- <csr-id-15b825ed80a4b099c9ea9f21f64f1b695e20554a/> python docs
- <csr-id-26ef86389490b3161546271bea194e4c8a4a8b7f/> python docs
- <csr-id-d953400d9c7f676fea70fee51264c331ba7e1067/> python docs
- <csr-id-10bf0df63acca5812e3d2d3ad5134bc75abe73b4/> python docs
- <csr-id-cdde18e3b119ef36d57feed2f4740b7bde30c011/> readme
- <csr-id-ac1987d33daf7fb7395ed1cf15b311390a15e60c/> add to changelog
- <csr-id-2f7c08e2b24a07054d547088ac2c96463a6229d3/> add to changelog
- <csr-id-082190756233e077b692839f979df466fd5c7239/> Release fibertools-rs version 0.2.5
- <csr-id-98a51ab3030ed03ce6adc7e160ee7feed49a7222/> Release fibertools-rs version 0.2.4
### Bug Fixes
- <csr-id-066ca9427211f5147f9528e66a342111e273296f/> rework fiberdata to consume bam record to avoid extra copy
- <csr-id-2e1fe93f48b357fbb3459f5206fc5a994325d7a4/> unify api anming for liftover, optimize for inclusion in pyft
- <csr-id-3e6aa945cb643e5d0559fac59b14a649e0de34b1/> reduce number of copies for nuc and msp.
- <csr-id-eea28d57a9eac79e3e3e0d9d16ede6dce51d242e/> move nuc and msp logic out of extract into ranges struct and simplify. We ran on a whole genome ft extract to confirm results dont change.
- <csr-id-9fe3676efa853b79af85e2e1f6bb7849c013a0ec/> speed options
### Commit Statistics
<csr-read-only-do-not-edit/>
- 150 commits contributed to the release over the course of 17 calendar days.
- 17 days passed between releases.
- 81 commits were understood as [conventional](https://www.conventionalcommits.org).
- 0 issues like '(#ID)' were seen in commit messages
### Commit Details
<csr-read-only-do-not-edit/>
<details><summary>view details</summary>
* **Uncategorized**
- Release bio-io version 0.2.0 ([`6bb4c5c`](https://github.com/fiberseq/fibertools-rs/commit/6bb4c5c8b041c24743d2f89283c005f011084452))
- Change ([`019e9de`](https://github.com/fiberseq/fibertools-rs/commit/019e9de0212ef414c69834b45c3dd3ebb29bcd5c))
- Change ([`11c3915`](https://github.com/fiberseq/fibertools-rs/commit/11c39153fd5da5a5d630baca764b37eac884e872))
- Change ([`20d9aa7`](https://github.com/fiberseq/fibertools-rs/commit/20d9aa70ff741fe198978abe4e8b8e46f7a9dd8e))
- Change ([`de36de7`](https://github.com/fiberseq/fibertools-rs/commit/de36de75483774c8f89b5371c13d6000276a788b))
- Release bamlift version 0.2.0 ([`36a975a`](https://github.com/fiberseq/fibertools-rs/commit/36a975a57afd5be38e4eb66429fc5b7f84ebe32d))
- Change ([`70c9606`](https://github.com/fiberseq/fibertools-rs/commit/70c9606273dd05d1cafd7ef7e1a1ba49f1aa5aa5))
- Change ([`49871ce`](https://github.com/fiberseq/fibertools-rs/commit/49871cef83c7229dd1754365876a7de33c1cdac1))
- Change ([`cbf0de8`](https://github.com/fiberseq/fibertools-rs/commit/cbf0de8d74f0cb14b6d71b5bb6b3378666f29580))
- Change ([`0a0c37b`](https://github.com/fiberseq/fibertools-rs/commit/0a0c37b4e62ed49048d78a836ddadcaa5911a844))
- Change ([`4a5e5c4`](https://github.com/fiberseq/fibertools-rs/commit/4a5e5c4ecdcfcb82c86d9df0899ce3e3c4ef5e34))
- Readme ([`99aeada`](https://github.com/fiberseq/fibertools-rs/commit/99aeadae8ba61da26d961a8f6318065e0a9ad442))
- Improve fetch error msg ([`6332770`](https://github.com/fiberseq/fibertools-rs/commit/633277099e1fde8684733c05d6b192434ee01c10))
- Update so pyft works with options results ([`a09faa2`](https://github.com/fiberseq/fibertools-rs/commit/a09faa2d68a6f13b2330b4a8e302fd40f3765c55))
- Update so pyft works with options results ([`f225f9d`](https://github.com/fiberseq/fibertools-rs/commit/f225f9d8828b69b2af1a3c11b471fed84132e4d6))
- Change the result of liftovers to be an Option<i64>. ([`9d07122`](https://github.com/fiberseq/fibertools-rs/commit/9d07122e49b817f531b4a412ae77dced2e936f3a))
- Docs ([`07882ea`](https://github.com/fiberseq/fibertools-rs/commit/07882ea5396c178354ba735b651311a476c29cbc))
- Docs ([`776713b`](https://github.com/fiberseq/fibertools-rs/commit/776713bf647ec6a361bb6bde34de412c6ec8af8c))
- Change ([`ad0340e`](https://github.com/fiberseq/fibertools-rs/commit/ad0340e8d9f8b0ac744aea4785b9530c14572045))
- Readme ([`6595c36`](https://github.com/fiberseq/fibertools-rs/commit/6595c3696dda1288f0f763fdc54d7311dfb790c9))
- Add qual to ft cetner, and clean the ft center code more ([`b9f4950`](https://github.com/fiberseq/fibertools-rs/commit/b9f4950f2839c5d8df61593ec58997e439fc5c6a))
- Docs ([`1a1f260`](https://github.com/fiberseq/fibertools-rs/commit/1a1f260323e262772ce7ecfaed2df52ab2597b5d))
- Docs ([`2ab1645`](https://github.com/fiberseq/fibertools-rs/commit/2ab16455268ef311fbc60a17a7831e05b2f2cf8a))
- Simplifed center with new api. ([`6fe2beb`](https://github.com/fiberseq/fibertools-rs/commit/6fe2beb91b2552292563fdae391c5ce026eded1d))
- Refactor a large part of the code base to reduce redudance. TODO simplify center and basemods with this new api. ([`df3ffba`](https://github.com/fiberseq/fibertools-rs/commit/df3ffba3aafa8403cdc95b6e0c31de07ac0a8114))
- Improve docs ([`96b4fc0`](https://github.com/fiberseq/fibertools-rs/commit/96b4fc0638e991ec6c29dffbb1678b99ffc00b1d))
- Adding ft center to the python module! ([`96f251b`](https://github.com/fiberseq/fibertools-rs/commit/96f251b7f370f68e729357f52d3f2b6400d1af33))
- Drop darkmode ([`1436dbf`](https://github.com/fiberseq/fibertools-rs/commit/1436dbfb05c542aa1f4c862d46113e43d0b396d8))
- Fix docs and fetch ([`04b1e9b`](https://github.com/fiberseq/fibertools-rs/commit/04b1e9b02059718fea91b0aef71efc0d9d86f744))
- Clean ([`1d5872d`](https://github.com/fiberseq/fibertools-rs/commit/1d5872dc510a370c065076e533af1913ccbc764f))
- Reorganize pyft api and docs ([`9da4fa3`](https://github.com/fiberseq/fibertools-rs/commit/9da4fa3b27e991250185463de48ba0ebea866bce))
- Check for sorted ([`8fbdc7c`](https://github.com/fiberseq/fibertools-rs/commit/8fbdc7c1a4af7039e62f249c49a4ca226023eefb))
- Check for sorted ([`624dd33`](https://github.com/fiberseq/fibertools-rs/commit/624dd3317814594b47835be120a8d4bcadc775f6))
- Block index ([`ab59d1d`](https://github.com/fiberseq/fibertools-rs/commit/ab59d1d3a650530c75d50b507a594ee7cc74eddc))
- Regex update ([`f73a36a`](https://github.com/fiberseq/fibertools-rs/commit/f73a36a716023835e16da50838752d74a2768843))
- Readme ([`8bf2168`](https://github.com/fiberseq/fibertools-rs/commit/8bf2168969acf67fa5069fb578f94941bd01e3f4))
- Readme ([`15d535a`](https://github.com/fiberseq/fibertools-rs/commit/15d535ae7dc90f86bec99a18015a22376c195788))
- Readme ([`aba1d75`](https://github.com/fiberseq/fibertools-rs/commit/aba1d7572a6109bb2e7d2acffea5f5e5c4f1ced6))
- Readme ([`9ea0b5f`](https://github.com/fiberseq/fibertools-rs/commit/9ea0b5f04f21cf74ab40a0ff1097eac996cc5b8b))
- Readme ([`69d87ea`](https://github.com/fiberseq/fibertools-rs/commit/69d87ea41febf0bd88380708cacea4232ae57f24))
- Readme ([`970c41f`](https://github.com/fiberseq/fibertools-rs/commit/970c41f9ba4a8c26bf980f0ce87f635dd4f68bd3))
- Readme ([`49180bc`](https://github.com/fiberseq/fibertools-rs/commit/49180bccd2dffdc49313e0b259dcdd0e80682bba))
- Readme ([`c8a2ab4`](https://github.com/fiberseq/fibertools-rs/commit/c8a2ab45cbff913c41bde48903c129b6e4d2f70a))
- Readme ([`168c951`](https://github.com/fiberseq/fibertools-rs/commit/168c9517b5137dbd58950f341d96a420c7d50935))
- Readme ([`f5a65a6`](https://github.com/fiberseq/fibertools-rs/commit/f5a65a612b8978f9742dab6990a8d52c6df7645a))
- Clippy ([`9f71158`](https://github.com/fiberseq/fibertools-rs/commit/9f711585d39c66ff45598d85dbf3783aca6ee44c))
- Clippy ([`b4278e4`](https://github.com/fiberseq/fibertools-rs/commit/b4278e4599a6634f37f05874a7e2e860c0b6a45a))
- Adding liftover to pyft ([`248bf4e`](https://github.com/fiberseq/fibertools-rs/commit/248bf4e56c5b10c2dd4613888818a995e6f75529))
- Unify api anming for liftover, optimize for inclusion in pyft ([`2e1fe93`](https://github.com/fiberseq/fibertools-rs/commit/2e1fe93f48b357fbb3459f5206fc5a994325d7a4))
- Unify api anming for liftover, optimize for inclusion in pyft ([`1c32392`](https://github.com/fiberseq/fibertools-rs/commit/1c32392c0bb24adfb3dc4bc78ab290e5405e2a62))
- Clean ([`0e2a574`](https://github.com/fiberseq/fibertools-rs/commit/0e2a574cfd8e1b832a3f157b51c22a60713039a9))
- Speed up and clean up approximate liftover and add a real test ([`c1ac44e`](https://github.com/fiberseq/fibertools-rs/commit/c1ac44e0a188a77900f9bf1dfef2dfbc42b3fdb9))
- Update with ranges ([`cae1a41`](https://github.com/fiberseq/fibertools-rs/commit/cae1a415a2dac4aca1558d14a50eaa0cba258b09))
- Very large improvment in speed of lifting over ranges, some liftover results differ from before by 1bp but it is rare. ([`6a695ec`](https://github.com/fiberseq/fibertools-rs/commit/6a695ec7a71e5002709d5496c8aade541e737514))
- Hide more deps under features for pyft ([`a80fe51`](https://github.com/fiberseq/fibertools-rs/commit/a80fe514ff3d4bf860dedbf7130a21d97b9537ab))
- Clean writes in center. ([`0d19ac1`](https://github.com/fiberseq/fibertools-rs/commit/0d19ac12281dd7fef0b571a745a3e6240bc771a3))
- Reduce number of copies for nuc and msp. ([`3e6aa94`](https://github.com/fiberseq/fibertools-rs/commit/3e6aa945cb643e5d0559fac59b14a649e0de34b1))
- Move nuc and msp logic out of extract into ranges struct and simplify. We ran on a whole genome ft extract to confirm results dont change. ([`eea28d5`](https://github.com/fiberseq/fibertools-rs/commit/eea28d57a9eac79e3e3e0d9d16ede6dce51d242e))
- Example py-ft ([`c55fcc5`](https://github.com/fiberseq/fibertools-rs/commit/c55fcc59749216e0f65c3d9c07efc14f32fb5fdf))
- Release fibertools-rs v0.2.6 ([`3beecf6`](https://github.com/fiberseq/fibertools-rs/commit/3beecf697eafa9707abf5be30a2b773479125069))
- Release fibertools-rs v0.2.6 ([`e973f17`](https://github.com/fiberseq/fibertools-rs/commit/e973f17def31e7c4731ae10143e6c5be5e01425a))
- Release fibertools-rs v0.2.6 ([`ba8df9b`](https://github.com/fiberseq/fibertools-rs/commit/ba8df9b8e918be85beef13411cb3aab588634056))
- Release fibertools-rs v0.2.6 ([`1b5dcfa`](https://github.com/fiberseq/fibertools-rs/commit/1b5dcfa18eef69a8e4a3f7e3e514bb5d5ae87b7f))
- Release fibertools-rs v0.2.6 ([`5aa1908`](https://github.com/fiberseq/fibertools-rs/commit/5aa19089b0cf0614a7a8d0b4f8dc477d6e808ea5))
- Release fibertools-rs v0.2.6 ([`656682a`](https://github.com/fiberseq/fibertools-rs/commit/656682a1b70871df4ca52484351d8296755cbe02))
- Release fibertools-rs v0.2.6 ([`2d2f0f9`](https://github.com/fiberseq/fibertools-rs/commit/2d2f0f96800779088138f6671ab81acfb61cdacc))
- Release fibertools-rs v0.2.6 ([`b80d856`](https://github.com/fiberseq/fibertools-rs/commit/b80d8567ee7ee899734fa5d2c5fd2b6604d45c78))
- Release fibertools-rs v0.2.6 ([`14562fd`](https://github.com/fiberseq/fibertools-rs/commit/14562fd4b9552752ddba160cd3cba04e5f90102b))
- Try again ([`4aa06eb`](https://github.com/fiberseq/fibertools-rs/commit/4aa06eb00c66afb2e5c0273247b81dbabfa15417))
- Release fibertools-rs v0.2.6 ([`e247747`](https://github.com/fiberseq/fibertools-rs/commit/e24774703e6addefabcbe4b1a4df0a91383bdfa8))
- Try again ([`09da733`](https://github.com/fiberseq/fibertools-rs/commit/09da733566d266063c7d74cbd610da2fe33b5f2f))
- Release fibertools-rs v0.2.6 ([`9b1c3f2`](https://github.com/fiberseq/fibertools-rs/commit/9b1c3f2241dce70ece8ded8feeed19251687d1b1))
- Release fibertools-rs v0.2.6 ([`0c525b5`](https://github.com/fiberseq/fibertools-rs/commit/0c525b5e0d6d81a1a82dd14a7fb6ea3c500c8c35))
- Py-ft release ([`4de2b11`](https://github.com/fiberseq/fibertools-rs/commit/4de2b11dbcdec8836b53d0abef5444f87fd8c372))
- Py-ft release ([`b909bc8`](https://github.com/fiberseq/fibertools-rs/commit/b909bc8df6adda1e0cef2ce6198c14e44ba6cbeb))
- Larger chunks not worth ([`911bf40`](https://github.com/fiberseq/fibertools-rs/commit/911bf40a22eaace2afe659efc1000808078792fa))
- Larger chunks ([`171cf51`](https://github.com/fiberseq/fibertools-rs/commit/171cf5104464aea984c8c1266835a2f385e49fa0))
- Speed options ([`9fe3676`](https://github.com/fiberseq/fibertools-rs/commit/9fe3676efa853b79af85e2e1f6bb7849c013a0ec))
- Rework fiberdata to consume bam record to avoid extra copy ([`066ca94`](https://github.com/fiberseq/fibertools-rs/commit/066ca9427211f5147f9528e66a342111e273296f))
- Clippy ([`ecd0a61`](https://github.com/fiberseq/fibertools-rs/commit/ecd0a61bf1518476fa19be4c77554c68076b96fd))
- Update rusthtslib version ([`d262afa`](https://github.com/fiberseq/fibertools-rs/commit/d262afac986cf53e97f3a53d41c87d605231c03e))
- Move bam tags into bio_io ([`abcbcda`](https://github.com/fiberseq/fibertools-rs/commit/abcbcda65a9006c21c892bfdff509cf6e7e55c55))
- Add logging and iterator and aligned blocks ([`7671998`](https://github.com/fiberseq/fibertools-rs/commit/76719983d8104a04cabd9846a5529f8e65fc7f96))
- Rename iterator ([`66b98f9`](https://github.com/fiberseq/fibertools-rs/commit/66b98f9f3c2644e79bf72de2ed070fba75b2ba38))
- Rename iterator ([`9e8cda2`](https://github.com/fiberseq/fibertools-rs/commit/9e8cda2fb47eff101eb3d458cf4599543e7d05a2))
- Rename iterator ([`23e6b12`](https://github.com/fiberseq/fibertools-rs/commit/23e6b12a7601afb4aa21454048a53d803ca1bcdf))
- Rename iterator ([`b03df77`](https://github.com/fiberseq/fibertools-rs/commit/b03df77d99a8f28ecd6d43509a43ff92fb300329))
- Docs ([`6e8cd6f`](https://github.com/fiberseq/fibertools-rs/commit/6e8cd6f9f25dcabc15ef2a25595b3a3ee86de241))
- Docs ([`79ca845`](https://github.com/fiberseq/fibertools-rs/commit/79ca845b0e72e832cdc57b1e1b58090a09417936))
- Add cpg to python modele and make easier access in the rust basemod api ([`3ea32b0`](https://github.com/fiberseq/fibertools-rs/commit/3ea32b01fda3e12f0cacae90d5a52495cec0b6bd))
- Docs ([`41bcd27`](https://github.com/fiberseq/fibertools-rs/commit/41bcd27e9de8654fd46bfb50d3c7efabad59a17e))
- Docs ([`66338fd`](https://github.com/fiberseq/fibertools-rs/commit/66338fd576a66ee230aa4234d072a93b3a3b21d5))
- Docs ([`6f910c5`](https://github.com/fiberseq/fibertools-rs/commit/6f910c53a4e0cb7be411b724385e540517f21306))
- Docs ([`85d471d`](https://github.com/fiberseq/fibertools-rs/commit/85d471df45a0c88567857427725852c491c041ff))
- Docs ([`c5eb60a`](https://github.com/fiberseq/fibertools-rs/commit/c5eb60a8d42616eacfafb871cf4f46fb2fa924c8))
- Docs ([`5bd6803`](https://github.com/fiberseq/fibertools-rs/commit/5bd6803c346a409150daea7713878af46995e836))
- Docs ([`a59f41d`](https://github.com/fiberseq/fibertools-rs/commit/a59f41d0b2d4b97b277b738f04b23010be8d6449))
- Docs ([`7a633d7`](https://github.com/fiberseq/fibertools-rs/commit/7a633d71272a9425ae276d9b846fcda38f6526e5))
- Docs ([`8d16055`](https://github.com/fiberseq/fibertools-rs/commit/8d16055edc4bf9bc5f94d5be42b86b2a2df712c8))
- Docs ([`467072a`](https://github.com/fiberseq/fibertools-rs/commit/467072ae6419b3ece8329f587467d0d0bf316911))
- Docs ([`09994bd`](https://github.com/fiberseq/fibertools-rs/commit/09994bdbdd3949186d44ecef36199a8d228ea280))
- Docs ([`8ea9fb1`](https://github.com/fiberseq/fibertools-rs/commit/8ea9fb1efc4897e191468ee10aa66500456fa0fc))
- Docs ([`82399e6`](https://github.com/fiberseq/fibertools-rs/commit/82399e6e702033acbb455ef6aea3a9935338d77f))
- Docs ([`fd115b7`](https://github.com/fiberseq/fibertools-rs/commit/fd115b7fdb6754d6f6885e901bc34d7364bfc7df))
- Docs ([`1d25caf`](https://github.com/fiberseq/fibertools-rs/commit/1d25caf7e8c19f97d39dec8eb69de7219e85621b))
- Docs ([`e73e00c`](https://github.com/fiberseq/fibertools-rs/commit/e73e00c849726e4577344ec8e964b3eda93ddbc6))
- Docs ([`a3f29cd`](https://github.com/fiberseq/fibertools-rs/commit/a3f29cd798fcbeb071fce7ea7041c4e71a98f8f6))
- Docs ([`e85afd9`](https://github.com/fiberseq/fibertools-rs/commit/e85afd963f513fe578b2d0f3e368a7ae56b59d84))
- Docs ([`580968a`](https://github.com/fiberseq/fibertools-rs/commit/580968a9da3c2a66740d01dfcc0d8c574bfd46c8))
- Docs ([`6b1e714`](https://github.com/fiberseq/fibertools-rs/commit/6b1e714ccda049aef3199563c03d6f5ec1df9dfa))
- Docs ([`c8502ac`](https://github.com/fiberseq/fibertools-rs/commit/c8502ac7cf87d375a5aa9fcf3494a3cf8f43105c))
- Docs ([`b9274c2`](https://github.com/fiberseq/fibertools-rs/commit/b9274c2a7064cd615b079b3cc0b44d9e2f4b5e50))
- Docs ([`eb44bda`](https://github.com/fiberseq/fibertools-rs/commit/eb44bdaf8280689eb06e536266b64802f509a7b3))
- Rtd theme ([`44f93a4`](https://github.com/fiberseq/fibertools-rs/commit/44f93a42b1d5cb30fefad99e1b4dcf19f4f7f0c0))
- Python docs ([`b98edf9`](https://github.com/fiberseq/fibertools-rs/commit/b98edf9f855ae24f81389a5ea481bf0b16dcd794))
- Python docs ([`32f0182`](https://github.com/fiberseq/fibertools-rs/commit/32f01826bbf06ac726464d59eee2769dfe80b138))
- Python docs ([`94dfd52`](https://github.com/fiberseq/fibertools-rs/commit/94dfd521a3f637df47c996fd046d1de3cde85776))
- Python docs ([`b3fa1c3`](https://github.com/fiberseq/fibertools-rs/commit/b3fa1c3b218379a3290fbed2382572b5e1c3e091))
- Python docs ([`d4b75b1`](https://github.com/fiberseq/fibertools-rs/commit/d4b75b1a569d694495bc1e87de651c1bb4e63778))
- Python docs ([`73c918f`](https://github.com/fiberseq/fibertools-rs/commit/73c918f9344fe362f602fa5356b11c9574c5ffec))
- Python docs ([`5f635e0`](https://github.com/fiberseq/fibertools-rs/commit/5f635e04085c012d39d8afa362416ca3642fc7c5))
- Python docs ([`c86cc58`](https://github.com/fiberseq/fibertools-rs/commit/c86cc585993506c55bd0243936767afe4a5f671c))
- Python docs ([`15b825e`](https://github.com/fiberseq/fibertools-rs/commit/15b825ed80a4b099c9ea9f21f64f1b695e20554a))
- Python docs ([`26ef863`](https://github.com/fiberseq/fibertools-rs/commit/26ef86389490b3161546271bea194e4c8a4a8b7f))
- Python docs ([`d953400`](https://github.com/fiberseq/fibertools-rs/commit/d953400d9c7f676fea70fee51264c331ba7e1067))
- Python docs ([`10bf0df`](https://github.com/fiberseq/fibertools-rs/commit/10bf0df63acca5812e3d2d3ad5134bc75abe73b4))
- Readme ([`cdde18e`](https://github.com/fiberseq/fibertools-rs/commit/cdde18e3b119ef36d57feed2f4740b7bde30c011))
- I have a minimal working python package yay! ([`1f6fea3`](https://github.com/fiberseq/fibertools-rs/commit/1f6fea3cf07e1e798649df45d944a5396bf82902))
- Start a python package ([`7e5fbde`](https://github.com/fiberseq/fibertools-rs/commit/7e5fbde9f0f52496fd1f2facbbd55d80d0b64a26))
- Add to changelog ([`ac1987d`](https://github.com/fiberseq/fibertools-rs/commit/ac1987d33daf7fb7395ed1cf15b311390a15e60c))
- Add to changelog ([`2f7c08e`](https://github.com/fiberseq/fibertools-rs/commit/2f7c08e2b24a07054d547088ac2c96463a6229d3))
- Merge pull request #19 from fiberseq/development ([`202025d`](https://github.com/fiberseq/fibertools-rs/commit/202025dcdefdf88e0754ac78be03731c707c0b1b))
- Update docs ([`c61762b`](https://github.com/fiberseq/fibertools-rs/commit/c61762b423129c7428ca946981febec491a9d853))
- Update changelog ([`75a3a32`](https://github.com/fiberseq/fibertools-rs/commit/75a3a320729cfcedb3c99fd084cb2db16104ed70))
- Unsed ([`4bc52a2`](https://github.com/fiberseq/fibertools-rs/commit/4bc52a229ef8be46eac45f765cfec6842d5d1d36))
- Start a changelog ([`2aa57f5`](https://github.com/fiberseq/fibertools-rs/commit/2aa57f5fc1d7c38701964afea6ed5c20a76eb0d2))
- Reorganize test data ([`966ac80`](https://github.com/fiberseq/fibertools-rs/commit/966ac80890e820da571164e01e360fc4c5507845))
- Merge pull request #18 from fiberseq/development ([`2369f27`](https://github.com/fiberseq/fibertools-rs/commit/2369f2702c9caeb18d6c8475c9d1a52a6cbe423e))
- Release fibertools-rs version 0.2.5 ([`0821907`](https://github.com/fiberseq/fibertools-rs/commit/082190756233e077b692839f979df466fd5c7239))
- Irnogre ([`938df0e`](https://github.com/fiberseq/fibertools-rs/commit/938df0e7e1aa88d05eb8b7e247eb88370e11d2b7))
- Correct path ([`ac0166b`](https://github.com/fiberseq/fibertools-rs/commit/ac0166bb5cc1ac8b0b93df71ced2f8fd7689564f))
- Better var name ([`fb3ad6d`](https://github.com/fiberseq/fibertools-rs/commit/fb3ad6d7c35e930cfb1ead67d494844eea62de93))
- Fix off by one that sometimes happened in the final msp when doing nuc/msp calling ([`da5763d`](https://github.com/fiberseq/fibertools-rs/commit/da5763d24a322db2f1e6bdc53af57358776a51f4))
- Fix off by one in minus strand nuc and msp coordiantes ([`91e2bc5`](https://github.com/fiberseq/fibertools-rs/commit/91e2bc558ab94b85e1ede25dccb2bf0e2878a023))
- Merge pull request #17 from fiberseq/development ([`8f3d278`](https://github.com/fiberseq/fibertools-rs/commit/8f3d278d3285f8b5eafd429d5e6174b79adbbc49))
- Check for bgz ([`14724dd`](https://github.com/fiberseq/fibertools-rs/commit/14724dd9270db0af9c12434fbc40252fd684b2fd))
- Rewrite ft center so I can use threads? ([`7180f8e`](https://github.com/fiberseq/fibertools-rs/commit/7180f8e126a72fa49c4761e166bde1535c306aa2))
- Rewrite ft center so I can use threads? ([`4485c5e`](https://github.com/fiberseq/fibertools-rs/commit/4485c5e46534b3bcdebf2295709e06830b404279))
- Merge pull request #16 from fiberseq/development ([`759ee9f`](https://github.com/fiberseq/fibertools-rs/commit/759ee9fae9484f20255ae90b431587302c1f1cba))
- Release fibertools-rs version 0.2.4 ([`98a51ab`](https://github.com/fiberseq/fibertools-rs/commit/98a51ab3030ed03ce6adc7e160ee7feed49a7222))
</details>
## v0.1.0 (2023-07-11)
### Chore
- <csr-id-6bb81e5a15f2f18bfe1a31b2ba207248e6a4e7b2/> Release fibertools-rs version 0.2.3
- <csr-id-7cd3d115ffa9c824218ac8ea9f2454682cb91ca9/> Release fibertools-rs version 0.2.2
- <csr-id-53094a13be5fdc883bd87e46940bf93d48e41b1c/> Release fibertools-rs version 0.2.1
- <csr-id-cd387947c4aafd5d70d087650e1e5fe929808e81/> Release fibertools-rs version 0.2.0
- <csr-id-4f95956d0a60a75b6b1a4d446829935426b2ffaf/> Release fibertools-rs version 0.1.4
- <csr-id-84e4ee9e1ae31396f8743d9d02c1af02dbe84bb7/> Release fibertools-rs version 0.1.3
- <csr-id-7df4056ecc335f5be92f5688215a156623f927cd/> Release fibertools-rs version 0.1.2
- <csr-id-9f8f35b4f75ae3a944d137a8fd7bb562529a634e/> Release fibertools-rs version 0.1.1
- <csr-id-d8f2ea597075a4f13be9d1d68c173c2476c02f63/> Release fibertools-rs version 0.1.1-alpha.4
- <csr-id-c1161138edd4b1bd7153a1cc5b724bb2eef29a4c/> Release fibertools-rs version 0.1.1-alpha.3
- <csr-id-dda2ea4236a46e4cba2ac0f7415a871c09f5777a/> Release fibertools-rs version 0.1.1-alpha.2
- <csr-id-c6f50df845bcd931b61cfa8151e4d38b1c9ccbdd/> Release fibertools-rs version 0.1.1-alpha.1
- <csr-id-3eede8cd716b8a03090a6f5dcc593460c6a943a1/> Release fibertools-rs version 0.1.1-alpha
### Commit Statistics
<csr-read-only-do-not-edit/>
- 681 commits contributed to the release over the course of 352 calendar days.
- 13 commits were understood as [conventional](https://www.conventionalcommits.org).
- 0 issues like '(#ID)' were seen in commit messages
### Commit Details
<csr-read-only-do-not-edit/>
<details><summary>view details</summary>
* **Uncategorized**
- Unsed deps ([`4603bb6`](https://github.com/fiberseq/fibertools-rs/commit/4603bb6920fd42e0c74d2b8d240d50b2d34c8a02))
- Unsed deps ([`b542514`](https://github.com/fiberseq/fibertools-rs/commit/b542514c3353d5afba985763a51645a10cacdf1e))
- Ci ([`60c065e`](https://github.com/fiberseq/fibertools-rs/commit/60c065e0515df493957929a0de16f916300df761))
- Bio-io updates ([`8615452`](https://github.com/fiberseq/fibertools-rs/commit/8615452ba8743caa7b46c39f7acb583abe7ee129))
- Merge pull request #15 from fiberseq/development ([`d8cfd67`](https://github.com/fiberseq/fibertools-rs/commit/d8cfd6773c37691c4aac73837a5124f9c7f4c6b7))
- Change extract defaults ([`b009dda`](https://github.com/fiberseq/fibertools-rs/commit/b009ddacc3c07f9f86562ce25d987d04ab717c11))
- CI ([`57880cc`](https://github.com/fiberseq/fibertools-rs/commit/57880cc16b29cbc250f9dfbf68dffd3c99f3c0fa))
- Rename ([`a00e0d3`](https://github.com/fiberseq/fibertools-rs/commit/a00e0d30cf80d6ac987d4bfbcaa0bf46b128a067))
- Set vars ([`eedb613`](https://github.com/fiberseq/fibertools-rs/commit/eedb613c2f4374ba826d1a8bca5402b97d5ccdee))
- Fix version in bamwriter ([`c3e3781`](https://github.com/fiberseq/fibertools-rs/commit/c3e378118394b9d2deb8d7dde45ac7de28b48a3b))
- Adding a compressed bgzip writer for files with .gz ([`e425ee3`](https://github.com/fiberseq/fibertools-rs/commit/e425ee32388b2870ae80e644af3f83d6ec167279))
- Adding a buff reader that can be compressed optionally ([`4235b77`](https://github.com/fiberseq/fibertools-rs/commit/4235b7768e2530e0721cf70c9181811066ff9b75))
- Making my own io package ([`d001c7f`](https://github.com/fiberseq/fibertools-rs/commit/d001c7f1e2cbd34bb5000093ba9565dc69ec3f65))
- Help update ([`cfb85d9`](https://github.com/fiberseq/fibertools-rs/commit/cfb85d9a92af7765cf9921a474c6d1a1597abcd3))
- Merge pull request #13 from Dylan-DPC/patch-1 ([`5bae1a1`](https://github.com/fiberseq/fibertools-rs/commit/5bae1a1195b14c7207a8cdff358fa23a3088f8f2))
- Update Cargo.toml ([`14d0629`](https://github.com/fiberseq/fibertools-rs/commit/14d0629d03b98bbddc73f933158f472984aea34b))
- Update docker to avoid double building in CI actions ([`19711d0`](https://github.com/fiberseq/fibertools-rs/commit/19711d0737e18354660c2a272d4b260a303a4a7f))
- Merge pull request #12 from lvclark/patch-1 ([`dc8e230`](https://github.com/fiberseq/fibertools-rs/commit/dc8e2309953b0abcc51f5741be716202d2592a92))
- Add HTSlib ([`fd058ba`](https://github.com/fiberseq/fibertools-rs/commit/fd058bac7084510f4c652c1da7e59df0db26bc77))
- Put ft in a path that doesn't need root access ([`b024da2`](https://github.com/fiberseq/fibertools-rs/commit/b024da202fe250d89c59d4860639b9429ace8a36))
- Uncomment compile line ([`d792d98`](https://github.com/fiberseq/fibertools-rs/commit/d792d98b46ec2b46c36ba3837a06db424c3acba7))
- Release fibertools-rs version 0.2.3 ([`6bb81e5`](https://github.com/fiberseq/fibertools-rs/commit/6bb81e5a15f2f18bfe1a31b2ba207248e6a4e7b2))
- Update bamfile for release ([`5213be8`](https://github.com/fiberseq/fibertools-rs/commit/5213be8b2d0467c48086624cbd94b1a20573d2dc))
- Fixing addition of nucleosomes to m6a in predict ([`7c50fab`](https://github.com/fiberseq/fibertools-rs/commit/7c50fabb8ccf2ae217d653fb642c23593964878e))
- Add test ([`2545e26`](https://github.com/fiberseq/fibertools-rs/commit/2545e26b45521d19ecd13e0f01c9676a44cfc18a))
- Add a command to srtip out basemods ([`8ecf75c`](https://github.com/fiberseq/fibertools-rs/commit/8ecf75cc9967d42c3125771e6c39704fcb77fef7))
- Docker works :) ([`44016a7`](https://github.com/fiberseq/fibertools-rs/commit/44016a72c1dbbbff212ef206b7594319d053320d))
- Update actions tool chain ([`24793fd`](https://github.com/fiberseq/fibertools-rs/commit/24793fd15a94bc3f64b074d91dfc62b98a568974))
- Update actions tool chain ([`ee48a2d`](https://github.com/fiberseq/fibertools-rs/commit/ee48a2d266a1e7a95c8c8760383b17375e9b04af))
- Update actions tool chain ([`3b15a91`](https://github.com/fiberseq/fibertools-rs/commit/3b15a9139bb898eb81aa858890865912fc8e0f89))
- Ignore ([`2c1bcb4`](https://github.com/fiberseq/fibertools-rs/commit/2c1bcb46d432b2d5304adc4e909ef55ecab0ed98))
- Fix docker env var ([`fc629e3`](https://github.com/fiberseq/fibertools-rs/commit/fc629e330af5dd620ba0d1ae85a66739bf3053d8))
- Docker not needed here ([`4b89e52`](https://github.com/fiberseq/fibertools-rs/commit/4b89e52aaf5b264408f8cb21310afc685e26d30f))
- Try to make gh actions use docker ([`57bb27d`](https://github.com/fiberseq/fibertools-rs/commit/57bb27d2bf8517aeaba9bce122a860d91151ab23))
- Update docker ([`b28fe63`](https://github.com/fiberseq/fibertools-rs/commit/b28fe63de61c93f3a1c0d2785b460c0f161f9773))
- Update docker ([`0e28b17`](https://github.com/fiberseq/fibertools-rs/commit/0e28b1739465f8ac791684d77b0125eec0b0c258))
- Update docker ([`aba3f95`](https://github.com/fiberseq/fibertools-rs/commit/aba3f95b80caae822bff9ce97368243c97542690))
- Update docker ([`1223538`](https://github.com/fiberseq/fibertools-rs/commit/1223538ac7c616950ebf6e6777548a4ddeca319d))
- Simplify ([`5920f5b`](https://github.com/fiberseq/fibertools-rs/commit/5920f5bdc2af15812a5b335a5703be53dacc86ca))
- Moving bamlift to its own crate ([`efd2a8b`](https://github.com/fiberseq/fibertools-rs/commit/efd2a8b6bf4e7ffe16ad3f91701cace194ea3967))
- Moving bamlift to its own crate ([`ccd0969`](https://github.com/fiberseq/fibertools-rs/commit/ccd096963fe46b7ccbe00781b0da99cab87388ef))
- Release fibertools-rs version 0.2.2 ([`7cd3d11`](https://github.com/fiberseq/fibertools-rs/commit/7cd3d115ffa9c824218ac8ea9f2454682cb91ca9))
- Add run tests and fix comments in bed files for center ([`8e00047`](https://github.com/fiberseq/fibertools-rs/commit/8e00047cdd769ad03a7e79197bfeb0e4bf00e6c4))
- Add run tests ([`b5d1e8e`](https://github.com/fiberseq/fibertools-rs/commit/b5d1e8eca77d7fefec5eece5330f00a1e50abac9))
- Hide some subcommands ([`03e7006`](https://github.com/fiberseq/fibertools-rs/commit/03e7006ab662e8fbb2ed0d3e11f7ffe1946ba4f1))
- Release fibertools-rs version 0.2.1 ([`53094a1`](https://github.com/fiberseq/fibertools-rs/commit/53094a13be5fdc883bd87e46940bf93d48e41b1c))
- Readme update ([`24e26e8`](https://github.com/fiberseq/fibertools-rs/commit/24e26e857c3778c5e36c7a9afb0f68afba0b2d59))
- Remove unused libs ([`fedd892`](https://github.com/fiberseq/fibertools-rs/commit/fedd892e1d360acb93b26f42a8b4d369c3fa8a48))
- Bring back the colors ([`d336911`](https://github.com/fiberseq/fibertools-rs/commit/d3369115667fc7887eaf786de9f78a9f5504399f))
- Bring back the colors ([`0af601a`](https://github.com/fiberseq/fibertools-rs/commit/0af601a8b6f8905be3ec79a0cc6db96bba940e61))
- Release fibertools-rs version 0.2.0 ([`cd38794`](https://github.com/fiberseq/fibertools-rs/commit/cd387947c4aafd5d70d087650e1e5fe929808e81))
- Update version ([`d8e67d9`](https://github.com/fiberseq/fibertools-rs/commit/d8e67d9739ab0ad205050ffcef7ce2606854c80d))
- Update version ([`6f541d3`](https://github.com/fiberseq/fibertools-rs/commit/6f541d31aad21e1b064203d10f6eeb8bb9d93b2d))
- Update version ([`1931652`](https://github.com/fiberseq/fibertools-rs/commit/19316529bd0b427ab8da1007e7a6b263688ecd4e))
- Update tch version ([`49983c3`](https://github.com/fiberseq/fibertools-rs/commit/49983c3ac085900397c505a702037790a28e9d50))
- Add HP tag ([`3c845b4`](https://github.com/fiberseq/fibertools-rs/commit/3c845b40e17642c60c36774cbed8b1ddfcfc70cf))
- Add HP tag ([`a6787ba`](https://github.com/fiberseq/fibertools-rs/commit/a6787ba6728d8dbc3d60b003ef4a9b34bf3ce954))
- Add HP tag ([`9895f1c`](https://github.com/fiberseq/fibertools-rs/commit/9895f1c10c85fd32a9f12da1f8d59c2bae300447))
- Add HP tag ([`4c78005`](https://github.com/fiberseq/fibertools-rs/commit/4c780051e44ee3f35a5539004f5ad03973638b48))
- Add HP tag ([`6d9b74d`](https://github.com/fiberseq/fibertools-rs/commit/6d9b74d8c3d632fcde1e47242e33db00fb4a18d0))
- Update for new revio model ([`08fcd9e`](https://github.com/fiberseq/fibertools-rs/commit/08fcd9e5d1890b0aa2c4243d9ddd097cf02adfae))
- Cite ([`ce139ac`](https://github.com/fiberseq/fibertools-rs/commit/ce139ac5333ac1db84ab80d65b2f138301537d2e))
- Fixing ignored min ml option ([`71f7799`](https://github.com/fiberseq/fibertools-rs/commit/71f77997a68dbb2b69f802375c49fba4ed4d865b))
- Updating to new revio models ([`b0e7539`](https://github.com/fiberseq/fibertools-rs/commit/b0e753999c0885b0450c9d0bd4b42520380820da))
- Updating to new revio models ([`b127d80`](https://github.com/fiberseq/fibertools-rs/commit/b127d8033e0d4a489a98009745d88bb791e31674))
- Make logging more clear ([`daefc06`](https://github.com/fiberseq/fibertools-rs/commit/daefc067e979bfc95550149da557a3cb11013ef3))
- Make logging more clear ([`ed8785a`](https://github.com/fiberseq/fibertools-rs/commit/ed8785ab203c7566426f220e2f6095e7bd6078b2))
- Readme ([`2e25423`](https://github.com/fiberseq/fibertools-rs/commit/2e2542385974f2e584fcfe42b0bd76dedfefa6f3))
- Readme ([`715e25d`](https://github.com/fiberseq/fibertools-rs/commit/715e25d9bbe82b36910984944b9ff3108a8f3bf3))
- Release fibertools-rs version 0.1.4 ([`4f95956`](https://github.com/fiberseq/fibertools-rs/commit/4f95956d0a60a75b6b1a4d446829935426b2ffaf))
- Simplify ([`288ff21`](https://github.com/fiberseq/fibertools-rs/commit/288ff21d15508baaf035d962efad9702d7300190))
- Simplify ([`687f41d`](https://github.com/fiberseq/fibertools-rs/commit/687f41d47ab003e6cd7cae5f7831d68fdc45e5a6))
- Simplify ([`24f5930`](https://github.com/fiberseq/fibertools-rs/commit/24f5930a1e1827e3cdd7e1fb9533215c9ecf41b8))
- New nucleosome caller is ready ([`2a856a7`](https://github.com/fiberseq/fibertools-rs/commit/2a856a796324bfe51934e9eaf70d945508a2f298))
- New nucleosome caller is ready ([`6a5a370`](https://github.com/fiberseq/fibertools-rs/commit/6a5a3705457bce06f44ab149bed291f5a98c8add))
- New nucleosome caller is ready ([`b4ee350`](https://github.com/fiberseq/fibertools-rs/commit/b4ee35093d0b0b8d7a2076feacd22fe074db8e2e))
- New nucleosome caller is ready ([`39f045d`](https://github.com/fiberseq/fibertools-rs/commit/39f045da8c231a4ea4af30a1d03f71a408465575))
- New nucleosome caller is ready ([`387fc4e`](https://github.com/fiberseq/fibertools-rs/commit/387fc4eab0613f7c47f9889789d26c44611c05b9))
- New nucleosome caller is ready ([`ceb371c`](https://github.com/fiberseq/fibertools-rs/commit/ceb371c0a8c3401a0a4439f394bb427f71c13f15))
- Skip double combine ([`b33dcae`](https://github.com/fiberseq/fibertools-rs/commit/b33dcaea2febcd99e5e4ce4d4d7f793380048f5e))
- Skip double combine ([`80f421c`](https://github.com/fiberseq/fibertools-rs/commit/80f421c1ce3831bdf709752804506d3d4b6553be))
- Skip double combine ([`330361c`](https://github.com/fiberseq/fibertools-rs/commit/330361c0fc96926730996ededf5b679da052347d))
- Skip double combine ([`c63ba23`](https://github.com/fiberseq/fibertools-rs/commit/c63ba23b3bfa8a88e39971a5e6f69a2da7731c2d))
- Skip double combine ([`7f2f23b`](https://github.com/fiberseq/fibertools-rs/commit/7f2f23bc4b4bc87b148247046b208b73f416e487))
- Comdine over solitary m6a more agressiby ([`5cce88a`](https://github.com/fiberseq/fibertools-rs/commit/5cce88abed5f4e1fc82f7aa98c0be5f270e75f69))
- Add rg to center ([`15d9ff1`](https://github.com/fiberseq/fibertools-rs/commit/15d9ff145a92970daf927dfa88d0b3e5515d52b6))
- Fix forward rev ([`d953cec`](https://github.com/fiberseq/fibertools-rs/commit/d953cec6f129a9c1bdd6f3a7b2aac399433b3578))
- Make dseg optional ([`feace70`](https://github.com/fiberseq/fibertools-rs/commit/feace70c6d331bfddc951979be6561eee41780eb))
- Make dseg optional ([`d67754e`](https://github.com/fiberseq/fibertools-rs/commit/d67754ea94552e5e419c21438f959f33fb638d1e))
- Make dseg optional ([`8e6a19e`](https://github.com/fiberseq/fibertools-rs/commit/8e6a19e1febe2ce0b068f98735a8b0a7d1f076c3))
- Make dseg optional ([`2a3971b`](https://github.com/fiberseq/fibertools-rs/commit/2a3971b63b1b7091b12d15d4cd4b6ba769a91932))
- Make dseg optional ([`a3291b9`](https://github.com/fiberseq/fibertools-rs/commit/a3291b9bfaef32cb9182ba57d8e0c0cacce44f27))
- Make dseg optional ([`59f3f9f`](https://github.com/fiberseq/fibertools-rs/commit/59f3f9fde5ae717de0e295e4ec25da7cbae9b5f2))
- Make dseg optional ([`ef5c7d2`](https://github.com/fiberseq/fibertools-rs/commit/ef5c7d2903809f04193705edc107859e7b8d8254))
- Make dseg optional ([`e38363c`](https://github.com/fiberseq/fibertools-rs/commit/e38363c0d113ae31493550839f5414e301679aa9))
- Make dseg optional ([`c5e42ed`](https://github.com/fiberseq/fibertools-rs/commit/c5e42ed3a6c0ffa14cb755bcf67aef3fa6adef5b))
- D-seg paramenter on cmd line ([`eba6409`](https://github.com/fiberseq/fibertools-rs/commit/eba640965823d1c9650697195918a655971bb1a9))
- Try dsegment ([`56cce35`](https://github.com/fiberseq/fibertools-rs/commit/56cce355483a8f92b790a23fd2c4ab76fbe5c9dc))
- Update docs ([`404d60e`](https://github.com/fiberseq/fibertools-rs/commit/404d60edc217a49846a375a58916115fdde04bf4))
- Improve help ([`b2e8f3e`](https://github.com/fiberseq/fibertools-rs/commit/b2e8f3e12aecf32253b164540a109726254ce70f))
- Move nuc options to cli for predict-m6a ([`5c6c17b`](https://github.com/fiberseq/fibertools-rs/commit/5c6c17b502c679db52ae4d5d300375988911ca41))
- Test update ([`4cfc00a`](https://github.com/fiberseq/fibertools-rs/commit/4cfc00aa14d1a1ba8c34b7b6178151d8286d878d))
- Options change ([`ae86e48`](https://github.com/fiberseq/fibertools-rs/commit/ae86e4803d178d021ca1b59db0dccaf13e108142))
- Add cli arguments ([`6530b50`](https://github.com/fiberseq/fibertools-rs/commit/6530b50522ced29ddb8cc0028df0177a67a3146e))
- Test negatives ([`5d41679`](https://github.com/fiberseq/fibertools-rs/commit/5d41679c825e8a38cbdb3451e49c9e1c1af0a5f4))
- Test negatives ([`86ea24c`](https://github.com/fiberseq/fibertools-rs/commit/86ea24cf3a899d30974bcf6c7b235238678fc357))
- Test negatives ([`8acbfaf`](https://github.com/fiberseq/fibertools-rs/commit/8acbfaf0c31425b55ce889bbff8203c7f2622a6b))
- Test negatives ([`b5cae9b`](https://github.com/fiberseq/fibertools-rs/commit/b5cae9b4b84fefd252a9be8e6ef81bc14df3aed2))
- Test negatives ([`d17ccf2`](https://github.com/fiberseq/fibertools-rs/commit/d17ccf2896942f67b92dbd2dcbd160be64786583))
- Test negatives ([`a178975`](https://github.com/fiberseq/fibertools-rs/commit/a178975974d8562cdc5d20974967b9d642ba26d6))
- Adding a command that lets me add simple nuc calls ([`819a90b`](https://github.com/fiberseq/fibertools-rs/commit/819a90bd1255bbd8298ee60fde55b16a1bfccfe2))
- Adding a command that lets me add simple nuc calls ([`33e0ee8`](https://github.com/fiberseq/fibertools-rs/commit/33e0ee84f8457d85ea52f45a430a61fcdc20dd8c))
- Adding a command that lets me add simple nuc calls ([`cd3ec8f`](https://github.com/fiberseq/fibertools-rs/commit/cd3ec8fb718cf9353f43348b2b2c9741117f96d1))
- Release fibertools-rs version 0.1.3 ([`84e4ee9`](https://github.com/fiberseq/fibertools-rs/commit/84e4ee9e1ae31396f8743d9d02c1af02dbe84bb7))
- Docs ([`2d97f26`](https://github.com/fiberseq/fibertools-rs/commit/2d97f26b66bd8f5e08fc66daacf74a925ff16677))
- Ign ([`ae94728`](https://github.com/fiberseq/fibertools-rs/commit/ae94728e602bedfd1fdabb636078cd97e5aed968))
- Adding 3.2 models ([`1193a76`](https://github.com/fiberseq/fibertools-rs/commit/1193a76e3ea8ac5f2225253d96ae770ebc0f7a07))
- Further clean model chem seelection ([`32530e5`](https://github.com/fiberseq/fibertools-rs/commit/32530e50cbb3a4e23d1a304cc16b88c94c55b4a1))
- Simplify model loading into the predict options ([`b60bf8b`](https://github.com/fiberseq/fibertools-rs/commit/b60bf8b8d43bb154a3f93be48f03d022e68238a3))
- Try adding a reference option to ft center ([`ca015e0`](https://github.com/fiberseq/fibertools-rs/commit/ca015e01d5c6db82a982d919c3edbc60fc5af375))
- Add the option to read the ML models from env variables FT_MODEL and FT_JSON ([`8314d8e`](https://github.com/fiberseq/fibertools-rs/commit/8314d8e62b21efe929c4e16c7509e7dd2bc312e4))
- Add RG to extract ([`355088e`](https://github.com/fiberseq/fibertools-rs/commit/355088e59eac4c726b1d30212da3cc46d8bc59c2))
- Theads help msg ([`595db94`](https://github.com/fiberseq/fibertools-rs/commit/595db94ef3b844ce49d829c25d79ee4b6d97f44d))
- Release fibertools-rs version 0.1.2 ([`7df4056`](https://github.com/fiberseq/fibertools-rs/commit/7df4056ecc335f5be92f5688215a156623f927cd))
- Remvoe libtorch check since it is packaged in conda now ([`28c3614`](https://github.com/fiberseq/fibertools-rs/commit/28c3614ee3913451b3eb81697f904f104160930b))
- Update url for new repo ([`021ae38`](https://github.com/fiberseq/fibertools-rs/commit/021ae389cf520391b5d3ccb066ffa8952ea32997))
- Release fibertools-rs version 0.1.1 ([`9f8f35b`](https://github.com/fiberseq/fibertools-rs/commit/9f8f35b4f75ae3a944d137a8fd7bb562529a634e))
- Bioconda now working ([`583ed05`](https://github.com/fiberseq/fibertools-rs/commit/583ed054e2b2cc5233f80e98e44c2fcabf8cec14))
- Bioconda now working ([`d0f4943`](https://github.com/fiberseq/fibertools-rs/commit/d0f494361fa3f39a5d0cf85e1e0148ab27e4950a))
- Fix ci ([`2d6fa56`](https://github.com/fiberseq/fibertools-rs/commit/2d6fa5617c814b651ee1f0e8f7214696c772d271))
- Release fibertools-rs version 0.1.1-alpha.4 ([`d8f2ea5`](https://github.com/fiberseq/fibertools-rs/commit/d8f2ea597075a4f13be9d1d68c173c2476c02f63))
- Restor version of ubunut ([`6ace556`](https://github.com/fiberseq/fibertools-rs/commit/6ace556673fe953e3bbdc50fbe9abff59e59aa0a))
- Release fibertools-rs version 0.1.1-alpha.3 ([`c116113`](https://github.com/fiberseq/fibertools-rs/commit/c1161138edd4b1bd7153a1cc5b724bb2eef29a4c))
- Older version of ubunut ([`a043398`](https://github.com/fiberseq/fibertools-rs/commit/a04339858db5f2944f3a46be44eb2c3c367f1939))
- Release fibertools-rs version 0.1.1-alpha.2 ([`dda2ea4`](https://github.com/fiberseq/fibertools-rs/commit/dda2ea4236a46e4cba2ac0f7415a871c09f5777a))
- Adding libtorch enviorment checks ([`3d0c77c`](https://github.com/fiberseq/fibertools-rs/commit/3d0c77c3bc89b1e6cce43e27ef1e92190339dcb2))
- Release fibertools-rs version 0.1.1-alpha.1 ([`c6f50df`](https://github.com/fiberseq/fibertools-rs/commit/c6f50df845bcd931b61cfa8151e4d38b1c9ccbdd))
- Change targets ([`1ad406a`](https://github.com/fiberseq/fibertools-rs/commit/1ad406a1de44d64ea84002442a9cab1d269d1ef8))
- Change precommit ([`0b00d2d`](https://github.com/fiberseq/fibertools-rs/commit/0b00d2d69814fa25f5ecd0520e720b4b52fe81f0))
- Release fibertools-rs version 0.1.1-alpha ([`3eede8c`](https://github.com/fiberseq/fibertools-rs/commit/3eede8cd716b8a03090a6f5dcc593460c6a943a1))
- Default use cnn ([`9946f0f`](https://github.com/fiberseq/fibertools-rs/commit/9946f0fc7dc875392cd6ef55a537c4ead2f80970))
- Testing a release manager ([`723bc6f`](https://github.com/fiberseq/fibertools-rs/commit/723bc6f0d7f7f7d808b041a6f6b8c50b6b2dd1db))
- Testing a release manager ([`faf0620`](https://github.com/fiberseq/fibertools-rs/commit/faf062072eba594d006c2b4c50cea3b898193957))
- Hide prediction under a new predict feature instead of partically under cnn ([`f86e1cf`](https://github.com/fiberseq/fibertools-rs/commit/f86e1cf628a3c3cb4db9a6ecd297467137d8dd4a))
- Make test smaller ([`45196f1`](https://github.com/fiberseq/fibertools-rs/commit/45196f1a62b9e7d0e007b6f5bd8729164dc729a9))
- V0.1 ([`3f65061`](https://github.com/fiberseq/fibertools-rs/commit/3f65061287fd64e5176de2daff4466cdcc774ee9))
- Check ([`14bb95f`](https://github.com/fiberseq/fibertools-rs/commit/14bb95f9bf4ca2f6a8369631369d22c3fe790dfb))
- Fix default model and model setting flags in clap ([`a1bc54d`](https://github.com/fiberseq/fibertools-rs/commit/a1bc54d136647163f6ac7685b4093b4a28848338))
- Change deafult to semi supervized cnn ([`ddfdc6e`](https://github.com/fiberseq/fibertools-rs/commit/ddfdc6e53f1620604d4197ec090bdd952e7229a3))
- Fixing sequences reported by center that are on the reverse complement and check 6th column for strand and update docs ([`7bc77cc`](https://github.com/fiberseq/fibertools-rs/commit/7bc77ccdeeaef3269e24727ec735cb40cc2b0879))
- Going back ([`e3a729e`](https://github.com/fiberseq/fibertools-rs/commit/e3a729ec15524fd4109cf98e50107fa852a60b37))
- Add min ec coverage ([`1dbc5ed`](https://github.com/fiberseq/fibertools-rs/commit/1dbc5ed4badc14af6c7b476435acfe7b7bee6207))
- Models ([`18f7634`](https://github.com/fiberseq/fibertools-rs/commit/18f7634b4ced91d78751f5b2eff95ababe6bcd63))
- Models ([`7fe8cd4`](https://github.com/fiberseq/fibertools-rs/commit/7fe8cd45670fa31cf9c86b9d8e77775cf5bc032b))
- Models ([`ceb21ef`](https://github.com/fiberseq/fibertools-rs/commit/ceb21efb7210d6f1340f3c5e0bd8381854a802ff))
- Models ([`53ab799`](https://github.com/fiberseq/fibertools-rs/commit/53ab7994ec3602a09b9365ce69c4d5f8432673c2))
- Try 225 initalization ([`909a5bc`](https://github.com/fiberseq/fibertools-rs/commit/909a5bc575667c16484f0faf375a416a011f1753))
- Try 225 initalization ([`45f087b`](https://github.com/fiberseq/fibertools-rs/commit/45f087bff15f82b8b073c3045fd8f84c5526616d))
- Try 225 initalization ([`3f7f202`](https://github.com/fiberseq/fibertools-rs/commit/3f7f202543c821cd93147170b04ac70e600ba819))
- Try 225 initalization ([`61be875`](https://github.com/fiberseq/fibertools-rs/commit/61be8754f452b65ccd9b83cacb8d731512dc2354))
- Try 225 initalization ([`d06f478`](https://github.com/fiberseq/fibertools-rs/commit/d06f4780bb04116e416c4910f6015c0c29bb5714))
- Try 225 initalization ([`4d17b9d`](https://github.com/fiberseq/fibertools-rs/commit/4d17b9dd0037fdb36f56f8ee7ec0365da6dc3d10))
- Try 225 initalization ([`2d59ffe`](https://github.com/fiberseq/fibertools-rs/commit/2d59ffecf0c42032316b954e994cca0b3a25d0c3))
- Try 225 initalization ([`6837a01`](https://github.com/fiberseq/fibertools-rs/commit/6837a01aff9efdc3483b12f1cc89a253bd2537bb))
- Try 225 initalization ([`b191f5f`](https://github.com/fiberseq/fibertools-rs/commit/b191f5f754dddf5c791692b334ac5765646882c0))
- Try 225 initalization ([`f31840d`](https://github.com/fiberseq/fibertools-rs/commit/f31840d1b53deefde8f4c0e525f26b8251efbc1d))
- Try 225 initalization ([`5c46adc`](https://github.com/fiberseq/fibertools-rs/commit/5c46adcfbb4978eb1b581d95027e947012934574))
- Try 225 initalization ([`e66bdd0`](https://github.com/fiberseq/fibertools-rs/commit/e66bdd0989cd35ce4f8e9bc7d1a481de7d98a550))
- Try 225 initalization ([`3837507`](https://github.com/fiberseq/fibertools-rs/commit/3837507d25124cebce728b630eb5e2ce7f295944))
- Try 225 initalization ([`f920711`](https://github.com/fiberseq/fibertools-rs/commit/f920711d084c7e0a19257c6bde99fa5913cc16eb))
- Try 225 initalization ([`2bcb25b`](https://github.com/fiberseq/fibertools-rs/commit/2bcb25bf43e95cc2136880655b19e9424bf77590))
- Try 225 initalization ([`54fa3fb`](https://github.com/fiberseq/fibertools-rs/commit/54fa3fbea666be44f744374ed47abf3820ff2316))
- Try 225 initalization ([`548655a`](https://github.com/fiberseq/fibertools-rs/commit/548655a897d04edbabe6563b305ff1d43e763629))
- Try 225 initalization ([`e97ab5a`](https://github.com/fiberseq/fibertools-rs/commit/e97ab5a6aabe5ad282235b9bef32538a7c083328))
- Try 225 initalization ([`729e9e4`](https://github.com/fiberseq/fibertools-rs/commit/729e9e4e23a94fb1f2f0450af3d8734033d3ed23))
- Try 225 initalization ([`fbc82f5`](https://github.com/fiberseq/fibertools-rs/commit/fbc82f51d3c0499434b9febfaec2cb42885b7226))
- Try 225 initalization ([`31926e6`](https://github.com/fiberseq/fibertools-rs/commit/31926e601c894a8605433bb2c23442bcca4c2d43))
- Try 225 initalization ([`2086b51`](https://github.com/fiberseq/fibertools-rs/commit/2086b51c003b6ae30a34ebf55c169de40a7949ae))
- Revio models ([`aebd08e`](https://github.com/fiberseq/fibertools-rs/commit/aebd08e94a6a0e53fd5acab43a9b0886aae2e672))
- Revio models ([`37d99ec`](https://github.com/fiberseq/fibertools-rs/commit/37d99ec537ae8e0422ffb42aad8306fe456e9044))
- Revio models ([`b891f68`](https://github.com/fiberseq/fibertools-rs/commit/b891f68ff9663c9efe550052aa554cd56d4e1c67))
- Revio models ([`94a73fa`](https://github.com/fiberseq/fibertools-rs/commit/94a73fa1b46d24a98fe9b5bb6cc9206d172359cd))
- Revio models ([`0cafca8`](https://github.com/fiberseq/fibertools-rs/commit/0cafca8076ccab29c7ac133e1750a6c911c95672))
- Adding a subset of sequence to center ([`7a2f2f4`](https://github.com/fiberseq/fibertools-rs/commit/7a2f2f4e6d655206c34280ad9f8072bfe4aef7d6))
- Adding batch of 10 reads all at once to gpu ([`c1947d5`](https://github.com/fiberseq/fibertools-rs/commit/c1947d5b2f6c36f9de6ef6189e9d586472c56efc))
- Clean progress bar ([`9349850`](https://github.com/fiberseq/fibertools-rs/commit/9349850fcdb58a57b0c3014240daef23b02767e7))
- Progress bar ([`f8763fb`](https://github.com/fiberseq/fibertools-rs/commit/f8763fb327695c32880662dfbda5cc346c9e3e07))
- Add a clear kinetics command ([`c4d0103`](https://github.com/fiberseq/fibertools-rs/commit/c4d0103000a803784a85f5e358cceb25586827f0))
- Add a optional distance filter to ft center ([`366ccc6`](https://github.com/fiberseq/fibertools-rs/commit/366ccc68ee06855b38dfa3870743d6c7f6503602))
- Doc update ([`08b0878`](https://github.com/fiberseq/fibertools-rs/commit/08b08782c7ed714154c4ab339112503cdec48975))
- Try next pytorch version ([`8d2a822`](https://github.com/fiberseq/fibertools-rs/commit/8d2a8225fc24834ff0a386749acc2494aeef718f))
- Merge pull request #10 from mrvollger/dev ([`e3ef1e6`](https://github.com/fiberseq/fibertools-rs/commit/e3ef1e6411a0f603ea71f998493a8940e36dddd6))
- Try next pytorch version ([`2e4eaca`](https://github.com/fiberseq/fibertools-rs/commit/2e4eaca457ad8ae6eb9a68ba94c07a8c7e7e8403))
- Static link? ([`f68a4ec`](https://github.com/fiberseq/fibertools-rs/commit/f68a4ec59a95bc3bd263fd4843ac578b99df790c))
- Adding a ml filter ([`839a4d2`](https://github.com/fiberseq/fibertools-rs/commit/839a4d24287357d1fe80c87e251212cf50f7c631))
- Adding pb u16 converter ([`5f8d877`](https://github.com/fiberseq/fibertools-rs/commit/5f8d877700d3ec4fcdaf9905c4c262d0b5398c22))
- Final (fingers crossed) values for ml filters for 2.0 and 2.2 chem ([`ee55a17`](https://github.com/fiberseq/fibertools-rs/commit/ee55a1711013061bf41d36d9824592ceba1266f4))
- Update tables for models ([`265dce1`](https://github.com/fiberseq/fibertools-rs/commit/265dce1ddc59c40eea80c5c332b41a8ef62cdf0d))
- Models out of date wrt tables ([`3d25480`](https://github.com/fiberseq/fibertools-rs/commit/3d25480d1793a9d13df1baa14e3d8258f777a2c1))
- Read in a json prediction conversion table and apply it to the semi suppervized approach ([`8a57047`](https://github.com/fiberseq/fibertools-rs/commit/8a5704715f7deb291ac5799212f0ca81adc88af7))
- Fmt ([`2e93877`](https://github.com/fiberseq/fibertools-rs/commit/2e93877a1fcbf95113e1e7f60e74029f8d30c7d4))
- Fmt ([`fb78c73`](https://github.com/fiberseq/fibertools-rs/commit/fb78c730918e870eed40d9056e3b1fe9d0423c42))
- Framework for converting floats to u8 precision calls ([`95185fa`](https://github.com/fiberseq/fibertools-rs/commit/95185faa33f27d807386203a1ddea220c757c6fa))
- Limit width ([`49b90a9`](https://github.com/fiberseq/fibertools-rs/commit/49b90a95bb3aefbe2b9f1c373e7415347281bcbd))
- Logos ([`d3d7f23`](https://github.com/fiberseq/fibertools-rs/commit/d3d7f23328610598dee9fba64342391d6a1c5222))
- Updating default values for models based on chemsitry ([`f706aef`](https://github.com/fiberseq/fibertools-rs/commit/f706aef82e67d32774a9d19899740b3327199864))
- Fix overwirrten model and add new 2.2 model ([`d6b479d`](https://github.com/fiberseq/fibertools-rs/commit/d6b479dff23d054a8d1f88551bd91e4b98d8b0ef))
- Fix overwirrten model and add new 2.2 model ([`efa2b51`](https://github.com/fiberseq/fibertools-rs/commit/efa2b51302482b11887e988e5f86e711daa96d9b))
- Fix overwirrten model and add new 2.2 model ([`d8a1ce3`](https://github.com/fiberseq/fibertools-rs/commit/d8a1ce389824a757856eda4c03510c0c0cec3715))
- Adjust suggested value for semi ([`95af6b9`](https://github.com/fiberseq/fibertools-rs/commit/95af6b9abdcedf5951f10728ed54db0d927705b7))
- Update model ([`eca5448`](https://github.com/fiberseq/fibertools-rs/commit/eca5448da750ed163fb3cd082b31958a4c0b38f3))
- Update model ([`660a1ac`](https://github.com/fiberseq/fibertools-rs/commit/660a1ac6fa18c0c619e2d9eb0c57e2f394ac99dc))
- Update model ([`08b35bd`](https://github.com/fiberseq/fibertools-rs/commit/08b35bdfe5c06b0191c73c74036ddf421cd9b50a))
- Update model ([`c58c252`](https://github.com/fiberseq/fibertools-rs/commit/c58c252845dcb185c8e204f720384caf9ef83ef3))
- Update model ([`33df823`](https://github.com/fiberseq/fibertools-rs/commit/33df823c8588d0fd149bbfd8f7bd3dd6928b1cce))
- Update model ([`fb0ef59`](https://github.com/fiberseq/fibertools-rs/commit/fb0ef598a8529c355c0af6e2a65fbc91931ce826))
- Update model ([`42d7be0`](https://github.com/fiberseq/fibertools-rs/commit/42d7be0a5d5910a644686b0ae44f178a87eb800e))
- Update model ([`0e709cc`](https://github.com/fiberseq/fibertools-rs/commit/0e709cc0d480788bb8fa6ab484f111a052c7ad3b))
- Update model ([`7602cb6`](https://github.com/fiberseq/fibertools-rs/commit/7602cb6f03943d32084644981ea04d6531776657))
- Update model ([`8642198`](https://github.com/fiberseq/fibertools-rs/commit/8642198dd0a9d0871db02accd6c0d3602645e99e))
- Update model ([`263ff71`](https://github.com/fiberseq/fibertools-rs/commit/263ff71a8473a6fcd9b246f840ce347a4ea6c9fe))
- Update model ([`2e84b17`](https://github.com/fiberseq/fibertools-rs/commit/2e84b174f8fe2671ca8e2cafd63f0013e51eb048))
- Update model ([`c2c637e`](https://github.com/fiberseq/fibertools-rs/commit/c2c637e9adedaa31de28998e5db684365f8a20d8))
- Update model ([`d86c1c9`](https://github.com/fiberseq/fibertools-rs/commit/d86c1c92a23148d92a27f4ffac3534005d8d5fb8))
- Update model ([`1d5568e`](https://github.com/fiberseq/fibertools-rs/commit/1d5568e9ee7c55ae5a76a6b4d66fa4f031c2314d))
- Update model ([`652992c`](https://github.com/fiberseq/fibertools-rs/commit/652992c2e200f5c0d37bfdc614e0625a3dfba431))
- Update model ([`7c83e6f`](https://github.com/fiberseq/fibertools-rs/commit/7c83e6fc3d5b1265ede574f9cadfed43f9f92032))
- Update model ([`d1a480a`](https://github.com/fiberseq/fibertools-rs/commit/d1a480a01dc9de5482cb7e30c85f1b20800f59f1))
- Update model ([`9d57185`](https://github.com/fiberseq/fibertools-rs/commit/9d571856b63e49dcb1baa6ac950cba0612de5de1))
- Update model ([`1532b69`](https://github.com/fiberseq/fibertools-rs/commit/1532b69e85ae81d60812b33153d4172af23e48c3))
- Update model ([`aed4e39`](https://github.com/fiberseq/fibertools-rs/commit/aed4e3951e0c2f974088b67de4a290f23841cefa))
- Update model ([`ace39e1`](https://github.com/fiberseq/fibertools-rs/commit/ace39e1799efb15821e0d11a022bd99ee16730c2))
- Update model ([`3838aad`](https://github.com/fiberseq/fibertools-rs/commit/3838aad6941ad934d2a12156d8ff72ea31ca40fa))
- Update model ([`1bed0db`](https://github.com/fiberseq/fibertools-rs/commit/1bed0dbf9b33ffe439571386960bd35680bd765d))
- Update model ([`ab4a2af`](https://github.com/fiberseq/fibertools-rs/commit/ab4a2af0964a89b3d25ee5539f26d3dd834654fd))
- Update model ([`6a093dc`](https://github.com/fiberseq/fibertools-rs/commit/6a093dc0a6f795f69492e2afb1747d123d4e1a97))
- Update model ([`b137ca1`](https://github.com/fiberseq/fibertools-rs/commit/b137ca120c123d72dd8a21b5522da2431a17493a))
- Update model ([`7123d61`](https://github.com/fiberseq/fibertools-rs/commit/7123d6170ddf39797d3860acfd3df11666743227))
- Update model ([`83c0b2e`](https://github.com/fiberseq/fibertools-rs/commit/83c0b2ec82f601a0094e3a2ebb5e71f2aac56303))
- Update model ([`383d09f`](https://github.com/fiberseq/fibertools-rs/commit/383d09f06e31dbbc18bad0c715eae04cfdd6e39f))
- Update model ([`a801f7a`](https://github.com/fiberseq/fibertools-rs/commit/a801f7ab147edfb96c1d9f99a300cfa0a770d52e))
- Update model ([`f6c1513`](https://github.com/fiberseq/fibertools-rs/commit/f6c15134b20d82fdf4854115c86d759aa2a7ec24))
- No semi score ([`d2f58b2`](https://github.com/fiberseq/fibertools-rs/commit/d2f58b235c783989021783d30f946bdc0bfc28fe))
- Custom semi adjust ([`0a9ef81`](https://github.com/fiberseq/fibertools-rs/commit/0a9ef81fc31c172a8c11b18628f39302a46a5955))
- Custom semi adjust ([`0758311`](https://github.com/fiberseq/fibertools-rs/commit/07583118d82194caeb89914724156c4e3c9689b2))
- Custom semi adjust ([`7bb553e`](https://github.com/fiberseq/fibertools-rs/commit/7bb553e76e17c56b9f29ae9abc9e6d5e676c219c))
- Custom semi adjust ([`c0b3b73`](https://github.com/fiberseq/fibertools-rs/commit/c0b3b7303f45116ab3994ff1648ca9ce718156bf))
- Custom semi adjust ([`25b8811`](https://github.com/fiberseq/fibertools-rs/commit/25b88110e6848b46cfbb5c134ca1d16a6f4da687))
- Custom semi adjust ([`b28f2dc`](https://github.com/fiberseq/fibertools-rs/commit/b28f2dcedf5b3b550edc3caac5c5f21a558b135a))
- Custom semi adjust ([`f7ddc51`](https://github.com/fiberseq/fibertools-rs/commit/f7ddc51372ea7ea5b9f0e5be3ec33e3ba73b38bc))
- Custom semi adjust ([`29b9f2c`](https://github.com/fiberseq/fibertools-rs/commit/29b9f2c3163ac7be3523593286fa7408f09d85fd))
- Custom semi adjust ([`de586ff`](https://github.com/fiberseq/fibertools-rs/commit/de586ff65d324a9f5c7c74eaa3e9997fa2a0a766))
- Custom semi adjust ([`66fec59`](https://github.com/fiberseq/fibertools-rs/commit/66fec59a0e718566d90578fde7d3d9e52f86b939))
- Custom semi adjust ([`db55c50`](https://github.com/fiberseq/fibertools-rs/commit/db55c5056d421f4006399b6356b6fd68ca28c1b5))
- Custom semi adjust ([`27bb5d1`](https://github.com/fiberseq/fibertools-rs/commit/27bb5d1f413ca47179d984976800f79342490e80))
- Custom semi adjust ([`758be9b`](https://github.com/fiberseq/fibertools-rs/commit/758be9b529643fc26248851284bf769756e942cf))
- Custom semi adjust ([`a595d70`](https://github.com/fiberseq/fibertools-rs/commit/a595d70b8f4b7e8e1a2dddb0637aef1d28585729))
- Custom semi adjust ([`6a1e6f1`](https://github.com/fiberseq/fibertools-rs/commit/6a1e6f1b106013b921cfe50333e47bb0d35370d6))
- Larger full float ([`1a2f942`](https://github.com/fiberseq/fibertools-rs/commit/1a2f9425888140427a5555daa6d9e33030032866))
- Restore full float if needed ([`5ec3156`](https://github.com/fiberseq/fibertools-rs/commit/5ec31564fdafaf5a1d9da956dda06ee869c4952c))
- Sam flag docs and man page generation ([`29d21d9`](https://github.com/fiberseq/fibertools-rs/commit/29d21d9fe758df7e0d522889064896f1136b1c07))
- Add completions as a subcommand ([`0cbc39a`](https://github.com/fiberseq/fibertools-rs/commit/0cbc39a48aea83a3f4c98733e74ed4dcb00b37e1))
- Adding a sam flag, fixes #9 ([`6643419`](https://github.com/fiberseq/fibertools-rs/commit/66434192371259e42b872f0c1dd8647c1d38b20d))
- Update 2.0 semi model ([`f9f1275`](https://github.com/fiberseq/fibertools-rs/commit/f9f127595becd27c9e26bccf9831e5a3632ec7a6))
- Fix for unaligned ([`01fd136`](https://github.com/fiberseq/fibertools-rs/commit/01fd13615116a652712f25e2fc10da6f92b3b115))
- Move target name into fiberdata so I can use a par iter, since HeaderView does not have sync... ([`a57548c`](https://github.com/fiberseq/fibertools-rs/commit/a57548cc03c10fcc8751176997364ecebe23f3d2))
- Use bam iterator in ft extract ([`13b0b35`](https://github.com/fiberseq/fibertools-rs/commit/13b0b35f7f40e67c87675687ab14cd1f72118092))
- Dont mess with gpu, nvm ([`574c66d`](https://github.com/fiberseq/fibertools-rs/commit/574c66dcbb9e9eda80501e76027c34b54a7fe96c))
- Dont mess with gpu ([`f6dfd7f`](https://github.com/fiberseq/fibertools-rs/commit/f6dfd7fb710c905bf853c70d705db214356344d1))
- Comment ([`46ceed8`](https://github.com/fiberseq/fibertools-rs/commit/46ceed8fbf39c94a515f7f98ccf54fb29cf5ff5c))
- Make sure tch is only useing 1 thread so rayon can use all the other ones ([`bc45715`](https://github.com/fiberseq/fibertools-rs/commit/bc45715126e80688d92a6eb769dd5e68b3dbebb4))
- Simplify predict chunk for cnn, maybe ([`0db8233`](https://github.com/fiberseq/fibertools-rs/commit/0db8233c134f78747a1192c609a52bca71613292))
- Actually that slowed it down ([`8e4bfdf`](https://github.com/fiberseq/fibertools-rs/commit/8e4bfdf8a8366b2518167c79c3648906ff4ef860))
- Speed up cpu cnn model by reducing batch size ([`8e1f47a`](https://github.com/fiberseq/fibertools-rs/commit/8e1f47a4b46cfea91eaebbcb8eeb6da3f4302b2a))
- Fake model quickly ([`c24a678`](https://github.com/fiberseq/fibertools-rs/commit/c24a67862e1bcfd616e060d7ae81ef76d84a3743))
- Inital adding of a m6A ML filter during prediction ([`95e17f0`](https://github.com/fiberseq/fibertools-rs/commit/95e17f0ccb71ec6a4d3ca819aeaddb31824d9b7f))
- Inital adding of a m6A ML filter during prediction ([`d9dbcad`](https://github.com/fiberseq/fibertools-rs/commit/d9dbcad107291b8bf903b5d7908a226bfd0c638f))
- Merge pull request #8 from mrvollger/main ([`6e28135`](https://github.com/fiberseq/fibertools-rs/commit/6e281357ed98c204f58b4f90d91960f06f3368df))
- Ignore ([`a427005`](https://github.com/fiberseq/fibertools-rs/commit/a42700559815dbee6ef047625065f41d11cb33d8))
- Merge pull request #7 from mrvollger/dev ([`794a668`](https://github.com/fiberseq/fibertools-rs/commit/794a66898105fbaffc3b91a9a7a5086800c06ecb))
- Merge pull request #6 from mrvollger/main ([`168d985`](https://github.com/fiberseq/fibertools-rs/commit/168d985e8c317080c76bc8249962d571278c5f14))
- Doc update ([`5b85aff`](https://github.com/fiberseq/fibertools-rs/commit/5b85aff92564fd37e7074fefb98397b34dd5caa0))
- Merge pull request #5 from mrvollger/dev ([`64f5111`](https://github.com/fiberseq/fibertools-rs/commit/64f51111c6e8c9a6be63fb9132124f8da682622c))
- Change to install from main ([`4e8c53d`](https://github.com/fiberseq/fibertools-rs/commit/4e8c53de5fcbe0f53074d2cc5c8e65fab7d9eb66))
- Nuc readme details ([`34395e7`](https://github.com/fiberseq/fibertools-rs/commit/34395e7e3e3f79c3376db163533a03ab59ddead8))
- 2.2 model final ([`83e4d0d`](https://github.com/fiberseq/fibertools-rs/commit/83e4d0dba3e690ba63fe3f44e64601c4c7f85f07))
- ML filters ([`7b1e479`](https://github.com/fiberseq/fibertools-rs/commit/7b1e479a81f800dac631c14d8cfcf4d99efb8c8f))
- ML filters ([`02742c0`](https://github.com/fiberseq/fibertools-rs/commit/02742c0c619d3f47d46863612a8a345b92ed6a0d))
- Todo ([`cc3c1ea`](https://github.com/fiberseq/fibertools-rs/commit/cc3c1eab598b4c5e4f03a98347a068d39c9e687a))
- Semi model update ([`d4f8146`](https://github.com/fiberseq/fibertools-rs/commit/d4f8146e94940eaba350cc93e06c568fd38b8656))
- Adding use of namedtempfile ([`663f296`](https://github.com/fiberseq/fibertools-rs/commit/663f2961441dde81f8a3e0e44c7166b3315b0146))
- Update model ([`d3c2590`](https://github.com/fiberseq/fibertools-rs/commit/d3c259054dafe09b11bf4bedd3327ddab9bc9c48))
- Trying new website themes ([`1ead9fd`](https://github.com/fiberseq/fibertools-rs/commit/1ead9fdfe807fd1beedc6cdcb1ebba9a3aa1e579))
- Add logo ([`7fd71b2`](https://github.com/fiberseq/fibertools-rs/commit/7fd71b2531648106c6d2a8b938302d695d34b901))
- Move images ([`005ea70`](https://github.com/fiberseq/fibertools-rs/commit/005ea70a53a8a83d3f49e5298eeb5b76b3e4f510))
- Adding 2.2 model ([`00a4461`](https://github.com/fiberseq/fibertools-rs/commit/00a44610df1362f5635aa276e830ada54c4a2eeb))
- Adding semi model file ([`1ffae74`](https://github.com/fiberseq/fibertools-rs/commit/1ffae74badbf89e67d5d320fc734f048e66e98be))
- Logging ([`dad490d`](https://github.com/fiberseq/fibertools-rs/commit/dad490d3a78295dae2959c684450dfb8eb8b2256))
- Add and change env vars ([`ee2a687`](https://github.com/fiberseq/fibertools-rs/commit/ee2a687543e47caf657fa22374516e0be0993ce5))
- Fmt ([`4392f1f`](https://github.com/fiberseq/fibertools-rs/commit/4392f1f4b7eb5c005afc59aeb294a690db44f198))
- Add version to git hash ([`3b19223`](https://github.com/fiberseq/fibertools-rs/commit/3b192236793fe62b20b4693876dcc296a0749821))
- Add git hash for long version ([`54cb7ae`](https://github.com/fiberseq/fibertools-rs/commit/54cb7ae89bbc6e106807b96aa7df20c52766ff39))
- Add option for semi supervized ([`a80df7b`](https://github.com/fiberseq/fibertools-rs/commit/a80df7ba665207ac9fe256733728d19054faf367))
- Add colors ([`aef5a7e`](https://github.com/fiberseq/fibertools-rs/commit/aef5a7e77276e09f68500950841daf541f510b15))
- Ci ([`297ff99`](https://github.com/fiberseq/fibertools-rs/commit/297ff9981b6a99e362371fcdacd93d30e847702c))
- Docs ([`98dd885`](https://github.com/fiberseq/fibertools-rs/commit/98dd885d0bae12eda518968e8c301a957a5eefae))
- Moving base mods and adding function to get forward bases ([`eac73c6`](https://github.com/fiberseq/fibertools-rs/commit/eac73c65bdacccb8aa612bd5cf753da5dacde327))
- Description ([`76aba78`](https://github.com/fiberseq/fibertools-rs/commit/76aba78e1eae1591d2c526112adb01711b5584e5))
- Ideas for v0.0.11 ([`1a9114d`](https://github.com/fiberseq/fibertools-rs/commit/1a9114d82fbd5dd1b65507c27b9e60976110c244))
- Files moved ([`ff85512`](https://github.com/fiberseq/fibertools-rs/commit/ff855127f77673e445ac14b2fddcf4080e1c6031))
- Docs ([`d3b8e62`](https://github.com/fiberseq/fibertools-rs/commit/d3b8e629449dd40764f2e2ebb58d89fd797f3cd9))
- Merge pull request #4 from mrvollger/gpu ([`778ad7a`](https://github.com/fiberseq/fibertools-rs/commit/778ad7aafa0ad4d69808594f85b75c2fe6c57179))
- Remove unused and check secondary ([`828e684`](https://github.com/fiberseq/fibertools-rs/commit/828e6840ddfb8483cfa233a3e4f25b9db9b33df7))
- Fix sucsess counter ([`3688365`](https://github.com/fiberseq/fibertools-rs/commit/3688365655c95e68cc43109b6ff8bafb91fbee7c))
- Move model shape into consts ([`37d8167`](https://github.com/fiberseq/fibertools-rs/commit/37d81677cc77c5ddb628089f86df0a05648b27d5))
- Progress ([`db2b2e0`](https://github.com/fiberseq/fibertools-rs/commit/db2b2e0827559641342e5b8b6d81281b70994125))
- Batchsize ([`7e2cd39`](https://github.com/fiberseq/fibertools-rs/commit/7e2cd39b5c1929b8a96c13595a47e4e5ddd5375f))
- Msg ([`a4e96b0`](https://github.com/fiberseq/fibertools-rs/commit/a4e96b026ae9469468aa55da24a70dd68435fb9d))
- Msg ([`ead03fa`](https://github.com/fiberseq/fibertools-rs/commit/ead03faf56aeee5ac8f49be40d6a283cea930ff1))
- Msg ([`9c88c03`](https://github.com/fiberseq/fibertools-rs/commit/9c88c03690a694fe19c5d39b9218a4ac76960e41))
- Change xgb batch size to 1 because it is fastest on cpu ([`5f83ef4`](https://github.com/fiberseq/fibertools-rs/commit/5f83ef4a609c57cf43abbc6655cc66c819d4f355))
- Add zero check ([`3a8c74b`](https://github.com/fiberseq/fibertools-rs/commit/3a8c74b74fd3c7073149042a5be9f9dd02661006))
- Make batch size defaults ([`c45eeda`](https://github.com/fiberseq/fibertools-rs/commit/c45eeda30cdf9eb38fefbd51ffc71d61332cf24a))
- Make batch size an option ([`5b5c86d`](https://github.com/fiberseq/fibertools-rs/commit/5b5c86d7c3298bbe931373389cb946aaed07a500))
- Chunk ([`bb79e62`](https://github.com/fiberseq/fibertools-rs/commit/bb79e62b4e069aab8d4240b2702b16deecf40cd2))
- Move progress ([`5d09a54`](https://github.com/fiberseq/fibertools-rs/commit/5d09a54d5d2d1f47e3b3cda8b764fa7974867db8))
- Adding batch of 10 reads all at once to gpu ([`34c8cbe`](https://github.com/fiberseq/fibertools-rs/commit/34c8cbe6ae75e9c46e390849075cd33ca4940729))
- Adding more install instructions for gpu ([`66d0eae`](https://github.com/fiberseq/fibertools-rs/commit/66d0eae9a7a86e6d05180506e88f305dac575abb))
- Comment ([`ec4c1e9`](https://github.com/fiberseq/fibertools-rs/commit/ec4c1e990d87fa63f1bad1d0d07ae9f085a0ec4f))
- Merge pull request #3 from mrvollger/gpu ([`1529b9e`](https://github.com/fiberseq/fibertools-rs/commit/1529b9ea32c01004a8e458bac4eb6a74c5194cf0))
- Move prgress to after map ([`765ba52`](https://github.com/fiberseq/fibertools-rs/commit/765ba52016a8d43d2b508e091e7b944e08dff4c1))
- Move model to gpu? ([`a928875`](https://github.com/fiberseq/fibertools-rs/commit/a928875bb494e27a65a1b6d178f70923fc9e446f))
- Move vec to gpu? ([`b5853d5`](https://github.com/fiberseq/fibertools-rs/commit/b5853d5f45ea67d144476e78e05488e3e23496a1))
- Move vec to gpu? ([`a213c7c`](https://github.com/fiberseq/fibertools-rs/commit/a213c7c03d5163a701246ce5dbc630db4337ebf9))
- Check device ([`77d5cac`](https://github.com/fiberseq/fibertools-rs/commit/77d5cac9bed0537d8045867b29de13cbbc56aa78))
- Remove dash ([`31728e6`](https://github.com/fiberseq/fibertools-rs/commit/31728e688be9831c62b770f377c8be7bf5fc1874))
- Reorder readme ([`79c4974`](https://github.com/fiberseq/fibertools-rs/commit/79c497452e3c52a7ffef0c781ce23a1ad67a5831))
- More details on cnn install ([`5bcbef8`](https://github.com/fiberseq/fibertools-rs/commit/5bcbef8ee5d9db7626dafcf82b4782053f67c8e7))
- Fix program line for ft ([`c30ffa3`](https://github.com/fiberseq/fibertools-rs/commit/c30ffa3bdcbada6d2932656bae72e82dd033cf51))
- Caps ([`ac9ecfb`](https://github.com/fiberseq/fibertools-rs/commit/ac9ecfbbb4ed22d423954348419ae48f50c98c88))
- Clean ([`93839d3`](https://github.com/fiberseq/fibertools-rs/commit/93839d3e6667966fb51a9a9e7c3924d9ce84b6f5))
- Clean ([`3f5fbec`](https://github.com/fiberseq/fibertools-rs/commit/3f5fbec24ce2e63ec7517d5abafb011a245f1072))
- Clean ([`25d11b0`](https://github.com/fiberseq/fibertools-rs/commit/25d11b025c3e907c5f0d11a3e2a28628bd4742f6))
- Get ready for the next version ([`540b76c`](https://github.com/fiberseq/fibertools-rs/commit/540b76c1e8789f7323fb46f42637ec3977dcb2bb))
- Typo ([`0fc22d1`](https://github.com/fiberseq/fibertools-rs/commit/0fc22d1d6f5fb7715f0d5adb48515815eadd24fc))
- Add doc strings ([`bcdd7d0`](https://github.com/fiberseq/fibertools-rs/commit/bcdd7d0ec4a077693fe117ecb7eb3a4dd73cb45a))
- Docs ([`ddd998f`](https://github.com/fiberseq/fibertools-rs/commit/ddd998fe135da32f5e6ffa7b85d5f8a2e34c2de8))
- Adding a PG tag to the m6a output ([`3d004aa`](https://github.com/fiberseq/fibertools-rs/commit/3d004aaffbac11b156e2ea67ea8a0abb99e6a770))
- Typo ([`14d69aa`](https://github.com/fiberseq/fibertools-rs/commit/14d69aab04fc180cf158e8b0d30b7f70a64dc6d7))
- Update release script for CNN ([`5c25138`](https://github.com/fiberseq/fibertools-rs/commit/5c25138922fd06b11e4f91509d2b336242cabe35))
- A new release for bioconda which will hopefully allow the cnn by default ([`85305ab`](https://github.com/fiberseq/fibertools-rs/commit/85305ab668c9298008b7d8c7116c88f108b02218))
- Increase chunk size ([`a028151`](https://github.com/fiberseq/fibertools-rs/commit/a028151da378709cc81085417a145df2e53d7982))
- For #2 try 2 ([`950d7db`](https://github.com/fiberseq/fibertools-rs/commit/950d7db10a84b9c55f4c53f854ac84c91e8b06bb))
- For #2 ([`de08a90`](https://github.com/fiberseq/fibertools-rs/commit/de08a90f752b1a94b15486bdced4a42b6a093d21))
- Stadardize message formating ([`178ef3c`](https://github.com/fiberseq/fibertools-rs/commit/178ef3cadd5922fa65b56398bd41b5700745d25e))
- Stadardize message formating ([`0fc4761`](https://github.com/fiberseq/fibertools-rs/commit/0fc4761a6892e862e3dbb1c5c0e96677e1250f4e))
- Add conda-forge to channel ([`dd65ce9`](https://github.com/fiberseq/fibertools-rs/commit/dd65ce9fab9ddc5e9ff9035eb60fd1653508b73d))
- Add detail to cli ([`e081131`](https://github.com/fiberseq/fibertools-rs/commit/e081131fe8643caf0b2050f19c31a1ef58517f07))
- Adding more headings in CLI ([`c8922fd`](https://github.com/fiberseq/fibertools-rs/commit/c8922fd4354e335bc138458916366d0d5e1c349a))
- Making some options global so they can go anywhere on the cli ([`1ac197d`](https://github.com/fiberseq/fibertools-rs/commit/1ac197dde3e03289f2669829bfb2e1c1d651774b))
- Making some options global so they can go anywhere on the cli ([`1f68cbe`](https://github.com/fiberseq/fibertools-rs/commit/1f68cbe5544c8eb0ac63f8aeada140bf56364dac))
- Allow bam reading and writing from stdin for m6a-predict ([`c977510`](https://github.com/fiberseq/fibertools-rs/commit/c9775102d429f0e6ce0afae9219107b3f78aa4f0))
- Add warning for missing hifi kinetics ([`21fe212`](https://github.com/fiberseq/fibertools-rs/commit/21fe212d8c51faffc74f7806cfc2f710f142aeb4))
- Update install ([`3890f37`](https://github.com/fiberseq/fibertools-rs/commit/3890f379a35303edf2f51ebbcafb7863916f819d))
- Update install ([`e4d0aad`](https://github.com/fiberseq/fibertools-rs/commit/e4d0aad2f8aeb273c9660e7150a366d2384d03a4))
- Prep for release ([`5a79467`](https://github.com/fiberseq/fibertools-rs/commit/5a7946757ea13b261e65bb0a5298442674149a62))
- Prep for release ([`95c34ca`](https://github.com/fiberseq/fibertools-rs/commit/95c34ca6cc7bbffc6ab1637593c31e7b68fb4308))
- Prep for release ([`f387eb4`](https://github.com/fiberseq/fibertools-rs/commit/f387eb432f8d22bf020c018396524cff791627fe))
- Prep for release ([`7057bdf`](https://github.com/fiberseq/fibertools-rs/commit/7057bdf64fc40a3b345cef80f39f331c29e7b69b))
- Check for RG ([`2a32603`](https://github.com/fiberseq/fibertools-rs/commit/2a32603dc7caaa3928de4a4fc84c29341fe8a49d))
- Typo ([`812dff2`](https://github.com/fiberseq/fibertools-rs/commit/812dff2de3d75378d6e940aa4cff651362387209))
- War messages ([`7ff93b0`](https://github.com/fiberseq/fibertools-rs/commit/7ff93b0420fdb67e3bd814f431f365b6ee203a20))
- Updating docs for predict-m6a ([`41ac119`](https://github.com/fiberseq/fibertools-rs/commit/41ac119e82923f5148390c6c96b0fd6cb0a5eac7))
- Updating docs for predict-m6a ([`d9aecda`](https://github.com/fiberseq/fibertools-rs/commit/d9aecdabad3fa75bfe3623e674830222c3ccaece))
- Updating docs for predict-m6a ([`18213df`](https://github.com/fiberseq/fibertools-rs/commit/18213dff5bcb78c70d2b8ed3df96535378cafdf6))
- Add predict to docs ([`4ccb774`](https://github.com/fiberseq/fibertools-rs/commit/4ccb7743d4aef11c2818a66d73e400982d3338e8))
- Secondary check ([`8e34095`](https://github.com/fiberseq/fibertools-rs/commit/8e34095bb3be8642be75fec0e656bec888fce659))
- Cleaning up ([`1ee535d`](https://github.com/fiberseq/fibertools-rs/commit/1ee535dd6212baee988b5dc15d64e3f5d84e6e64))
- Filter for alignment types ([`d504543`](https://github.com/fiberseq/fibertools-rs/commit/d5045431cd4380267ed50aa0ea3e01b1503fe1f5))
- Clippy ([`3c4088d`](https://github.com/fiberseq/fibertools-rs/commit/3c4088d449aec818cb0d00c04e72170d1a7ab7e9))
- Rev qual? ([`603adb4`](https://github.com/fiberseq/fibertools-rs/commit/603adb48cdbe74b83e53f61182b0ff6e269f2714))
- Rename ([`9ad12a7`](https://github.com/fiberseq/fibertools-rs/commit/9ad12a7ee31499b1a7dd91e579fcf4d000d29003))
- Remove filter ([`0b58b77`](https://github.com/fiberseq/fibertools-rs/commit/0b58b77fe7f56680b2fbbb8edd61a4b8f8ac155f))
- Updating basemod class ([`b86d481`](https://github.com/fiberseq/fibertools-rs/commit/b86d481431764a3c533f692f582524bd59674bbe))
- New bigger ML models ([`00257fa`](https://github.com/fiberseq/fibertools-rs/commit/00257fa814c7a3794701e877863e0040f4ac7094))
- I can now write ML MM tags using the BaseMods data structure ([`e0d546a`](https://github.com/fiberseq/fibertools-rs/commit/e0d546acdaa74d1613dc730dbf1da2093e16bb1f))
- Filter mapped reads out of the process since it doesnt work right now ([`657b72a`](https://github.com/fiberseq/fibertools-rs/commit/657b72afbb7b5901c13e84d03048ca3536539c3a))
- Check for missing liftovers, fiz ([`38a7dc3`](https://github.com/fiberseq/fibertools-rs/commit/38a7dc34202d11a63890bd4fcb5b297a1a20a6ba))
- Check for missing liftovers, fiz ([`e91f54a`](https://github.com/fiberseq/fibertools-rs/commit/e91f54ad68a74162144e606a5e0116b1ac05673e))
- Check for missing liftovers ([`0ce2c08`](https://github.com/fiberseq/fibertools-rs/commit/0ce2c0816ef9884f1b60091bc4db18bd5c59a0bf))
- Fix prediction for mapped data? ([`ec6ec5a`](https://github.com/fiberseq/fibertools-rs/commit/ec6ec5aa91610df6bdb6dfd80a9f16eaac8b63c9))
- Fix for real RC values with qual ([`db2aad9`](https://github.com/fiberseq/fibertools-rs/commit/db2aad93f753c078e1be7a6c7233a038873e5c7f))
- Clean unused files and rename things in cnn ([`a340879`](https://github.com/fiberseq/fibertools-rs/commit/a340879415fab6ffb4cca167aa53466840a3b671))
- Clean unused files and rename things in cnn ([`ce6335f`](https://github.com/fiberseq/fibertools-rs/commit/ce6335ffd2a8fad8af11d84ee4e3ea579cf12d35))
- Clean unused files and rename things ([`4e7c710`](https://github.com/fiberseq/fibertools-rs/commit/4e7c710ffa395e9773cd3411bf8d003758b314da))
- Remove filter ([`812a93e`](https://github.com/fiberseq/fibertools-rs/commit/812a93e3718ed719cddd3febade167b8248c4138))
- Remove filter ([`bc4b80c`](https://github.com/fiberseq/fibertools-rs/commit/bc4b80c77fa7ce0d212e64abe7e5f8596dc11ff8))
- Remove filter ([`9a7f5ff`](https://github.com/fiberseq/fibertools-rs/commit/9a7f5ff577f8c87cc7c5fe22f94b1de31320142d))
- Remove filter ([`fc175ee`](https://github.com/fiberseq/fibertools-rs/commit/fc175eee6f26ea4040a25d1582998bf105250abe))
- Remove filter ([`30a3119`](https://github.com/fiberseq/fibertools-rs/commit/30a31192b3a329405d91f062d6cd90f64064c522))
- Remove filter ([`910014c`](https://github.com/fiberseq/fibertools-rs/commit/910014c15d3b9b4f1db027547e7384e4d7ba901c))
- Remove filter ([`fbaf936`](https://github.com/fiberseq/fibertools-rs/commit/fbaf936eea3b965c0c10ddd187508aee90578cd0))
- Remove filter ([`c7ab03d`](https://github.com/fiberseq/fibertools-rs/commit/c7ab03df80d2e2c6779fca75d14734894ca34dc8))
- Remove filter ([`ce61ed5`](https://github.com/fiberseq/fibertools-rs/commit/ce61ed51d07f912a9bb17ac986c7ce14c60787b3))
- Remove filter ([`e5df2bf`](https://github.com/fiberseq/fibertools-rs/commit/e5df2bf8fce36c6b5b6a294bb90e6b0fa2fe64ac))
- Remove filter ([`b52f7e7`](https://github.com/fiberseq/fibertools-rs/commit/b52f7e7097374c29200eb2aa38430931103a3b8d))
- Remove filter ([`e51d1c8`](https://github.com/fiberseq/fibertools-rs/commit/e51d1c8c988bc0ad5562bea38e817345ef39c5bc))
- Remove filter ([`df4ef9a`](https://github.com/fiberseq/fibertools-rs/commit/df4ef9a4e9c9fb49e822c0dd8d8039f29fa9c9b2))
- Remove filter ([`d8dcf92`](https://github.com/fiberseq/fibertools-rs/commit/d8dcf929ad5d4d87b390740651fbc9cef2cf94ef))
- Remove filter ([`88a02c8`](https://github.com/fiberseq/fibertools-rs/commit/88a02c8b6e416ac586bb544cfda9c0902992a0f4))
- Remove filter ([`a28e051`](https://github.com/fiberseq/fibertools-rs/commit/a28e0515f52fc0d5145217700d075e73118dd4bd))
- Remove filter ([`9b2ea36`](https://github.com/fiberseq/fibertools-rs/commit/9b2ea36b8d0ab60e57230c8abe47a6aac4eeda00))
- Remove filter ([`44ca3c7`](https://github.com/fiberseq/fibertools-rs/commit/44ca3c7d6c7369a6ad46dd954775be45624c4e41))
- Remove filter ([`308f881`](https://github.com/fiberseq/fibertools-rs/commit/308f88133df22b1e0d60df1eb232d3894e46e1c2))
- Assert ([`333494c`](https://github.com/fiberseq/fibertools-rs/commit/333494c30b0315e89ff249fecd87c1ede5ae8672))
- Making a combined output for pos, ref_pos, and qual ([`3bbc7a1`](https://github.com/fiberseq/fibertools-rs/commit/3bbc7a16d8ff66fc2d53a41d08badcf3c1ab460c))
- Making a combined output for pos, ref_pos, and qual ([`39e5d3a`](https://github.com/fiberseq/fibertools-rs/commit/39e5d3aee3a00d5b6dd8565ef2fdc3134483ee19))
- Making a combined output for pos, ref_pos, and qual ([`537e38e`](https://github.com/fiberseq/fibertools-rs/commit/537e38e4f5c6b9fdd6b81a4f49854cbc57e2f7c6))
- Making a combined output for pos, ref_pos, and qual ([`1c4c5b7`](https://github.com/fiberseq/fibertools-rs/commit/1c4c5b72d7096b975089cce4c6bff9d5927997dc))
- Making a combined output for pos, ref_pos, and qual ([`34d3a82`](https://github.com/fiberseq/fibertools-rs/commit/34d3a8285e9b7cc839c012b7a07647fc5c68da52))
- Making a combined output for pos, ref_pos, and qual ([`8c09829`](https://github.com/fiberseq/fibertools-rs/commit/8c09829e4de4763f12fa0c9cf1409227c9b5514d))
- Another try ([`1d4d939`](https://github.com/fiberseq/fibertools-rs/commit/1d4d93971b17be4c11b6ab43ce061c479f4ecfe2))
- Clear earlier ([`7d262ef`](https://github.com/fiberseq/fibertools-rs/commit/7d262efb1223cc7110c34619b973ace0c20d82d3))
- Here ([`9d1a815`](https://github.com/fiberseq/fibertools-rs/commit/9d1a8155b189a5ef66331a2f6e39c0a4e1904a83))
- Removing remove ([`488d5d5`](https://github.com/fiberseq/fibertools-rs/commit/488d5d5303d363d69f99de060ac010414242c343))
- Moving basemods ([`ac2ecca`](https://github.com/fiberseq/fibertools-rs/commit/ac2eccae144d150a192ee85b41958c300e289412))
- Fix qual? ([`00828e1`](https://github.com/fiberseq/fibertools-rs/commit/00828e11f51639608b97cabe5c00b6f54f608a61))
- Fix qual? ([`8bd2e41`](https://github.com/fiberseq/fibertools-rs/commit/8bd2e41723aa2005495164ca0431193acf80d7e0))
- Fix qual? ([`d69e61d`](https://github.com/fiberseq/fibertools-rs/commit/d69e61d0544d08b6d57925646f99ef26b73f627d))
- Add missing 255 ([`048eb6d`](https://github.com/fiberseq/fibertools-rs/commit/048eb6dbc9a686cfb7030f9425963d275e5c655d))
- Adding ability to extract full probablities from mp tag if it is there and requested ([`e981381`](https://github.com/fiberseq/fibertools-rs/commit/e981381b76cb8fb2a1265fef3cce3ae18353c2ef))
- Optionally add full float ml prediction to bam ([`3b8f463`](https://github.com/fiberseq/fibertools-rs/commit/3b8f463f09ad8878c1040f7909983a959c341f63))
- Add model for 2.2 chemsitry with xgb ([`8ae2a96`](https://github.com/fiberseq/fibertools-rs/commit/8ae2a96c5b63965c91eb8ebad679184effbc23f4))
- Check for unmapped ([`300ca87`](https://github.com/fiberseq/fibertools-rs/commit/300ca8748d63aeddbbd2bf68e13488b0dee5cb05))
- Refactor xgb into its own file ([`1f38ace`](https://github.com/fiberseq/fibertools-rs/commit/1f38aced0b2c59d0e9135474f0d737297d8c092d))
- Move cnn into a feature and its own file, and compile xgb predict by deafult ([`e4c3be2`](https://github.com/fiberseq/fibertools-rs/commit/e4c3be2c36feb5ee5c2c821a8ac085b2352e9be0))
- Move cnn into a feature and its own file, and compile xgb predict by deafult ([`005327b`](https://github.com/fiberseq/fibertools-rs/commit/005327b5c878d850b813c4297b432097ed66a5ad))
- Hide cnn predictions behind a feature flag, aka not compiled by default ([`8a811ca`](https://github.com/fiberseq/fibertools-rs/commit/8a811ca7780c8721847746157d046c681bb06f4a))
- Updating docs with new help messages ([`a0dfed9`](https://github.com/fiberseq/fibertools-rs/commit/a0dfed979ecbdcd131a854fb6860224e6f81805a))
- Adding seq remove option and quality addition option for extract-alll ([`6490336`](https://github.com/fiberseq/fibertools-rs/commit/6490336b9cd1b88f70725239098b35db8580e122))
- Log scale scores ([`45ed225`](https://github.com/fiberseq/fibertools-rs/commit/45ed225ea3e67f2adf34f7bd3e470558c3f7f3cd))
- Log scale scores ([`e1550ea`](https://github.com/fiberseq/fibertools-rs/commit/e1550eae9d4bef31f951783574fbe38b4d87c17e))
- Log scale scores ([`e6775b9`](https://github.com/fiberseq/fibertools-rs/commit/e6775b94933c69e84cf205185beed39384741228))
- Log scale scores ([`99c2307`](https://github.com/fiberseq/fibertools-rs/commit/99c23070b95f706c150d4eca8e45ee32cffc1e1d))
- Log scale scores ([`a219299`](https://github.com/fiberseq/fibertools-rs/commit/a219299b53a08cf9782d6000622b77966b67479f))
- Log scale scores ([`7fe2f64`](https://github.com/fiberseq/fibertools-rs/commit/7fe2f64ca0a3f9dfa1e0d6735081edeec719d477))
- Log scale scores ([`fa3fe52`](https://github.com/fiberseq/fibertools-rs/commit/fa3fe52ebca70a948707c6ad6a510399d08edcef))
- Log scale scores ([`d0c765f`](https://github.com/fiberseq/fibertools-rs/commit/d0c765f64ea07fcc6d5c7949596fcf1f26fdb699))
- Log scale scores ([`7599a95`](https://github.com/fiberseq/fibertools-rs/commit/7599a957f9a2a55b784eca8d1d3fd1e7e6b424eb))
- Log scale scores ([`cd19887`](https://github.com/fiberseq/fibertools-rs/commit/cd1988728a79595fdee65efa8eeae0accc5195d4))
- Log scale scores ([`55c9d76`](https://github.com/fiberseq/fibertools-rs/commit/55c9d76d75630b5e72669cdd0a51177ab482c39c))
- Log scale scores ([`7302915`](https://github.com/fiberseq/fibertools-rs/commit/73029154ad45b76b64833bc52ef2e4035bd68120))
- Log scale scores ([`671fd39`](https://github.com/fiberseq/fibertools-rs/commit/671fd39bf67b32071abec8fd8610cd7da48de4c7))
- Log scale scores ([`bace110`](https://github.com/fiberseq/fibertools-rs/commit/bace110f61504ce7e50e7e9507a045b7c5303638))
- Log scale scores ([`b16e97a`](https://github.com/fiberseq/fibertools-rs/commit/b16e97a859ba0dcd724c47b4f99e941416e411b7))
- Log scale scores ([`b896405`](https://github.com/fiberseq/fibertools-rs/commit/b896405d638955cfc173c946fe1792b76d82918a))
- Log scale scores ([`fa6080e`](https://github.com/fiberseq/fibertools-rs/commit/fa6080ec45281967d1e41f88ff6dd1f516f45937))
- Log scale scores ([`c5a6dc9`](https://github.com/fiberseq/fibertools-rs/commit/c5a6dc9360a8b7edffd68aa028cd80989e9dcf5d))
- Log scale scores ([`85cdc97`](https://github.com/fiberseq/fibertools-rs/commit/85cdc97adb7c1901d06e44baff256bdee9106c88))
- Log scale scores ([`682428c`](https://github.com/fiberseq/fibertools-rs/commit/682428cdb60717827b4364df2590cdfb62f59bf4))
- Log scale scores ([`304cd12`](https://github.com/fiberseq/fibertools-rs/commit/304cd124dc39db3b7a543ba4cc3c11c92026ffb8))
- Log scale scores ([`b1b07b6`](https://github.com/fiberseq/fibertools-rs/commit/b1b07b6e6d0fc7467200a711b7af9e3ccb339b6e))
- Log scale scores ([`0f8605e`](https://github.com/fiberseq/fibertools-rs/commit/0f8605e86c329ac9e7d6232dee9365eb872d69e8))
- Log scale scores ([`2d57517`](https://github.com/fiberseq/fibertools-rs/commit/2d57517b48f0a098a628bee0b065fabb1d8561ce))
- Log scale scores ([`520405a`](https://github.com/fiberseq/fibertools-rs/commit/520405a4488297abe9223252ccd40419dd1f711d))
- Log scale scores ([`3bdd3dc`](https://github.com/fiberseq/fibertools-rs/commit/3bdd3dc6ba3f3ea6276e24919f8eaf2791f6410f))
- Log scale scores ([`0b1e12a`](https://github.com/fiberseq/fibertools-rs/commit/0b1e12a57d2f7cbd7882d750b9984e8dd9153612))
- Log scale scores ([`b1cec34`](https://github.com/fiberseq/fibertools-rs/commit/b1cec34ec17a6ac686c12c52406fb4d6ad11a3ad))
- Log scale scores ([`84df281`](https://github.com/fiberseq/fibertools-rs/commit/84df281b53031c3f6e4b54a5b3dbfb22857f50d3))
- Log scale scores ([`9f9271e`](https://github.com/fiberseq/fibertools-rs/commit/9f9271e92f916b64c7cb69f9069a81d3c56cac87))
- Log scale scores ([`8bb047c`](https://github.com/fiberseq/fibertools-rs/commit/8bb047ce971b1ad34d58d501269e8dae3e66c113))
- Log scale scores ([`707cada`](https://github.com/fiberseq/fibertools-rs/commit/707cada84d493e8b637a155d871f109dd93631d3))
- Log scale scores ([`368cf43`](https://github.com/fiberseq/fibertools-rs/commit/368cf438dd3e3cc59f2d5602fead89ef990cba83))
- Log scale scores ([`efed35f`](https://github.com/fiberseq/fibertools-rs/commit/efed35f1e1e02701bec4becc2130671de27543ee))
- Log scale scores ([`897cc0e`](https://github.com/fiberseq/fibertools-rs/commit/897cc0e9c917a7d4b6144322cea065b567983f91))
- Log scale scores ([`0534a44`](https://github.com/fiberseq/fibertools-rs/commit/0534a449e3b1cfcbc35c0649f08defaef4b2b44a))
- Log scale scores ([`2cc55d6`](https://github.com/fiberseq/fibertools-rs/commit/2cc55d6e1089fdf689bb43d886043305772b1d6b))
- Log scale scores ([`9bc80b0`](https://github.com/fiberseq/fibertools-rs/commit/9bc80b0231095c1f0d5391c13724202ffd5a840d))
- Log scale scores ([`e8ef551`](https://github.com/fiberseq/fibertools-rs/commit/e8ef55148364e0042ef70da970a9007553e0ff1d))
- Log scale scores ([`ee5645d`](https://github.com/fiberseq/fibertools-rs/commit/ee5645dd2e35ffd86958bf59a0914367457a4a01))
- Log scale scores ([`44a4a5d`](https://github.com/fiberseq/fibertools-rs/commit/44a4a5d17fcb1e410c70f1bbabe038f74c1474d3))
- Log scale scores ([`5a02c02`](https://github.com/fiberseq/fibertools-rs/commit/5a02c0287b28ef3467514f94542e606b997e902e))
- Log scale scores ([`7ef8d25`](https://github.com/fiberseq/fibertools-rs/commit/7ef8d256e62f9b541630fc87acc757ec5f4fd86f))
- Log scale scores ([`bfb113f`](https://github.com/fiberseq/fibertools-rs/commit/bfb113fcf6b4fabaddb2a5eccca68a400f49dacd))
- Log scale scores ([`686e6c4`](https://github.com/fiberseq/fibertools-rs/commit/686e6c4cb1af841c83caa3249148e644d3133dfd))
- Log scale scores ([`6d9c943`](https://github.com/fiberseq/fibertools-rs/commit/6d9c94345b347b1b77e8b29505552678be9fe088))
- Log scale scores ([`b0d8f3c`](https://github.com/fiberseq/fibertools-rs/commit/b0d8f3cac7ef61e2e4ee6092ea7103ae1e4f946c))
- Log scale scores ([`79078ab`](https://github.com/fiberseq/fibertools-rs/commit/79078abbf5a019c987dcff0b774c3ef89047cb34))
- Log scale scores ([`9049c72`](https://github.com/fiberseq/fibertools-rs/commit/9049c724f8f2d55e800b03cc078986672a794078))
- Log scale scores ([`add7ba8`](https://github.com/fiberseq/fibertools-rs/commit/add7ba8711c0d77abcba1b2fad2edfa32bf28f02))
- Log scale scores ([`fe90219`](https://github.com/fiberseq/fibertools-rs/commit/fe90219412724b1f6f8181f58a15bd136ccf9661))
- Log scale scores ([`83cae68`](https://github.com/fiberseq/fibertools-rs/commit/83cae683ca71556c2fe6a71544a196451d56077e))
- Log scale scores ([`523253c`](https://github.com/fiberseq/fibertools-rs/commit/523253c30aeff332d69cc20abcaa96acff8dbe88))
- Log scale scores ([`490d1d2`](https://github.com/fiberseq/fibertools-rs/commit/490d1d2a00ed9c7cf1e5eeeb68cf27ee3822fd24))
- Log scale scores ([`f5015d3`](https://github.com/fiberseq/fibertools-rs/commit/f5015d3490a20bd0aa0d7fe89f34ac4933a133d9))
- Log scale scores ([`02c90f8`](https://github.com/fiberseq/fibertools-rs/commit/02c90f8007c33ffe6ba1995113c84ff5954a9fa6))
- Log scale scores ([`aa39635`](https://github.com/fiberseq/fibertools-rs/commit/aa396350b08fc77e9a63d7997eecbe73ac063ddc))
- Log scale scores ([`595907a`](https://github.com/fiberseq/fibertools-rs/commit/595907a0ccf59e34cc35ccdd0a824afacd948a72))
- Log scale scores ([`25d2d20`](https://github.com/fiberseq/fibertools-rs/commit/25d2d205ce22f2376332c68124c0fcce5245ea23))
- Log scale scores ([`1325001`](https://github.com/fiberseq/fibertools-rs/commit/132500194e3e2984e1496a09be87602bd4366a22))
- Log scale scores ([`2319670`](https://github.com/fiberseq/fibertools-rs/commit/2319670bed73400af75c058248616a8719069c7b))
- Log scale scores ([`6d366ce`](https://github.com/fiberseq/fibertools-rs/commit/6d366cea42b8c9be9c0c7e2c7f21714d8f381aa0))
- Log scale scores ([`c1c5d7b`](https://github.com/fiberseq/fibertools-rs/commit/c1c5d7b64bfec0ab873c3969a107ff9ec11446db))
- Fix hotone encodeing? ([`13f3e19`](https://github.com/fiberseq/fibertools-rs/commit/13f3e19f462a291b94496f154ee2a243421226e7))
- Fix hotone encodeing? ([`549d7f1`](https://github.com/fiberseq/fibertools-rs/commit/549d7f1acb2914ad204e82e1953b57d9604450b6))
- Fix offest in leading count? ([`5d6ffe2`](https://github.com/fiberseq/fibertools-rs/commit/5d6ffe2390336d061e2490102ffff7cf8b095db0))
- Fix PW and IPW in the wrong direction on - strand ([`9d68bb2`](https://github.com/fiberseq/fibertools-rs/commit/9d68bb2ffbc5f4b449b50ec68e974c46f8c2afaa))
- Update ([`f3e742c`](https://github.com/fiberseq/fibertools-rs/commit/f3e742c48283f39c7216e3b4ef8c5158e0094408))
- Boost ([`ca24cfb`](https://github.com/fiberseq/fibertools-rs/commit/ca24cfb341d24cf1f5161a9a543a05f44654e687))
- Cnn model update ([`9466260`](https://github.com/fiberseq/fibertools-rs/commit/946626075d8782e9758c1c1646243d42b2fc4db4))
- Cnn model update ([`e235077`](https://github.com/fiberseq/fibertools-rs/commit/e235077bfb572f790b39a8b7a8a98f1d59da87e9))
- Cnn model update ([`faeb253`](https://github.com/fiberseq/fibertools-rs/commit/faeb2536fb4defaf2cef55b20daea1e80162a171))
- Cnn model update ([`b434fb1`](https://github.com/fiberseq/fibertools-rs/commit/b434fb16a6a91a237eb203a36f865db356a312ae))
- Cnn model update ([`ba23e9b`](https://github.com/fiberseq/fibertools-rs/commit/ba23e9bef2473f04af3a08b76bac60030a3189b7))
- Revetn cnn model ([`c6d907e`](https://github.com/fiberseq/fibertools-rs/commit/c6d907ece0a050663116912fb0cd4c74f39b7fe4))
- New cnn model ([`cc7cdd5`](https://github.com/fiberseq/fibertools-rs/commit/cc7cdd518bf0acac682e736de6e7354e028e47bc))
- Adding m6a qual to all output ([`e6bbdc8`](https://github.com/fiberseq/fibertools-rs/commit/e6bbdc85912ac2f471ea745cb4797cc1e8e204f8))
- Adding a new m6a call that also gets quals ([`93a005f`](https://github.com/fiberseq/fibertools-rs/commit/93a005fa1813b9571010429472bf7afa6bf6112b))
- New test ([`b74871c`](https://github.com/fiberseq/fibertools-rs/commit/b74871c1a344a4b1d4c0e77fca98bcc8adfccc92))
- New test ([`17dbc9d`](https://github.com/fiberseq/fibertools-rs/commit/17dbc9dcd430d0bd90635c240309f31a05d0595b))
- Larged model ([`f10c4d3`](https://github.com/fiberseq/fibertools-rs/commit/f10c4d3039996a5cce096ca62dda3f693ea3d7db))
- Adding comple flags for tch? ([`b81248a`](https://github.com/fiberseq/fibertools-rs/commit/b81248aec0e5fcf7235f34c2001577b5de2b6456))
- Adding comple flags for tch? ([`a6c324f`](https://github.com/fiberseq/fibertools-rs/commit/a6c324ff3bbcb9533a70b24ddafb7b38607054f4))
- Adding a cnn flag ([`1184418`](https://github.com/fiberseq/fibertools-rs/commit/1184418abfe60ba9a544843dee371e4cbfae47f2))
- Adding the cnn model? ([`f085bac`](https://github.com/fiberseq/fibertools-rs/commit/f085bac197e84e3a38deb8c8902d0b6ee039d64a))
- Adding out threads ([`da1f980`](https://github.com/fiberseq/fibertools-rs/commit/da1f98012e79b7b07a29f5cae0ccaf30541645b0))
- Remove tmep ([`458a062`](https://github.com/fiberseq/fibertools-rs/commit/458a06204e6b6e4f8bd4811b5538a8b8cfa6fe77))
- Log ([`6e8f9e6`](https://github.com/fiberseq/fibertools-rs/commit/6e8f9e6b73c831fed0efe530029bd98a75cab47d))
- Clippy ([`5670402`](https://github.com/fiberseq/fibertools-rs/commit/56704026d83a00fdae7eaad4213ab850c65e336b))
- Moved to a rust xgboost ([`0af3137`](https://github.com/fiberseq/fibertools-rs/commit/0af3137ee15d51afc025f7f422515ba2442f6d58))
- Added a basic m6a caller that adds to the bam tags ([`71e5812`](https://github.com/fiberseq/fibertools-rs/commit/71e58128417c909190726b624e5e1d32eda665a6))
- Clean ([`a723d61`](https://github.com/fiberseq/fibertools-rs/commit/a723d613358b6131185bb17a93b5fb4924e1dd4f))
- Added a proof of principle xgboost application to predicting m6A ([`e70e7b9`](https://github.com/fiberseq/fibertools-rs/commit/e70e7b956c36b5e2323370b0e78de57566d39802))
- Smaller ([`ab1ea68`](https://github.com/fiberseq/fibertools-rs/commit/ab1ea68bc5467c7a3a018a99b9a277bf755a9723))
- Versions ([`121e7c9`](https://github.com/fiberseq/fibertools-rs/commit/121e7c9837b76e2f7b7c72937bfa679881f06f14))
- Versions ([`72f7cdd`](https://github.com/fiberseq/fibertools-rs/commit/72f7cdded1903587ff2d839a4c4f91a1fd10290b))
- Versions ([`184fe65`](https://github.com/fiberseq/fibertools-rs/commit/184fe650e8a3d7ea03b97fe2c9b11c58ef6f65a5))
- Ignore ([`1a7a741`](https://github.com/fiberseq/fibertools-rs/commit/1a7a741f624dedfe4b3a5b32212f82db4e08ce9c))
- Makeing the 00.0.6 release ([`8847fe5`](https://github.com/fiberseq/fibertools-rs/commit/8847fe5e133b62eed66915ef5dfbcfb1dda2712b))
- Updating readme and docs ([`bd22fb1`](https://github.com/fiberseq/fibertools-rs/commit/bd22fb1ccf68614e3b211eafa2f07081ce513985))
- Updating readme and docs ([`b086baa`](https://github.com/fiberseq/fibertools-rs/commit/b086baa4644098c153672fd2fe5f255f80f8f902))
- Adding rq tag to all ([`9ae61bb`](https://github.com/fiberseq/fibertools-rs/commit/9ae61bb338ff89da9c3e0aa556c91ec6a9cd95c3))
- Todos ([`28775b6`](https://github.com/fiberseq/fibertools-rs/commit/28775b6bb9762847ec89ff5c85ce71b74ba24dcc))
- Fixing CI ([`279dcc2`](https://github.com/fiberseq/fibertools-rs/commit/279dcc2f252e861cb25113ffdd842fdf4616d226))
- Changing test file and expanding CI ([`44e4cb7`](https://github.com/fiberseq/fibertools-rs/commit/44e4cb7d56a12b4c4c1deb0b974db928481e3bb1))
- Changing test file and expanding CI ([`cfe8e4c`](https://github.com/fiberseq/fibertools-rs/commit/cfe8e4c7145511f32e5f28fc71fbc6dfcd03152a))
- Fixing CI ([`cc5efd2`](https://github.com/fiberseq/fibertools-rs/commit/cc5efd2b02ad3c2c5c11179d4c3ffaeb5554e671))
- Adding CI badge ([`4bbeb45`](https://github.com/fiberseq/fibertools-rs/commit/4bbeb45e9c7ab54c2b761932891c961536b179af))
- Adding CI ([`71b3ade`](https://github.com/fiberseq/fibertools-rs/commit/71b3adef427d601d1e96632b0403654490a2c029))
- Adding CI ([`03efba5`](https://github.com/fiberseq/fibertools-rs/commit/03efba5e4b994f58f8dd8bfd3fe29e26a44b8925))
- Adding CI ([`19b024d`](https://github.com/fiberseq/fibertools-rs/commit/19b024d887163ff66fe55342b737b4e5425ac7af))
- Making alpha version for cargo ([`0a68568`](https://github.com/fiberseq/fibertools-rs/commit/0a68568e0f097080e870c50239ca0779ef96d431))
- Making alpha version for cargo ([`818c6e0`](https://github.com/fiberseq/fibertools-rs/commit/818c6e05694e85c1b5e0bc7bef4f65dc773cfd64))
- Changeing writer to handle broken pipes, line with head, and removing some completed TODOs ([`074bcab`](https://github.com/fiberseq/fibertools-rs/commit/074bcab25a0874e81975042cb918d6cd8c9b5d60))
- Changeing writer to handle broken pipes, line with head, and removing some completed TODOs ([`8c7e31b`](https://github.com/fiberseq/fibertools-rs/commit/8c7e31b5278d92136b12f7311a771c4ad3602179))
- TODO ([`fa2c31c`](https://github.com/fiberseq/fibertools-rs/commit/fa2c31ce7f484d9551eac2a291c776331b148350))
- Fixing a suspected off by one issue on the reverse strand ([`63840dc`](https://github.com/fiberseq/fibertools-rs/commit/63840dcf47913ff01b43ed2f21b516fcb7f863a0))
- Adding total m6a, AT, and 5mc counts ([`32397e8`](https://github.com/fiberseq/fibertools-rs/commit/32397e8bab0d17e624c4c6a4c3454d342df04048))
- Replace missing contig with a . ([`1ea4769`](https://github.com/fiberseq/fibertools-rs/commit/1ea476947c79dab1570fec1a13db3cd8b969d8ab))
- Fixed segfault for unaligned reads trying to get reference info ([`ea05a59`](https://github.com/fiberseq/fibertools-rs/commit/ea05a59eb7c1ff485859bcd1e1ebccd554a46241))
- Improve install instructions ([`cc302d4`](https://github.com/fiberseq/fibertools-rs/commit/cc302d4f8baa88168d97fc56a3822998785c4b5c))
- Checking for unmapped in ranged liftover ([`52eae4b`](https://github.com/fiberseq/fibertools-rs/commit/52eae4bd1785756b1e23e723c7691714c0f4a5bf))
- Bump ([`b2c5663`](https://github.com/fiberseq/fibertools-rs/commit/b2c5663bda4b879fc635386ad858817d80a2d961))
- Adding links to automated help pages to help keep uptodate. Closes #1 ([`2ee0542`](https://github.com/fiberseq/fibertools-rs/commit/2ee0542ba6fdd68b0a12014808554ed96c0ae268))
- Made a large # of changes so that outputs are consistently in the orientation of the read stored in the bam rather than the original orientation ([`7c6f773`](https://github.com/fiberseq/fibertools-rs/commit/7c6f773d50a5d60a7dea4de7895ee7381115a90b))
- Fixed bug for missing reverse strand outputs ([`318aac5`](https://github.com/fiberseq/fibertools-rs/commit/318aac56263db53e570b91db0ef6bc77e80d8357))
- Removing filter to keep the -1 ([`38c8a77`](https://github.com/fiberseq/fibertools-rs/commit/38c8a77f6e53c218c923bfafe2e3327839411add))
- Renaming output to 5mC ([`23d4526`](https://github.com/fiberseq/fibertools-rs/commit/23d45268bc3df175e76e86b46c7f1f7fc3735bad))
- Adding a -1 value for positions that cannot be lifted over in extract all ([`b50df1b`](https://github.com/fiberseq/fibertools-rs/commit/b50df1b064ba42ac591cee72182dc0d910f52fad))
- Adding . for missing feilds ([`6f6ee28`](https://github.com/fiberseq/fibertools-rs/commit/6f6ee28a163fcd9e70f149f92b590e2fa64366b5))
- Remove tab at end of line ([`d52b388`](https://github.com/fiberseq/fibertools-rs/commit/d52b388570f5bc9e3e59af4b23ffe972afb7dce5))
- Removing duplicate headers ([`81de168`](https://github.com/fiberseq/fibertools-rs/commit/81de168625747b52c31e692c519a591b8c3ca964))
- Adding img ([`e219b79`](https://github.com/fiberseq/fibertools-rs/commit/e219b7909f8baebaad266872135cf77867b60d1e))
- Adding comment char for all header ([`07be127`](https://github.com/fiberseq/fibertools-rs/commit/07be127be30e3a229bdd0a5d83baeab947618e7e))
- Adding column names for --all ([`1f00737`](https://github.com/fiberseq/fibertools-rs/commit/1f007377ef92cb0c7cd91c787d61442cf5b02a88))
- Try again ([`f08170f`](https://github.com/fiberseq/fibertools-rs/commit/f08170f82b0a57345318bc6b3f1a3ba4e3dab7a6))
- Try again ([`e336377`](https://github.com/fiberseq/fibertools-rs/commit/e3363778e1e2085a5c52660ce06db5b8bc95cec3))
- Try again ([`20b2050`](https://github.com/fiberseq/fibertools-rs/commit/20b20501c15c90a71d8892e10f17809273c005da))
- Try again ([`66a506f`](https://github.com/fiberseq/fibertools-rs/commit/66a506f6eb8da407a50a4e6589ffdf5a2bdb6a25))
- Try again ([`7e7cad3`](https://github.com/fiberseq/fibertools-rs/commit/7e7cad3d8313fbd673226dab78c8a36163752332))
- Try again ([`fe0a6b4`](https://github.com/fiberseq/fibertools-rs/commit/fe0a6b4d65ce14a003f34461f65acd809bee6b3a))
- Try again ([`96f231a`](https://github.com/fiberseq/fibertools-rs/commit/96f231ac977f1f53c3adf12e4e4d8dd9d5ccc526))
- Try again ([`01e9ede`](https://github.com/fiberseq/fibertools-rs/commit/01e9edebe6d9967a9dc7d70b4880f2ba77229b9e))
- Try again ([`2f3a2fb`](https://github.com/fiberseq/fibertools-rs/commit/2f3a2fb433623e6fe7a18b79411ea9fe768f5b37))
- Try again ([`c27f71d`](https://github.com/fiberseq/fibertools-rs/commit/c27f71d4a5be58a2416849b97f3b28c46d0bdcd1))
- Try again ([`ae31d3c`](https://github.com/fiberseq/fibertools-rs/commit/ae31d3cd95a2fef2f160fc2e7cfc4df7a3d1b21a))
- Try again ([`c65d806`](https://github.com/fiberseq/fibertools-rs/commit/c65d806784814b0b994fddff711d5300d154c927))
- Try again ([`034e34a`](https://github.com/fiberseq/fibertools-rs/commit/034e34a387c0d534c65d2be376acf6ec4f243cc4))
- Try again ([`17d6705`](https://github.com/fiberseq/fibertools-rs/commit/17d6705d5b673819fcf8fda60e737bc10be5bbdd))
- Try again ([`fa6ee99`](https://github.com/fiberseq/fibertools-rs/commit/fa6ee99a5a00fcdd4df12abe0f06283451fa99f0))
- Try again ([`26132de`](https://github.com/fiberseq/fibertools-rs/commit/26132de803b678c6981408e722a5292d05edc3b2))
- Try again ([`aba1393`](https://github.com/fiberseq/fibertools-rs/commit/aba1393448fa008ba61400fd2fce05560b06df4f))
- Try again ([`b0d39db`](https://github.com/fiberseq/fibertools-rs/commit/b0d39dbdac9bda011983f2e185fab17f025f5c74))
- Try again ([`d460c52`](https://github.com/fiberseq/fibertools-rs/commit/d460c52190a47fd06c90960a88e932cf074fb91f))
- Try again ([`c6ea96b`](https://github.com/fiberseq/fibertools-rs/commit/c6ea96b20ac4906b827e626ed196bf5104d0c978))
- Try again ([`ff04b4d`](https://github.com/fiberseq/fibertools-rs/commit/ff04b4de7fafcc07bf378fddb3af38ca35aa3fb0))
- Try again ([`2ac517b`](https://github.com/fiberseq/fibertools-rs/commit/2ac517b8ecf997fc8b54b4946d546eabaf6798d6))
- Try again ([`e2faa05`](https://github.com/fiberseq/fibertools-rs/commit/e2faa0543a49ef7b7c2abb6f69d7b5ecba5b0eb8))
- Try again ([`f998631`](https://github.com/fiberseq/fibertools-rs/commit/f998631f15f30993e2f430dba6966fd247fa84fa))
- Try again ([`a876050`](https://github.com/fiberseq/fibertools-rs/commit/a8760507fc547e026d6f47f977bb6ba032bb0e5b))
- Try again ([`887fec5`](https://github.com/fiberseq/fibertools-rs/commit/887fec55bfeeeb6ff65cb8b83a4743b2b1e3eb13))
- Try again ([`5b10de4`](https://github.com/fiberseq/fibertools-rs/commit/5b10de4241691f8940721c9040aeaa6c065e96ea))
- Try again ([`52d7bd7`](https://github.com/fiberseq/fibertools-rs/commit/52d7bd714c8b0de7f3db5895d8ea00a7a54aaadf))
- Try again ([`4e05b62`](https://github.com/fiberseq/fibertools-rs/commit/4e05b62480ff1e70df6d76639962a4085c44b693))
- Try again ([`20d3e10`](https://github.com/fiberseq/fibertools-rs/commit/20d3e103b93baa19bc08ffb78a5e0d7a326664ef))
- Try again ([`e7f890c`](https://github.com/fiberseq/fibertools-rs/commit/e7f890cb77b8e7b841a3f304ad4e047c91be0d5a))
- Try again ([`cbd77e4`](https://github.com/fiberseq/fibertools-rs/commit/cbd77e473f4bf364e45759d93359d396fb4569f5))
- Try again ([`4c88f74`](https://github.com/fiberseq/fibertools-rs/commit/4c88f74e74a14fbafc632663e02276c86bb126f4))
- Try again ([`86c7202`](https://github.com/fiberseq/fibertools-rs/commit/86c720283166eaa6d6687e8b7cffcf5090d79eec))
- Try again ([`b090f10`](https://github.com/fiberseq/fibertools-rs/commit/b090f10710645fbd7e023a145c852590be9438c5))
- Try again ([`4b2e4f6`](https://github.com/fiberseq/fibertools-rs/commit/4b2e4f620ea8fa439e946494919d02b79c1f9d23))
- Try again ([`b47f660`](https://github.com/fiberseq/fibertools-rs/commit/b47f660e7418121a29410e187270828f0b7bcf5f))
- Try again ([`42aba01`](https://github.com/fiberseq/fibertools-rs/commit/42aba0163ab75b56b7744bbfc59a57949391369c))
- Try again ([`47b266e`](https://github.com/fiberseq/fibertools-rs/commit/47b266ebba89d06c4d611dc3ae30f16067604d9f))
- Try again ([`b21de47`](https://github.com/fiberseq/fibertools-rs/commit/b21de47fe60df83b92e4e76289e6f1e67434a749))
- Try again ([`d394151`](https://github.com/fiberseq/fibertools-rs/commit/d394151025a78c8ca888d5bf41e7df7995499a28))
- Try again ([`0b27603`](https://github.com/fiberseq/fibertools-rs/commit/0b2760336c609df0f06687b9f4c7e93c641e0cee))
- Try again ([`c60bcc5`](https://github.com/fiberseq/fibertools-rs/commit/c60bcc5db5bab3d23afda04fb84e194dd7236d2a))
- Try again ([`4b0ffca`](https://github.com/fiberseq/fibertools-rs/commit/4b0ffcafa9e84a6c0dc18444404a05d70f498963))
- Try again ([`852a562`](https://github.com/fiberseq/fibertools-rs/commit/852a56290e03e45fce6e5964c9f6a7156c9df25a))
- Try again ([`40cfdb0`](https://github.com/fiberseq/fibertools-rs/commit/40cfdb0d6a4d35e182e74110da35c86feef21aab))
- Try again ([`bc3c10f`](https://github.com/fiberseq/fibertools-rs/commit/bc3c10fb8dd47ee27f799b49e6d0c215a1d32693))
- Try again ([`f8d57b0`](https://github.com/fiberseq/fibertools-rs/commit/f8d57b0b7c24db853d0554a6552b1e54c44ea8d7))
- Try again ([`a7b022e`](https://github.com/fiberseq/fibertools-rs/commit/a7b022ed10d2cf5db382b5ad3b0b3c56e398fe1e))
- Try again ([`8f5e64a`](https://github.com/fiberseq/fibertools-rs/commit/8f5e64aab138e5ba6661736e02f512d354f60cc7))
- Try again ([`17fb908`](https://github.com/fiberseq/fibertools-rs/commit/17fb908a5d40e5d43b8363f3d540b492a78c83ba))
- Try again ([`e961e4c`](https://github.com/fiberseq/fibertools-rs/commit/e961e4c1043e7b9d32fe7f3f4f7a9a0051eb6874))
- Try again ([`c2baedf`](https://github.com/fiberseq/fibertools-rs/commit/c2baedf4e8096dd70c24d0b2a7f412941ac37eeb))
- Try again ([`a1c4a3c`](https://github.com/fiberseq/fibertools-rs/commit/a1c4a3cfbb6f41ee1636bda46388b7a43268a7f1))
- Try again ([`0beb42e`](https://github.com/fiberseq/fibertools-rs/commit/0beb42edf4758812ae39f8f26907cef7872d136b))
- Try again ([`010dbfd`](https://github.com/fiberseq/fibertools-rs/commit/010dbfde2f5dc91f6f63f16cf32384cdd76d3c91))
- Try again ([`b006a78`](https://github.com/fiberseq/fibertools-rs/commit/b006a78163709eb3682b6ff408ad4f3f6d217e5c))
- Try again ([`8b328bf`](https://github.com/fiberseq/fibertools-rs/commit/8b328bf3cf5b803c3b6f4f12ed2899b28918b174))
- Try again ([`5001a71`](https://github.com/fiberseq/fibertools-rs/commit/5001a719cc12ccd03c7f02af70062ed15473977b))
- Try again ([`c798640`](https://github.com/fiberseq/fibertools-rs/commit/c79864032038434534890db1d9686ad8566e8f2e))
- Try again ([`e8e1a38`](https://github.com/fiberseq/fibertools-rs/commit/e8e1a38ec3ce708a85fb3e27e7b8b7352f4f93f1))
- Try again ([`13ad33f`](https://github.com/fiberseq/fibertools-rs/commit/13ad33f58703bcc4e760e979f4684876c65b9d0a))
- Try again ([`de3267d`](https://github.com/fiberseq/fibertools-rs/commit/de3267d6d2d5396a98fa238ba5fe8327363f9b30))
- Try again ([`967533c`](https://github.com/fiberseq/fibertools-rs/commit/967533ce1a4c495ea89229962d1d30bb7c95156b))
- Try again ([`a9ebd24`](https://github.com/fiberseq/fibertools-rs/commit/a9ebd24948d303391c82d761246d49e9867426ce))
- Try again ([`157a2aa`](https://github.com/fiberseq/fibertools-rs/commit/157a2aafd1ce4ee25301d571f5e32d68e04dbf2c))
- Try again ([`6ac49c6`](https://github.com/fiberseq/fibertools-rs/commit/6ac49c6ae3dc43fc283faebdfc1b7d20973d99f6))
- Build# ([`7caf415`](https://github.com/fiberseq/fibertools-rs/commit/7caf4156dd4a385c275e679b8f1a88d021243d28))
- Adding ([`bfafb3b`](https://github.com/fiberseq/fibertools-rs/commit/bfafb3b812b8b4672c2ff278253e0032b8603067))
- Adding ([`5f03308`](https://github.com/fiberseq/fibertools-rs/commit/5f03308482d48c34f144b197aa8b935f21a820d4))
- Set theme jekyll-theme-minimal ([`3c3b11f`](https://github.com/fiberseq/fibertools-rs/commit/3c3b11f7087a90f095d0d610732e919fdac46746))
- Adding ([`493de98`](https://github.com/fiberseq/fibertools-rs/commit/493de98db23e567607d496422ece6ac89bfb497b))
- Adding ([`f0d4310`](https://github.com/fiberseq/fibertools-rs/commit/f0d43109d2101a9e415d95e1a6825bf62c74ef7b))
- Adding ([`116af9d`](https://github.com/fiberseq/fibertools-rs/commit/116af9df584a21ff0e0b9634f2a8e08d64ddb204))
- Adding ([`5e2dc3b`](https://github.com/fiberseq/fibertools-rs/commit/5e2dc3b62dd71d4c3c63d5ea06d1ff7a17fe9b66))
- Adding ([`5bb45b3`](https://github.com/fiberseq/fibertools-rs/commit/5bb45b397f817ce14310fdbd953ea03c99085124))
- Adding ([`81f6dfd`](https://github.com/fiberseq/fibertools-rs/commit/81f6dfd92a81976492fe2d0ec5eddc063bb3111d))
- Adding ([`17caed7`](https://github.com/fiberseq/fibertools-rs/commit/17caed707b099304802f3195d95beb5dbbf23e8d))
- Adding ([`131fb08`](https://github.com/fiberseq/fibertools-rs/commit/131fb0826cf7567395846d80db553ece267ba163))
- Adding ([`f1a51e9`](https://github.com/fiberseq/fibertools-rs/commit/f1a51e91255515bf0e28cae8f9dc65e77f477e3a))
- Adding ([`66951c7`](https://github.com/fiberseq/fibertools-rs/commit/66951c7b1f48425b97ab540e12ffca074ea94795))
- Adding ([`7c77792`](https://github.com/fiberseq/fibertools-rs/commit/7c777921ca3bd7dd29a71dd1b9d4aa765d238180))
- Adding ([`7ff38f9`](https://github.com/fiberseq/fibertools-rs/commit/7ff38f95c2a81811581b84706bc67974ff739929))
- Adding ([`e9234cd`](https://github.com/fiberseq/fibertools-rs/commit/e9234cddbc97ca2de160c5f98ea677cfa6b1781a))
- Adding ([`316bcbb`](https://github.com/fiberseq/fibertools-rs/commit/316bcbb578e6751c68ef1ed3300afdbe1426d2e2))
- Adding ([`1cbf8ab`](https://github.com/fiberseq/fibertools-rs/commit/1cbf8ab50a585d3bbbdfe0517683d5271849b2f4))
- Adding ([`02c9983`](https://github.com/fiberseq/fibertools-rs/commit/02c9983a5f55f57f93f2c739cfb4774218e82e03))
- Adding ([`cb24e21`](https://github.com/fiberseq/fibertools-rs/commit/cb24e21a5f72a4e166be88c2f4bbe25d1ec87297))
- Adding ([`9bf5ebc`](https://github.com/fiberseq/fibertools-rs/commit/9bf5ebc2930d4d9ba9b586f7294ffe63de185ec4))
- Adding ([`a7f3707`](https://github.com/fiberseq/fibertools-rs/commit/a7f3707d0bf8aa3c0e55079c05c9a194b59486a9))
- Adding ([`5984937`](https://github.com/fiberseq/fibertools-rs/commit/5984937945abcb7218f0f15fdeec9ba5a1f46045))
- Adding ([`e21e345`](https://github.com/fiberseq/fibertools-rs/commit/e21e34559b3b176f664a8fe511284353e6763126))
- Adding ([`d5fb531`](https://github.com/fiberseq/fibertools-rs/commit/d5fb531a6fba4466a08ed343e817ed939fbe7def))
- Adding ([`dad97a2`](https://github.com/fiberseq/fibertools-rs/commit/dad97a222bfb05003b441b9adcc92dc45af6848d))
- Adding ([`1384ff1`](https://github.com/fiberseq/fibertools-rs/commit/1384ff1ae8b3d5918ebf937c9c2971de2edae1e3))
- Adding ([`1040d32`](https://github.com/fiberseq/fibertools-rs/commit/1040d32c250fec34c048b051d2350baabd3ca45a))
- Adding ([`773be4e`](https://github.com/fiberseq/fibertools-rs/commit/773be4e7e183f4c26b0c7367f6f3828ec2251b2b))
- Adding ([`66b72f8`](https://github.com/fiberseq/fibertools-rs/commit/66b72f8ce9993974740c0e273f360db305ea0719))
- Adding ([`d3cbad4`](https://github.com/fiberseq/fibertools-rs/commit/d3cbad4d369f0466e3c45ac17e2555edbfcd3dd9))
- Adding ([`7045b27`](https://github.com/fiberseq/fibertools-rs/commit/7045b27483d453934956b66453d02769196d1c2b))
- Adding ([`5bbadf7`](https://github.com/fiberseq/fibertools-rs/commit/5bbadf78d149f487ad7e4e6a3bb0ad21635e8682))
- Adding ([`cc72a38`](https://github.com/fiberseq/fibertools-rs/commit/cc72a38bf8ed015355eb192398de65b5a9b89dfd))
- Adding ([`5a81075`](https://github.com/fiberseq/fibertools-rs/commit/5a810759ed4a2bd6f908c83d3d6348d0282bf5c0))
- Adding ([`832dd42`](https://github.com/fiberseq/fibertools-rs/commit/832dd427a8d560aba24c50529c98fb584f0fa080))
- Adding ([`477bc7e`](https://github.com/fiberseq/fibertools-rs/commit/477bc7e7323d923b6ff55bc003d28877103ff5b4))
- First commit ([`13746b2`](https://github.com/fiberseq/fibertools-rs/commit/13746b24d9b5a323c625909c61a1edcfcb1514aa))
</details>