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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and the project tries but probably doesn't to adhere to Semantic Versioning.

Unreleased

Commit Statistics

  • 1 commit contributed to the release.
  • 0 commits were understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

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  • Uncategorized

v0.2.5 (2023-07-18)

The default output for ft extract is now in reference coordinates instead of molecular.

ft extract can now produce compressed files by adding the gz extension. e.g.:

ft extract -t 16 --m6a m6a.bed.gz --cpg cpg.bed.gz --nuc nuc.bed.gz --msp msp.bed.gz --all all.bed.gz ../PS00243_ft.bam

And this is bgzp compression, so it is compatible with tabix indexing.

Chore

  • Release fibertools-rs version 0.2.5

Commit Statistics

  • 9 commits contributed to the release over the course of 5 calendar days.
  • 6 days passed between releases.
  • 1 commit was understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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  • Uncategorized
    • Release fibertools-rs version 0.2.5 (0821907)
    • Irnogre (938df0e)
    • Correct path (ac0166b)
    • Better var name (fb3ad6d)
    • Fix off by one that sometimes happened in the final msp when doing nuc/msp calling (da5763d)
    • Fix off by one in minus strand nuc and msp coordiantes (91e2bc5)
    • Check for bgz (14724dd)
    • Rewrite ft center so I can use threads? (7180f8e)
    • Rewrite ft center so I can use threads? (4485c5e)

v0.2.4 (2023-07-11)

Chore

  • Release fibertools-rs version 0.2.4

Commit Statistics

  • 21 commits contributed to the release over the course of 13 calendar days.
  • 17 days passed between releases.
  • 1 commit was understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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  • Uncategorized
    • Release fibertools-rs version 0.2.4 (98a51ab)
    • Unsed deps (4603bb6)
    • Unsed deps (b542514)
    • Ci (60c065e)
    • Bio-io updates (8615452)
    • Change extract defaults (b009dda)
    • CI (57880cc)
    • Rename (a00e0d3)
    • Set vars (eedb613)
    • Fix version in bamwriter (c3e3781)
    • Adding a compressed bgzip writer for files with .gz (e425ee3)
    • Adding a buff reader that can be compressed optionally (4235b77)
    • Making my own io package (d001c7f)
    • Help update (cfb85d9)
    • Merge pull request #13 from Dylan-DPC/patch-1 (5bae1a1)
    • Update Cargo.toml (14d0629)
    • Update docker to avoid double building in CI actions (19711d0)
    • Merge pull request #12 from lvclark/patch-1 (dc8e230)
    • Add HTSlib (fd058ba)
    • Put ft in a path that doesn't need root access (b024da2)
    • Uncomment compile line (d792d98)

v0.2.3 (2023-06-24)

Chore

  • Release fibertools-rs version 0.2.3

Commit Statistics

  • 20 commits contributed to the release over the course of 5 calendar days.
  • 8 days passed between releases.
  • 1 commit was understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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v0.2.2 (2023-06-15)

Chore

  • Release fibertools-rs version 0.2.2

Commit Statistics

  • 4 commits contributed to the release.
  • 1 commit was understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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  • Uncategorized
    • Release fibertools-rs version 0.2.2 (7cd3d11)
    • Add run tests and fix comments in bed files for center (8e00047)
    • Add run tests (b5d1e8e)
    • Hide some subcommands (03e7006)

v0.2.1 (2023-06-14)

Chore

  • Release fibertools-rs version 0.2.1

Commit Statistics

  • 5 commits contributed to the release over the course of 3 calendar days.
  • 3 days passed between releases.
  • 1 commit was understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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  • Uncategorized

v0.2.0 (2023-06-10)

Chore

  • Release fibertools-rs version 0.2.0

Commit Statistics

  • 19 commits contributed to the release over the course of 51 calendar days.
  • 52 days passed between releases.
  • 1 commit was understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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v0.1.4 (2023-04-19)

Chore

  • Release fibertools-rs version 0.1.4

Commit Statistics

  • 44 commits contributed to the release over the course of 3 calendar days.
  • 36 days passed between releases.
  • 1 commit was understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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v0.1.3 (2023-03-14)

Chore

  • Release fibertools-rs version 0.1.3

Commit Statistics

  • 10 commits contributed to the release over the course of 16 calendar days.
  • 29 days passed between releases.
  • 1 commit was understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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  • Uncategorized
    • Release fibertools-rs version 0.1.3 (84e4ee9)
    • Docs (2d97f26)
    • Ign (ae94728)
    • Adding 3.2 models (1193a76)
    • Further clean model chem seelection (32530e5)
    • Simplify model loading into the predict options (b60bf8b)
    • Try adding a reference option to ft center (ca015e0)
    • Add the option to read the ML models from env variables FT_MODEL and FT_JSON (8314d8e)
    • Add RG to extract (355088e)
    • Theads help msg (595db94)

v0.1.2 (2023-02-13)

Chore

  • Release fibertools-rs version 0.1.2

Commit Statistics

  • 3 commits contributed to the release over the course of 9 calendar days.
  • 10 days passed between releases.
  • 1 commit was understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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  • Uncategorized
    • Release fibertools-rs version 0.1.2 (7df4056)
    • Remvoe libtorch check since it is packaged in conda now (28c3614)
    • Update url for new repo (021ae38)

v0.1.1 (2023-02-02)

Chore

  • Release fibertools-rs version 0.1.1
  • Release fibertools-rs version 0.1.1-alpha.4

Commit Statistics

  • 6 commits contributed to the release.
  • 2 commits were understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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  • Uncategorized
    • Release fibertools-rs version 0.1.1 (9f8f35b)
    • Bioconda now working (583ed05)
    • Bioconda now working (d0f4943)
    • Fix ci (2d6fa56)
    • Release fibertools-rs version 0.1.1-alpha.4 (d8f2ea5)
    • Restor version of ubunut (6ace556)

v0.1.1-alpha.3 (2023-02-01)

Chore

  • Release fibertools-rs version 0.1.1-alpha.3

Commit Statistics

  • 2 commits contributed to the release.
  • 1 commit was understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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  • Uncategorized
    • Release fibertools-rs version 0.1.1-alpha.3 (c116113)
    • Older version of ubunut (a043398)

v0.1.1-alpha.2 (2023-02-01)

Chore

  • Release fibertools-rs version 0.1.1-alpha.2

Commit Statistics

  • 2 commits contributed to the release.
  • 1 commit was understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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  • Uncategorized
    • Release fibertools-rs version 0.1.1-alpha.2 (dda2ea4)
    • Adding libtorch enviorment checks (3d0c77c)

v0.1.1-alpha.1 (2023-02-01)

Chore

  • Release fibertools-rs version 0.1.1-alpha.1

Commit Statistics

  • 2 commits contributed to the release.
  • 1 commit was understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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  • Uncategorized
    • Release fibertools-rs version 0.1.1-alpha.1 (c6f50df)
    • Change targets (1ad406a)

v0.1.1-alpha (2023-02-01)

Chore

  • Release fibertools-rs version 0.1.1-alpha

Commit Statistics

  • 6 commits contributed to the release.
  • 1 day passed between releases.
  • 1 commit was understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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  • Uncategorized
    • Change precommit (0b00d2d)
    • Release fibertools-rs version 0.1.1-alpha (3eede8c)
    • Default use cnn (9946f0f)
    • Testing a release manager (723bc6f)
    • Testing a release manager (faf0620)
    • Hide prediction under a new predict feature instead of partically under cnn (f86e1cf)

v0.1.0 (2023-01-30)

Commit Statistics

  • 134 commits contributed to the release over the course of 52 calendar days.
  • 52 days passed between releases.
  • 0 commits were understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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v0.0.11 (2022-12-09)

Commit Statistics

  • 63 commits contributed to the release over the course of 17 calendar days.
  • 17 days passed between releases.
  • 0 commits were understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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v0.0.10 (2022-11-22)

Commit Statistics

  • 9 commits contributed to the release.
  • 0 commits were understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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v0.0.9 (2022-11-21)

Commit Statistics

  • 15 commits contributed to the release.
  • 1 day passed between releases.
  • 0 commits were understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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  • Uncategorized
    • A new release for bioconda which will hopefully allow the cnn by default (85305ab)
    • Increase chunk size (a028151)
    • For #2 try 2 (950d7db)
    • For #2 (de08a90)
    • Stadardize message formating (178ef3c)
    • Stadardize message formating (0fc4761)
    • Add conda-forge to channel (dd65ce9)
    • Add detail to cli (e081131)
    • Adding more headings in CLI (c8922fd)
    • Making some options global so they can go anywhere on the cli (1ac197d)
    • Making some options global so they can go anywhere on the cli (1f68cbe)
    • Allow bam reading and writing from stdin for m6a-predict (c977510)
    • Add warning for missing hifi kinetics (21fe212)
    • Update install (3890f37)
    • Update install (e4d0aad)

v0.0.8 (2022-11-20)

Commit Statistics

  • 68 commits contributed to the release over the course of 6 calendar days.
  • 11 days passed between releases.
  • 0 commits were understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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v0.0.7 (2022-11-08)

Commit Statistics

  • 105 commits contributed to the release over the course of 52 calendar days.
  • 54 days passed between releases.
  • 0 commits were understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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v0.0.6 (2022-09-15)

Commit Statistics

  • 13 commits contributed to the release over the course of 14 calendar days.
  • 14 days passed between releases.
  • 0 commits were understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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v0.0.6-alpha.1 (2022-08-31)

Commit Statistics

  • 11 commits contributed to the release over the course of 5 calendar days.
  • 7 days passed between releases.
  • 0 commits were understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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  • Uncategorized
    • Making alpha version for cargo (0a68568)
    • Making alpha version for cargo (818c6e0)
    • Changeing writer to handle broken pipes, line with head, and removing some completed TODOs (074bcab)
    • Changeing writer to handle broken pipes, line with head, and removing some completed TODOs (8c7e31b)
    • TODO (fa2c31c)
    • Fixing a suspected off by one issue on the reverse strand (63840dc)
    • Adding total m6a, AT, and 5mc counts (32397e8)
    • Replace missing contig with a . (1ea4769)
    • Fixed segfault for unaligned reads trying to get reference info (ea05a59)
    • Improve install instructions (cc302d4)
    • Checking for unmapped in ranged liftover (52eae4b)

v0.0.5 (2022-08-23)

Commit Statistics

  • 29 commits contributed to the release over the course of 23 calendar days.
  • 23 days passed between releases.
  • 0 commits were understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

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  • Uncategorized

v0.0.4 (2022-07-31)

Commit Statistics

  • 31 commits contributed to the release over the course of 2 calendar days.
  • 2 days passed between releases.
  • 0 commits were understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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v0.0.3-alpha (2022-07-28)

Commit Statistics

  • 18 commits contributed to the release over the course of 1 calendar day.
  • 1 day passed between releases.
  • 0 commits were understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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v0.0.2 (2022-07-27)

Commit Statistics

  • 6 commits contributed to the release.
  • 0 commits were understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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v0.0.1 (2022-07-27)

Commit Statistics

  • 35 commits contributed to the release over the course of 2 calendar days.
  • 0 commits were understood as conventional.
  • 0 issues like '(#ID)' were seen in commit messages

Commit Details

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