Ecosyste.ms: Issues

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

GitHub / zaeleus/noodles issues and pull requests

#302 - Error parsing vcf data from ncbi

Issue - State: closed - Opened by MoutainPL 12 days ago - 3 comments
Labels: vcf

#300 - Should writing Strings to INFO be escaped

Issue - State: closed - Opened by holtgrewe 25 days ago - 2 comments
Labels: bug, vcf

#299 - GTF parser fails when textual attributes contain semicolons

Issue - State: closed - Opened by kaizhang 27 days ago - 1 comment
Labels: bug, gtf

#297 - How to get tags

Issue - State: closed - Opened by Liripo about 1 month ago

#296 - util/alignment/async: Add async indexed reader

Issue - State: open - Opened by zaeleus about 1 month ago
Labels: enhancement, util

#294 - cram/async/io/writer: Add convenience method to write file definition and SAM header

Issue - State: closed - Opened by zaeleus about 1 month ago
Labels: enhancement, cram

#293 - cram/async/io/writer: Add alignment record writer

Issue - State: closed - Opened by zaeleus about 1 month ago
Labels: enhancement, cram

#292 - Add async alignment writer

Pull Request - State: closed - Opened by mbhall88 about 1 month ago - 2 comments
Labels: util

#291 - gtf parse error

Issue - State: closed - Opened by qingyun039 about 1 month ago - 1 comment
Labels: gtf

#291 - gtf parse error

Issue - State: closed - Opened by qingyun039 about 1 month ago - 1 comment
Labels: gtf

#290 - adds example for how to use the multi-threaded bgzf reader with bams

Pull Request - State: closed - Opened by bwlang about 1 month ago - 1 comment
Labels: bam

#290 - adds example for how to use the multi-threaded bgzf reader with bams

Pull Request - State: closed - Opened by bwlang about 1 month ago - 1 comment
Labels: bam

#289 - Convenience methods for SAM records

Issue - State: closed - Opened by mbhall88 about 2 months ago - 2 comments
Labels: sam

#288 - Add async alignment reader

Pull Request - State: closed - Opened by mbhall88 about 2 months ago - 2 comments
Labels: util

#287 - Support fastq comments/attributes/metadata

Issue - State: closed - Opened by d-cameron 2 months ago - 3 comments
Labels: enhancement, fastq

#286 - Unified async alignment reader/writer

Issue - State: closed - Opened by mbhall88 2 months ago - 3 comments
Labels: util

#285 - templeate_length() for long reads

Issue - State: closed - Opened by Psy-Fer 2 months ago - 2 comments
Labels: sam

#283 - sam/alignment/record/sequence: Add a method signature to return a single base at a given index

Issue - State: closed - Opened by zaeleus 2 months ago - 3 comments
Labels: bam, cram, sam

#282 - Trait bounds changes in noodles_sam 0.62.0

Issue - State: closed - Opened by mbhall88 3 months ago - 1 comment

#279 - Performance question

Issue - State: closed - Opened by anderspitman 3 months ago

#278 - Create test SAM data

Issue - State: closed - Opened by mbhall88 3 months ago - 2 comments
Labels: enhancement, sam

#277 - QualityScore conversion from fastq

Issue - State: open - Opened by d-cameron 3 months ago - 1 comment
Labels: fastq

#277 - QualityScore conversion from fastq

Issue - State: closed - Opened by d-cameron 3 months ago - 2 comments
Labels: fastq

#274 - How to write custom bam records

Issue - State: closed - Opened by SteampunkIslande 3 months ago - 1 comment

#274 - How to write custom bam records

Issue - State: closed - Opened by SteampunkIslande 3 months ago - 1 comment

#274 - How to write custom bam records

Issue - State: closed - Opened by SteampunkIslande 3 months ago - 4 comments

#273 - bgzf/async/reader: Add seeking to an uncompressed position

Issue - State: closed - Opened by zaeleus 3 months ago
Labels: enhancement, bgzf

#273 - bgzf/async/reader: Add seeking to an uncompressed position

Issue - State: closed - Opened by zaeleus 3 months ago
Labels: enhancement, bgzf

#273 - bgzf/async/reader: Add seeking to an uncompressed position

Issue - State: closed - Opened by zaeleus 3 months ago
Labels: enhancement, bgzf

#271 - BED name column limit

Issue - State: closed - Opened by ghuls 4 months ago - 1 comment
Labels: bed

#270 - bed/record: Return ParseError::MissingScore instead of ParseError::Mi…

Pull Request - State: closed - Opened by ghuls 4 months ago - 1 comment
Labels: bed

#270 - bed/record: Return ParseError::MissingScore instead of ParseError::Mi…

Pull Request - State: closed - Opened by ghuls 4 months ago - 1 comment
Labels: bed

#269 - Can support flush method on writer ?

Issue - State: closed - Opened by sharkLoc 4 months ago - 3 comments
Labels: enhancement, fasta

#269 - Can support flush method on writer ?

Issue - State: closed - Opened by sharkLoc 4 months ago - 3 comments
Labels: enhancement, fasta

#269 - Can support flush method on writer ?

Issue - State: closed - Opened by sharkLoc 4 months ago - 3 comments
Labels: enhancement, fasta

#268 - IUPAC codes in VCF REF field

Issue - State: closed - Opened by ACEnglish 4 months ago - 1 comment
Labels: vcf

#267 - fix: error on sequence complement

Pull Request - State: closed - Opened by sharkLoc 4 months ago - 1 comment
Labels: fasta

#266 - BCF and VCF `record_bufs` return different `RecordBuf`s

Issue - State: closed - Opened by tedil 4 months ago - 2 comments
Labels: bug, bcf

#265 - add queried reader

Pull Request - State: open - Opened by Crispy13 5 months ago

#264 - `gff::AsyncReader` gated by async feature

Issue - State: closed - Opened by tshauck 5 months ago - 2 comments
Labels: bug

#264 - `gff::AsyncReader` gated by async feature

Issue - State: closed - Opened by tshauck 5 months ago - 2 comments
Labels: bug

#264 - `gff::AsyncReader` gated by async feature

Issue - State: closed - Opened by tshauck 5 months ago - 2 comments
Labels: bug

#264 - `gff::AsyncReader` gated by async feature

Issue - State: closed - Opened by tshauck 5 months ago - 2 comments
Labels: bug

#264 - `gff::AsyncReader` gated by async feature

Issue - State: closed - Opened by tshauck 5 months ago - 2 comments
Labels: bug

#262 - Add Async GFF Reader and/or expose lazy record from string?

Issue - State: closed - Opened by tshauck 5 months ago - 2 comments
Labels: enhancement, gff

#260 - Reading entries of file into preallocated buffer

Issue - State: closed - Opened by rickymagner 5 months ago - 3 comments
Labels: bam

#259 - Missing newlines in `header::record::write_other` when writing collections

Issue - State: closed - Opened by tedil 5 months ago - 1 comment
Labels: bug, vcf

#258 - How to set tag with value in noodles::bam?

Issue - State: closed - Opened by Crispy13 5 months ago - 2 comments
Labels: bam, sam

#257 - `sam::header::programs` module is private

Issue - State: closed - Opened by jch-13 5 months ago - 1 comment
Labels: sam

#257 - `sam::header::programs` module is private

Issue - State: closed - Opened by jch-13 5 months ago - 1 comment
Labels: sam

#255 - Unexpected EOF on BCF File

Issue - State: closed - Opened by tshauck 5 months ago - 2 comments
Labels: bug, bcf

#254 - `impl<'a> From<bam::record::Name<'a>> for sam::alignment::record_buf::Name` includes trailing NUL

Issue - State: closed - Opened by jch-13 5 months ago - 1 comment
Labels: bug, bam

#254 - `impl<'a> From<bam::record::Name<'a>> for sam::alignment::record_buf::Name` includes trailing NUL

Issue - State: closed - Opened by jch-13 5 months ago - 1 comment
Labels: bug, bam

#254 - `impl<'a> From<bam::record::Name<'a>> for sam::alignment::record_buf::Name` includes trailing NUL

Issue - State: closed - Opened by jch-13 5 months ago - 1 comment
Labels: bug, bam

#253 - About method names of `noodles_sam::alignment::record::Flags`

Issue - State: closed - Opened by Crispy13 6 months ago - 2 comments

#253 - About method names of `noodles_sam::alignment::record::Flags`

Issue - State: closed - Opened by Crispy13 6 months ago - 2 comments
Labels: sam

#253 - About method names of `noodles_sam::alignment::record::Flags`

Issue - State: closed - Opened by Crispy13 6 months ago - 2 comments

#252 - Docs typo

Issue - State: closed - Opened by Crispy13 6 months ago - 2 comments
Labels: bam

#251 - Getting raw record lines with lazy records

Issue - State: closed - Opened by rkimoakbioinformatics 6 months ago - 2 comments
Labels: vcf

#249 - record_buf object to sam::Record object?

Issue - State: closed - Opened by larryns 6 months ago - 2 comments
Labels: sam

#248 - util feature

Issue - State: closed - Opened by larryns 6 months ago - 4 comments
Labels: util

#248 - util feature

Issue - State: closed - Opened by larryns 6 months ago - 4 comments
Labels: util

#247 - sam/io/writer/record: Increase visibility of SAM record CIGAR string serializer

Issue - State: closed - Opened by zaeleus 6 months ago - 2 comments
Labels: sam

#246 - bgzf MultiThreadedReader Missing Error Message

Issue - State: closed - Opened by asgray 6 months ago - 2 comments
Labels: bgzf

#245 - Add new BAM example for full PG entry

Pull Request - State: closed - Opened by jamestwebber 7 months ago - 2 comments
Labels: bam, sam

#244 - migrating from 0.49 to 0.65: generating invalid BAM files

Issue - State: closed - Opened by jamestwebber 7 months ago - 2 comments
Labels: bug, bam

#243 - Async BGZF readers eagerly evaluate blocks

Issue - State: closed - Opened by mmalenic 7 months ago - 2 comments
Labels: bgzf

#241 - Parsing VCF fails for ID in header

Issue - State: closed - Opened by apraga 7 months ago - 3 comments
Labels: vcf

#238 - bgzf/multithreaded_writer: Add builder

Issue - State: closed - Opened by zaeleus 7 months ago - 1 comment
Labels: enhancement, bgzf

#238 - bgzf/multithreaded_writer: Add builder

Issue - State: closed - Opened by zaeleus 7 months ago - 1 comment
Labels: enhancement, bgzf

#237 - BGZF invalid header really strict

Issue - State: closed - Opened by andypexai 7 months ago - 6 comments
Labels: bgzf

#236 - Why `Flags::PROPERLY_ALIGNED` instead of `Flags::PROPERLY_PAIRED` as name?

Issue - State: closed - Opened by ghuls 7 months ago - 2 comments
Labels: sam

#236 - Why `Flags::PROPERLY_ALIGNED` instead of `Flags::PROPERLY_PAIRED` as name?

Issue - State: closed - Opened by ghuls 7 months ago - 2 comments
Labels: sam

#235 - Fixed-length `Character` fields

Issue - State: open - Opened by holtgrewe 7 months ago - 2 comments
Labels: vcf, bcf

#234 - `Send`-able `Repository`?

Issue - State: closed - Opened by tshauck 7 months ago - 2 comments
Labels: bug, fasta

#233 - question: how to convert cigar from bytes.

Issue - State: closed - Opened by cauliyang 8 months ago - 4 comments
Labels: enhancement, sam

#231 - Installation error

Issue - State: closed - Opened by andyjslee 8 months ago - 2 comments

#230 - Alignment span calculation (bug or misunderstanding)

Issue - State: closed - Opened by rob-p 8 months ago - 4 comments
Labels: bug, bam

#229 - noodles bam failled to write record with large mapping position.

Issue - State: closed - Opened by natir 8 months ago - 1 comment
Labels: bug, bam

#228 - noodles sam successfully read the recording but failed to write it

Issue - State: closed - Opened by natir 8 months ago - 2 comments
Labels: sam

#227 - Seamless parsing of BAM/SAM

Issue - State: closed - Opened by mbhall88 8 months ago - 4 comments

#224 - fix: lazy vcf overreading into next record

Pull Request - State: closed - Opened by tshauck 8 months ago - 5 comments

#223 - fix: fix range for INFO for lazy vcf record bounds

Pull Request - State: closed - Opened by tshauck 8 months ago - 1 comment
Labels: vcf

#222 - Question: different coalescing of bytes for index queries?

Issue - State: closed - Opened by tshauck 9 months ago - 2 comments
Labels: csi

#221 - Lazy reading of BAM records requires reading of the header first

Issue - State: closed - Opened by markjschreiber 9 months ago - 1 comment

#220 - Add underlying reader access for CRAM `AsyncReader`

Issue - State: closed - Opened by mmalenic 10 months ago - 1 comment
Labels: enhancement

#219 - Concurrent reading/decompression of BAM files.

Issue - State: closed - Opened by Adoni5 10 months ago - 3 comments
Labels: bam

#218 - noodles implementation is slower than rust-htslib, did I do something suboptimal?

Issue - State: closed - Opened by bwlang 10 months ago - 5 comments
Labels: bam, bgzf

#217 - Build Error on Windows

Issue - State: closed - Opened by tshauck 11 months ago - 1 comment
Labels: bug, csi

#216 - csi/writer: End position of a chunk is using wrong virtual position

Issue - State: closed - Opened by zaeleus 11 months ago
Labels: bug, csi

#215 - csi: tabix header indices are off by one

Issue - State: closed - Opened by zaeleus 11 months ago - 2 comments
Labels: bug, csi

#214 - How to index a VCF statically or on the fly

Issue - State: open - Opened by nh13 11 months ago - 4 comments
Labels: enhancement, vcf

#213 - Nondeterministic TBI index creation

Issue - State: closed - Opened by holtgrewe 11 months ago - 1 comment
Labels: enhancement, csi

#213 - Nondeterministic TBI index creation

Issue - State: closed - Opened by holtgrewe 11 months ago - 1 comment
Labels: enhancement, csi