0.6.0 - 2024-11-14

Release Notes

• fix: do not report m6A predictions that happen within the first 7 or last 7 bp of a read. This is so the ML model only operates on real data. No changes to other calls. Will fix #65
• fix: report footprint codes even if there is no spanning msp, fixes #63
• feat: add a pyft utility that can take extract --all data and make it long format for plotting.
• feat: Add a shuffle option to pileup to help with the FDR calculations in FIRE
• feat: make nucleosomes and MSPs optional in pileup
• chore: use vergen for cli version
• feat: add phasing stats to QC
• feat: allow strip-base mods to filter on base mod quality.

Download fibertools-rs 0.6.0

File	Platform	Checksum
fibertools-rs-aarch64-apple-darwin.tar.xz	Apple Silicon macOS	checksum
fibertools-rs-x86_64-apple-darwin.tar.xz	Intel macOS	checksum
fibertools-rs-x86_64-unknown-linux-gnu.tar.xz	x64 Linux	checksum

0.5.4 - 2024-09-10

Release Notes

• Added filtering expressions to ft #57
• ADD ft qc #59
• Extended QC commands and added FIRE to prediction #60

Download fibertools-rs 0.5.4

File	Platform	Checksum
fibertools-rs-aarch64-apple-darwin.tar.xz	Apple Silicon macOS	checksum
fibertools-rs-x86_64-apple-darwin.tar.xz	Intel macOS	checksum
fibertools-rs-x86_64-unknown-linux-gnu.tar.xz	x64 Linux	checksum

0.5.3 - 2024-07-31

Release Notes

⚙️ Miscellaneous Tasks

• Update changelog with release
• Update changelog with release
• Update changelog with release
• Update changelog with release
• Update changelog with release

Download fibertools-rs 0.5.3

File	Platform	Checksum
fibertools-rs-aarch64-apple-darwin.tar.xz	Apple Silicon macOS	checksum
fibertools-rs-x86_64-apple-darwin.tar.xz	Intel macOS	checksum
fibertools-rs-x86_64-unknown-linux-gnu.tar.xz	x64 Linux	checksum

v0.5.0

Chore

• clippy
• clippy
• clippy
• unused
• cli
• cli
• cli
• update ctcf definition
• prep for bump
• pyft bump
• hide m5c #54
• hide m5c #54
• extend docs #54
• cargo dist

New Features

• skip empty regions
• skip empty regions
• add a ddda to m6a converter
• switch to generic cpu
• switch to generic cpu
• add ont fire heuristic test data and cli improments
• add ont fire heuristic
• add ont fire heuristic
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• starting the book
• add options motif_span
• more input bam functions
• more input bam functions
• InputBam now can make a template for an output bam
• InputBam now can make a template for an output bam
• allow the complexity of the pipeup to be adjusted
• pileup is now useable
• pileup is now useable
• pileup is now useable
• add a pyft way to iterate over a bam file one read at a time.
• allow fire opts to be read from env vars.
• inital fibertools pileup is complete
• inital fibertools pileup is complete
• inital fibertools pileup is complete

Bug Fixes

• make footprint u16 number of modules consistent
• use bit flag filter
• use min ml score in pileup
• check for end of chrom
• missing final base in pileup region
• clean up cli interactions with pileup
• clean up cli interactions with pileup
• clean up cli interactions with pileup
• clean up cli interactions with pileup
• clean up cli interactions with pileup
• clean up cli interactions with pileup
• clean up cli interactions with pileup
• clean up cli interactions with pileup
• clean up cli interactions with pileup
• fix label on FIRE vs LINKER for decorator tracks
• keep footprint code
• skip sites with zero spanning reads
• skip sites with zero spanning reads
• pileup thread error
• pileup thread error
• add target names to pyft
• add target names to pyft
• add target names to pyft
• add new check to avoid a new failure on unaligned bams
• py-ft build
• py-ft build

Other

• removing unneeded nesting
• Major change to the cli and adding a filtering tools that works like samtools view -F
• why are the revio tests failing?

Refactor

• move some tests
• update for fibertools refactor
• move some complexity into utils
• move some complexity into utils
• move some complexity into utils
• move some complexity into utils
• move some complexity into utils
• move the running of subcommands into a submodule called subcommands
• move the running of subcommands into a submodule called subcommands
• Breakout subcommands opts into different files
• Make the inputbam function a utility and add a FiberFilter structure that can be used to filter the input bam and therefore the output

Commit Statistics

• 1 commit contributed to the release.
• 131 days passed between releases.
• 0 commits were understood as conventional.
• 1 unique issue was worked on: #50

Commit Details

view details

• #50
  • Working on v0.5.0 (198cebe)

0.4.2 (2024-03-21)

Release Notes

Chore

• clean docs
• clean docs
• clean changelog
• update helps
• clean cargo config
• clean
• clean

Commit Statistics

• 9 commits contributed to the release over the course of 1 calendar day.
• 1 day passed between releases.
• 7 commits were understood as conventional.
• 1 unique issue was worked on: #47

Commit Details

view details

• #47
  • 0.4.2 (bb7eff1)
• Uncategorized
  • Version (47be701)
  • Clean docs (d98cfa8)
  • Clean docs (b4600cd)
  • Clean changelog (0222a23)
  • Update helps (fc4260d)
  • Clean cargo config (fee819a)
  • Clean (069c6c9)
  • Clean (a06a949)

0.4.1 (2024-03-20)

Release Notes

Chore

• make test data larger again since I remove the whole dir from cargo publish
• make test data larger again since I remove the whole dir from cargo publish
• make test data larger again since I remove the whole dir from cargo publish
• make test data larger again since I remove the whole dir from cargo publish
• make cargo publish smaller
• make cargo publish smaller
• make cargo publish smaller
• make cargo publish smaller
• make cargo publish smaller
• make test data smaller
• ignore notebook
• sync lock with branch
• sync lock with branch

New Features

• convert pytorch models to onnx to allow more backends
  This PR uses onnx files instead of pytorch files and moves the backend
  of m6a prediction to burn-rs instead of tch-rs.

  This allows us to use other ML backends in addition to pytorch, which
  means we can still run m6a prediction without the massive pytorch
  libraries and get the same results at the cost of some performance.

  I have also added tests for m6a predictions for each PacBio chemistry to
  ensure that the number and quality of predictions are identical to
  previous versions regardless of backend. Will also be a useful test in
  the future.

  I also add a lot of new functionality to pyft.

  This will be the basis of ft v0.4.0 when merged.

Commit Statistics

• 23 commits contributed to the release over the course of 7 calendar days.
• 20 days passed between releases.
• 14 commits were understood as conventional.
• 2 unique issues were worked on: #43, #46

Commit Details

view details

• #43
  • Footprinting (0429ff0)
• #46
  • Convert pytorch models to onnx to allow more backends (547b815)
• Uncategorized
  • Make test data larger again since I remove the whole dir from cargo publish (61967b4)
  • Make test data larger again since I remove the whole dir from cargo publish (93de92f)
  • Make test data larger again since I remove the whole dir from cargo publish (3a47fa8)
  • Make test data larger again since I remove the whole dir from cargo publish (0a9ab3f)
  • Release fibertools-rs v0.4.0 (5f5fac5)
  • Release fibertools-rs v0.4.0 (01748de)
  • Make cargo publish smaller (0b8f6a2)
  • Release fibertools-rs v0.4.0 (3656e4b)
  • Release fibertools-rs v0.4.0 (e4815ad)
  • Make cargo publish smaller (2be96e2)
  • Release fibertools-rs v0.4.0 (4c505e0)
  • Make cargo publish smaller (8a58172)
  • Release fibertools-rs v0.4.0 (31881bf)
  • Make cargo publish smaller (1d7de11)
  • Make cargo publish smaller (9a96cb3)
  • Release fibertools-rs v0.4.0 (9e29925)
  • Make test data smaller (cbdda1a)
  • Release fibertools-rs v0.4.0 (5eba406)
  • Ignore notebook (212b2c9)
  • Sync lock with branch (285db7d)
  • Sync lock with branch (17b8cb6)

v0.3.9

chore: Release fibertools-rs version 0.3.9

0.3.8 (2024-01-24)

Release Notes

Chore

• pyft lock
• readme and help pages
• readme and help pages
• whitespace
• simplify colos
• CI
• CI
• clippy
• improved error msg

New Features

• center and extract now include fire scores in the range of 0-255
• better fire paralization
• update pyft to have a writer function
• update pyft to have a writer function
• update pyft to have a writer function
• update pyft

Bug Fixes

• GBDT made a semvar breaking change, fixing and locking depandancies.

Commit Statistics

• 19 commits contributed to the release over the course of 14 calendar days.
• 14 days passed between releases.
• 16 commits were understood as conventional.
• 1 unique issue was worked on: #38

Commit Details

view details

• #38
  • Refactor (a24ce8e)
• Uncategorized
  • Release fibertools-rs v0.3.7 (aaca6be)
  • Pyft lock (81dcb9b)
  • GBDT made a semvar breaking change, fixing and locking depandancies. (16ef1b6)
  • Readme and help pages (56b0db1)
  • Readme and help pages (622a445)
  • Center and extract now include fire scores in the range of 0-255 (9bac006)
  • Better fire paralization (be89a61)
  • Whitespace (b093f3a)
  • Simplify colos (62f4f49)
  • CI (6393bd8)
  • CI (dc7c74a)
  • Clippy (616f8da)
  • Update pyft to have a writer function (ea06c18)
  • Update pyft to have a writer function (c83b5a0)
  • Update pyft to have a writer function (3bb2f45)
  • Update pyft (e98ceed)
  • Improved error msg (b6da9fe)
  • Unused (5824b74)

0.3.7 (2024-01-10)

Release Notes

Chore

• add trace to ml mm parser
• update.
• update.
• update.
• update.
• update.
• update.
• update.
• update.

New Features

• FIRE extract update
• FIRE extract update
• Adding a fire bed+ extract for the fire pipeline.
• FIRE now works in fibertools! TODO add info to extract, etc.
• adding rle information to fire feats
• adding rle information to fire feats
• adding rle information to fire feats
• adding rle information to fire feats
• adding rle information to fire feats
• adding rle information to fire feats
• adding rle information to fire feats
• adding rle information to fire feats
• adding rle information to fire feats
• adding rle information to fire feats
• adding rle information to fire feats
• adding rle information to fire feats
• adding rle information to fire feats
• adding rle information to fire feats
• adding rle information to fire feats
• adding rle information to fire feats
• adding rle information to fire feats
• adding rle information to fire feats
• adding rle information to fire feats
• update fire model
• use threads better, fire feats
• use threads better, fire feats
• use threads better, fire feats
• use threads better, fire feats
• start working on decorators
• start working on decorators
• FIRE io
• Speed up writing FIRE results
• add a min ML options to add-nucs and keep working on FIRE predictions
• fire progress indicator.
• Add ability to print FIRE features to a text file, TODO predict FIREs in rust.
• Move prediction into a feature only avalible through Cargo, since bioocnda wont let me do large installs anymore.
• add simplify options to center
• add hp tag to center
• add hp tag to center

Bug Fixes

• allow for the unaligned read start and read end
• allow for the unaligned read start and read end
• make an iterator for fiberseq records
• try and better use threads.
• try and better use threads.

Other

• adding code outline for footprinting tool
• cli
• clippy

Commit Statistics

• 72 commits contributed to the release over the course of 81 calendar days.
• 93 days passed between releases.
• 56 commits were understood as conventional.
• 0 issues like '(#ID)' were seen in commit messages

Commit Details

view details

• Uncategorized
  • Clippy (1f27489)
  • Release fibertools-rs v0.3.6 (2f4a9ce)
  • Clippy (ca10f3e)
  • Paths (78e9b44)
  • Release fibertools-rs v0.3.6 (cf6891e)
  • FIRE extract update (7ddcf19)
  • FIRE extract update (bfed259)
  • Adding code outline for footprinting tool (c733189)
  • Typo in wget (a7f24d8)
  • Update CI (6e3bf75)
  • Add skip no m6a opts (a98c064)
  • Clippy (026862a)
  • Speed up extracting decorators, and move make decorators a struct (7176aa4)
  • Adding a fire bed+ extract for the fire pipeline. (cebf54c)
  • FIRE now works in fibertools! TODO add info to extract, etc. (8db7b41)
  • Adding rle information to fire feats (3edee57)
  • Adding rle information to fire feats (b10a8c4)
  • Adding rle information to fire feats (c459196)
  • Adding rle information to fire feats (3a96904)
  • Adding rle information to fire feats (babb017)
  • Adding rle information to fire feats (f830405)
  • Adding rle information to fire feats (b954aab)
  • Adding rle information to fire feats (fd11b45)
  • Adding rle information to fire feats (7c7c2c3)
  • Adding rle information to fire feats (e1f9897)
  • Adding rle information to fire feats (7fac8c7)
  • Adding rle information to fire feats (be21ec1)
  • Adding rle information to fire feats (20985ab)
  • Adding rle information to fire feats (0166d77)
  • Adding rle information to fire feats (53ee8b4)
  • Adding rle information to fire feats (6ab4844)
  • Adding rle information to fire feats (e4510e0)
  • Adding rle information to fire feats ([ee27328](ee2732871e072271c...

0.3.6 (2023-10-09)

Release Notes

Chore

• update

Commit Statistics

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

Commit Details

view details

• Uncategorized
  • Update (32e9121)