rust-bio/rust-bio issues and pull requests

#618 - feat: Implementing From and TryInto for Phase

Pull Request - State: open - Opened by mys721tx 14 days ago

#617 - deps: update rand requirement from >=0.7.3, < 0.9 to >=0.7.3, < 0.10

Pull Request - State: open - Opened by dependabot[bot] 15 days ago
Labels: dependencies

#616 - feat: position-specific scoring matrix: support inputs with ambiguous monomers in from_seqs

Pull Request - State: open - Opened by hervold 28 days ago

#615 - deps: update petgraph requirement from >=0.4, <0.7 to >=0.4, <0.8

Pull Request - State: open - Opened by dependabot[bot] about 1 month ago
Labels: dependencies

#614 - deps: update itertools requirement from >=0.8, <0.14 to >=0.8, <0.15

Pull Request - State: open - Opened by dependabot[bot] about 1 month ago
Labels: dependencies

#613 - Accepting pull requests?

Issue - State: closed - Opened by ivnsch about 2 months ago - 1 comment

#612 - update to newest ndarray

Issue - State: open - Opened by jianshu93 about 2 months ago - 1 comment

#611 - Ability to write Occ to file

Issue - State: open - Opened by jamorrison 2 months ago

#610 - deps: update statrs requirement from >= 0.11, < 0.18 to >= 0.11, < 0.19

Pull Request - State: open - Opened by dependabot[bot] 2 months ago
Labels: dependencies

#609 - Allow record.id() to get the first field before the first "|" instead of white space

Issue - State: open - Opened by dawnmy 2 months ago

#608 - deps: update thiserror requirement from 1 to 2

Pull Request - State: open - Opened by dependabot[bot] 3 months ago
Labels: dependencies

#607 - Consider publishing intervaltree/datastructures implementation as a standalone crate

Issue - State: open - Opened by derekleverenz 4 months ago - 1 comment

#606 - Index out of bounds in `FMIndex::backwards_search`

Issue - State: open - Opened by RagnarGrootKoerkamp 5 months ago

#605 - fix: out of index fix for one character sequence inputs POA

Pull Request - State: open - Opened by lorewar2 5 months ago - 3 comments

#604 - chore: add clippy workflow

Pull Request - State: closed - Opened by johanneskoester 5 months ago - 1 comment

#603 - feat: added parser for bionano custom file formats

Pull Request - State: open - Opened by laurakuehle 5 months ago

#602 - chore(master): release 2.0.3

Pull Request - State: closed - Opened by github-actions[bot] 5 months ago - 1 comment
Labels: autorelease: tagged

#601 - chore(master): release 2.0.2

Pull Request - State: closed - Opened by github-actions[bot] 5 months ago - 1 comment
Labels: autorelease: tagged

#600 - refactor: imports

Pull Request - State: open - Opened by Guelakais 7 months ago - 6 comments

#599 - deps: update ndarray requirement from >=0.15, <0.16 to >=0.15, <0.17

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#598 - chore(master): release 2.0.1

Pull Request - State: closed - Opened by github-actions[bot] 7 months ago - 1 comment
Labels: autorelease: tagged

#597 - fix: Add missing method to access phase of gff record

Pull Request - State: closed - Opened by fxwiegand 7 months ago - 6 comments

#596 - deps: update bit-set requirement from 0.5 to 0.8

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago - 3 comments
Labels: dependencies

#595 - deps: update statrs requirement from >= 0.11, < 0.17 to >= 0.11, < 0.18

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago - 1 comment
Labels: dependencies

#594 - deps: update bit-set requirement from 0.5 to 0.6

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago - 1 comment
Labels: dependencies

#593 - refactor!: Refactor misleadingly named method io::gff::Record::frame to phase and improve typing

Pull Request - State: closed - Opened by fxwiegand 8 months ago

#592 - ❔ [Question]: Has anyone started wrapping a Python package around rust-bio?

Issue - State: open - Opened by galenseilis 8 months ago

#591 - POA consensus seems incorrect

Issue - State: closed - Opened by davidlougheed 8 months ago - 1 comment

#590 - deps: update itertools requirement from >=0.8, <0.13 to >=0.8, <0.14

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies

#589 - Integration of `PDBTBX`

Issue - State: open - Opened by OWissett 9 months ago

#588 - deps: update strum requirement from >= 0.16, < 0.26 to >= 0.16, < 0.27

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 3 comments
Labels: dependencies

#587 - deps: update multimap requirement from >=0.6, <0.10 to >=0.6, <0.11

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies

#586 - deps: update strum_macros requirement from >= 0.16, < 0.26 to >= 0.16, < 0.27

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies

#585 - chore(master): release 2.0.0

Pull Request - State: closed - Opened by github-actions[bot] 10 months ago - 1 comment
Labels: autorelease: tagged

#584 - fix: Fix clippy warnings

Pull Request - State: closed - Opened by albertsgarde 11 months ago

#583 - "Error(Deserialize" when reading records from file

Issue - State: closed - Opened by simonharnqvist 11 months ago - 2 comments

#582 - fix: Remove unnecessary and unsound use of unsafe

Pull Request - State: closed - Opened by albertsgarde 11 months ago

#581 - Unnecessary and unsound use of unsafe

Issue - State: closed - Opened by albertsgarde 11 months ago - 2 comments

#580 - ci: allow deps as semantic PR title prefix

Pull Request - State: closed - Opened by dcroote 11 months ago

#579 - Strange Behavior of the fasta reader module

Issue - State: closed - Opened by Guelakais 11 months ago - 5 comments

#578 - Performance issues with the pairwise alignment module

Issue - State: closed - Opened by Guelakais 11 months ago - 8 comments

#577 - fix: Make LogProb comparable

Pull Request - State: closed - Opened by Addimator 12 months ago - 1 comment

#576 - Which alignment algorithm is which?

Issue - State: closed - Opened by Guelakais almost 1 year ago - 3 comments

#575 - fix: POA reverse edge fix

Pull Request - State: closed - Opened by lorewar2 about 1 year ago - 17 comments

#574 - Question : how to get all the elements of Dbxref

Issue - State: open - Opened by simonpenel about 1 year ago

#573 - chore: release 1.6.0

Pull Request - State: closed - Opened by github-actions[bot] about 1 year ago - 1 comment
Labels: autorelease: tagged

#572 - POA panics on some sets of sequences

Issue - State: closed - Opened by davidlougheed about 1 year ago - 8 comments

#571 - POA method to get aligned sequences with gaps back?

Issue - State: open - Opened by davidlougheed about 1 year ago - 3 comments

#570 - Question: How does the rust-bio distance module handle ambiguous bases?

Issue - State: closed - Opened by nrminor about 1 year ago - 2 comments

#569 - feat: POA semi-global, local, and custom alignment

Pull Request - State: closed - Opened by lorewar2 about 1 year ago

#568 - POA end gap/semi-global alignment

Issue - State: open - Opened by ctsa about 1 year ago - 7 comments

#567 - refactor: remove getset

Pull Request - State: closed - Opened by serprex about 1 year ago

#566 - fix(ci): Fix Dependabot

Pull Request - State: closed - Opened by sjackman about 1 year ago - 2 comments

#565 - deps: update ordered-float requirement from 3.1 to 4.2

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 5 comments
Labels: dependencies

#564 - chore: release 1.5.0

Pull Request - State: closed - Opened by github-actions[bot] about 1 year ago - 1 comment
Labels: autorelease: tagged

#563 - feat: Add pretty output for poa

Pull Request - State: closed - Opened by lorewar2 about 1 year ago - 1 comment

#562 - deps: update itertools requirement from >=0.8, <0.12 to >=0.8, <0.13

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 6 comments
Labels: dependencies

#561 - Fixing cdylib

Pull Request - State: closed - Opened by mwiewior over 1 year ago

#560 - chore: release 1.4.1

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago
Labels: autorelease: pending

#559 - Update statrs version to 0.16 to avoid future rust incompatibility

Issue - State: open - Opened by robinpaul85 over 1 year ago

#558 - fix: minimum ndarray version is 0.15

Pull Request - State: closed - Opened by dcroote over 1 year ago

#557 - chore: temporarily disable coverage estimation until simd support has arrived in the stable rust stdlib

Pull Request - State: closed - Opened by johanneskoester over 1 year ago

#556 - Compat error with array depencency

Issue - State: closed - Opened by jakobnissen over 1 year ago - 2 comments

#555 - deps: update ordered-float requirement from 3.1 to 4.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#554 - chore: fix cargo tarpaulin usage

Pull Request - State: open - Opened by johanneskoester over 1 year ago

#553 - chore: fix MSRV

Pull Request - State: closed - Opened by johanneskoester over 1 year ago

#552 - fix: memory efficient poa bug fix

Pull Request - State: closed - Opened by lorewar2 over 1 year ago - 2 comments

#551 - chore: release 1.4.0

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#550 - feat: added public function for construction of suffix array from integer alphabets

Pull Request - State: closed - Opened by andynet over 1 year ago - 1 comment

#549 - POA index out of bounds

Issue - State: closed - Opened by wdecoster over 1 year ago - 26 comments

#548 - RankSelect uses double the space needed

Issue - State: open - Opened by jorgehermo9 over 1 year ago

#547 - Pretty format for multiple sequence alignment with POA

Issue - State: closed - Opened by jhrcook over 1 year ago - 1 comment

#546 - Cargo.toml instructions should suggest `bio = "1"` instead of `bio = "*"`

Issue - State: open - Opened by ChaiTRex over 1 year ago

#545 - Select operation on RankSelect structure may be broken

Issue - State: open - Opened by jorgehermo9 over 1 year ago

#544 - action-semantic-pull-request does not accept 'deps' as type

Issue - State: closed - Opened by dcroote over 1 year ago - 2 comments

#543 - Coverage CI test failing due to compiler bug (being addressed upstream)

Issue - State: open - Opened by dlaehnemann over 1 year ago - 1 comment

#542 - fix: make dependabot commit message follow conventional commits

Pull Request - State: closed - Opened by dlaehnemann over 1 year ago - 3 comments

#541 - build(deps): update multimap requirement from >=0.6, <0.9 to >=0.6, <0.10

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#540 - build(deps): update enum-map requirement from >=0.6.4, <2 to >=0.6.4, <3

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#539 - feat: Blastn with http request

Pull Request - State: open - Opened by CaroCardozo over 1 year ago - 2 comments

#538 - fix: Expand path variables when reading `fasta` files

Pull Request - State: closed - Opened by nleroy917 over 1 year ago - 3 comments

#537 - chore: release 1.3.2

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago
Labels: autorelease: pending

#536 - ci: Add dependabot

Pull Request - State: closed - Opened by SKY-ALIN over 1 year ago - 11 comments

#535 - build(deps): bump strum from 0.24.1 0.25.0

Pull Request - State: closed - Opened by sjackman over 1 year ago - 4 comments

#534 - build(deps): Depend on itertools >=0.8, <0.12

Pull Request - State: closed - Opened by sjackman over 1 year ago - 3 comments

#533 - fix: include `doctests` in the test coverage of code that tarpaulin calculates

Pull Request - State: closed - Opened by dlaehnemann over 1 year ago - 4 comments

#532 - feat: memory efficient banded poa

Pull Request - State: closed - Opened by lorewar2 over 1 year ago - 1 comment

#531 - docs: don't use wildcard version, replace 'extern crate' with 'use'

Pull Request - State: closed - Opened by yjhn over 1 year ago - 1 comment

#530 - chore: release 1.3.1

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 2 comments
Labels: autorelease: tagged

#529 - chore: release 1.3.0

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#528 - chore: update MSRV

Pull Request - State: closed - Opened by johanneskoester over 1 year ago - 1 comment

#527 - feat: Addition of Transcribe and Translate features

Pull Request - State: open - Opened by Cardosaum over 1 year ago - 1 comment

#526 - [Feature Request] Add Transcription & Translation capabilities

Issue - State: open - Opened by Cardosaum over 1 year ago

#525 - feat: Consensus sequence from partial order alignment graph

Pull Request - State: closed - Opened by lorewar2 over 1 year ago

#524 - feat: update to bio-types 1.0

Pull Request - State: closed - Opened by johanneskoester over 1 year ago - 1 comment

#523 - chore: release 1.2.0

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#522 - perf: improve alignment::distance::levenshtein and alignment::distance::bounded_levenshtein on strrings where distance is small

Pull Request - State: closed - Opened by nkkarpov over 1 year ago - 3 comments

GitHub / rust-bio/rust-bio issues and pull requests