Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

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

#429 - subsetting samples

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

#428 - feat: derive PartialEq and Eq for bam:: and bcf::Format

Pull Request - State: open - Opened by mbhall88 2 months ago - 1 comment

#427 - get sequence reads from rust_htslib::bam::record::Seq

Issue - State: closed - Opened by wdlv 3 months ago - 2 comments

#426 - chore(master): release 0.47.0

Pull Request - State: open - Opened by github-actions[bot] 3 months ago
Labels: autorelease: pending

#425 - Compiler issue on AArch64 Linux

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

#423 - error: could not compile `rust-htslib`

Issue - State: open - Opened by knakamura6222053 4 months ago

#422 - How to access read group info from `Record`?

Issue - State: open - Opened by Crispy13 4 months ago - 2 comments

#421 - chore(master): release 0.46.0

Pull Request - State: closed - Opened by github-actions[bot] 4 months ago - 1 comment
Labels: autorelease: tagged

#420 - fix: fix building libz-sys

Pull Request - State: closed - Opened by FelixMoelder 4 months ago - 2 comments

#419 - feat: making several RecordBuffer methods public

Pull Request - State: closed - Opened by Addimator 4 months ago - 1 comment

#418 - feat: Add fasta::build function + FaidxBuildError

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

#417 - fix: Panic on trailing omitted FORMAT records

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

#416 - Seek/Tell for BGZF Module

Issue - State: open - Opened by rmhubley 6 months ago

#415 - fix: Loosen acceptable types to support current linux build on aarch64

Pull Request - State: closed - Opened by rdeaton-freenome 6 months ago - 3 comments

#413 - chore(master): release 0.45.0

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

#411 - BCF reader partial unpacking for site-only queries

Issue - State: open - Opened by bguo068 8 months ago

#410 - feat: add faidx_seq_len function

Pull Request - State: closed - Opened by pblischak 9 months ago

#408 - feat: Add rust_htslib::bcf::index::build

Pull Request - State: closed - Opened by PB-DB 9 months ago - 5 comments

#407 - Panic on omitted trailing FORMAT fields

Issue - State: open - Opened by fennerm 11 months ago - 2 comments

#405 - How to operate on Format/Info fields for Records?

Issue - State: open - Opened by rickymagner 11 months ago - 2 comments

#404 - Reading bam from s3

Issue - State: open - Opened by wdecoster 11 months ago - 3 comments

#403 - Question: multi-threaded reading of BAM files

Issue - State: open - Opened by rashidalabri 11 months ago

#401 - [bug] Memory leak when using `faidx::Reader::fetch_seq()` ?

Issue - State: open - Opened by MaelLefeuvre 12 months ago - 10 comments

#400 - Are there filter options available for pileup?

Issue - State: open - Opened by Crispy13 12 months ago - 4 comments

#399 - chore(master): release 0.44.1

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

#398 - fix: use correct return value in bcf_get_format and bcf_get_info_values

Pull Request - State: closed - Opened by Marlin-Na about 1 year ago - 5 comments

#397 - fix: include doctests in test coverage calculations

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

#396 - fix: makes Header.to_hashmap() not call unwrap.

Pull Request - State: open - Opened by ArtRand about 1 year ago - 3 comments

#395 - chore(master): release 0.44.0

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

#394 - feat: implement Clone for bcf::Record

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

#393 - fix: strand() doesn't need mut.

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

#392 - chore(master): release 0.43.1

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

#391 - fix: implement Drop for faidx::Reader, destroying the fai handle

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

#390 - faidx file not closed when Reader goes out of scope: Too many open files

Issue - State: closed - Opened by wdecoster about 1 year ago - 3 comments

#389 - chore(master): release 0.43.0

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

#388 - feat: HeaderRecord::push_tag: Value may be owned

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

#387 - feat: Index for `bam::IndexedReader`

Pull Request - State: closed - Opened by tedil about 1 year ago - 5 comments

#386 - Accessing the index file from a `bam::IndexedReader`

Issue - State: closed - Opened by tedil about 1 year ago - 4 comments
Labels: help wanted, question

#385 - feat: implement htslib basemod api

Pull Request - State: closed - Opened by jts about 1 year ago - 25 comments

#384 - fix: Allow empty tags in BAM header

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

#383 - chore(master): release 0.42.0

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

#382 - How to: empty sequence and quality for BAM entries

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

#381 - faidx: expose n_seq and seqi

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

#380 - chore(master): release 0.41.1

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

#379 - chore(master): release 0.41.0

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

#378 - chore(master): release rust-htslib 0.41.0

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

#377 - feat: Add ability to fetch number of sequences and I-th sequence from FAI index

Pull Request - State: closed - Opened by jamorrison over 1 year ago - 7 comments

#376 - ci: Pin tarpaulin version

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

#375 - feat: Revised calculation of leading- and trailing-softclips

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

#374 - feat: Implement htslib basemod api

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

#373 - Question: VCF file indexing function

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

#372 - feat: exposes CigarStringView pos

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

#370 - Windows compatibility

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

#369 - Building conda recipe with rust-htslib as dependency: failure on osx

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

#368 - chore(master): release rust-htslib 0.40.2

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

#367 - chore(master): release hts-sys 2.0.3

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

#366 - perf: update htslib and corresponding bindings to 1.16

Pull Request - State: closed - Opened by johanneskoester over 1 year ago - 5 comments

#364 - chore(master): release rust-htslib 0.40.1

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago - 1 comment
Labels: autorelease: tagged

#363 - fix: fixed fn to_hashmap so it can avoid an error when @CO tag appeared

Pull Request - State: closed - Opened by shohei-kojima almost 2 years ago - 13 comments

#362 - Plans to support modified bases (MM and ML tags)?

Issue - State: closed - Opened by mrvollger almost 2 years ago - 3 comments

#361 - fix: bam::Record:new should return a valid record

Pull Request - State: open - Opened by nh13 about 2 years ago - 7 comments

#360 - bcf::header::rid2name outputs incorrect name

Issue - State: closed - Opened by ngleadall about 2 years ago - 1 comment

#359 - fastest way to locate reads which contain specify kemr use rust-htslib??

Issue - State: closed - Opened by nihilee about 2 years ago - 4 comments

#358 - refactor: move source into subfolder

Pull Request - State: open - Opened by johanneskoester about 2 years ago - 3 comments

#357 - chore(master): release rust-htslib 0.40.0

Pull Request - State: closed - Opened by github-actions[bot] about 2 years ago - 1 comment
Labels: autorelease: tagged

#356 - chore: release rust-htslib 0.39.5

Pull Request - State: closed - Opened by github-actions[bot] about 2 years ago - 2 comments
Labels: autorelease: tagged

#355 - chore: release rust-htslib 0.39.4

Pull Request - State: closed - Opened by github-actions[bot] about 2 years ago - 1 comment
Labels: autorelease: tagged

#354 - fix: Update Cargo.toml

Pull Request - State: closed - Opened by rob-p about 2 years ago - 1 comment

#353 - publishing updated versions to crates.io

Issue - State: closed - Opened by rob-p about 2 years ago - 2 comments

#352 - Compile issue on OSX / M1

Issue - State: closed - Opened by rob-p about 2 years ago - 2 comments

#351 - Build portability is complicated by recent zlib-ng updates

Issue - State: open - Opened by ctsa about 2 years ago

#349 - feat: Add wrapper of BGZF writer

Pull Request - State: closed - Opened by jemma-nelson over 2 years ago - 1 comment

#348 - Question about reference sequence

Issue - State: closed - Opened by nihilee over 2 years ago - 1 comment

#347 - Support for BGZF writer?

Issue - State: closed - Opened by jemma-nelson over 2 years ago - 2 comments

#346 - Modify allele of a vcf entry

Issue - State: closed - Opened by ebioman over 2 years ago - 1 comment

#345 - fix: Workaround Non-Threadsafe Use of `Rc` in `bam::record::Record`

Pull Request - State: open - Opened by jch-13 over 2 years ago - 1 comment

#344 - Most recent releases not published on crates.io

Issue - State: closed - Opened by jch-13 over 2 years ago

#343 - Merge VCF headers

Issue - State: open - Opened by wdesouza over 2 years ago - 2 comments

#342 - How should bcf::Record::push_info_float work?

Issue - State: open - Opened by xosxos over 2 years ago - 1 comment

#341 - build: Upgrade libdeflater

Pull Request - State: closed - Opened by sstadick over 2 years ago - 1 comment

#340 - Upgrade libdeflater

Issue - State: closed - Opened by sstadick over 2 years ago

#339 - Problem creating new BAM records (SAM=Segfault,BAM=silent failure)

Issue - State: open - Opened by ebioman over 2 years ago - 8 comments

#338 - chore: release rust-htslib 0.39.3

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

#337 - fix: change the type to c_char so it can be compiled for aarch64

Pull Request - State: closed - Opened by cschin over 2 years ago - 8 comments

#336 - chore: Exclude test files from crate package.

Pull Request - State: closed - Opened by adam-azarchs over 2 years ago - 1 comment

#335 - Add update_aux function to BAM records.

Issue - State: open - Opened by ghuls over 2 years ago - 2 comments

#334 - Quickest way for pileup at known position?

Issue - State: open - Opened by ebioman over 2 years ago

#333 - hts-sys can not be installed

Issue - State: closed - Opened by y9c almost 3 years ago - 5 comments

#332 - build: update htslib & fix build.rs

Pull Request - State: closed - Opened by pmarks almost 3 years ago - 2 comments

#331 - chore: release rust-htslib 0.39.2

Pull Request - State: closed - Opened by github-actions[bot] almost 3 years ago - 1 comment
Labels: autorelease: tagged

#330 - chore: release hts-sys 2.0.2

Pull Request - State: closed - Opened by github-actions[bot] almost 3 years ago - 1 comment
Labels: autorelease: tagged