zaeleus/noodles issues and pull requests

#346 - Error while parsing SVLEN field

Issue - State: closed - Opened by holtjma 15 days ago - 3 comments
Labels: bug, vcf

#345 - Quality score documentation

Issue - State: open - Opened by kaizhang about 1 month ago - 1 comment
Labels: bam, sam

#344 - vcf/variant/record_buf/builder: Change default variant start to missing

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

#343 - Zero position in VCF

Issue - State: open - Opened by drtconway about 1 month ago - 5 comments
Labels: enhancement, vcf

#342 - cargo add noodles -F bed fails

Issue - State: closed - Opened by drtconway about 2 months ago - 2 comments
Labels: bed

#341 - Question: handling absent chromosomes in VCF

Issue - State: closed - Opened by holtjma about 2 months ago - 1 comment
Labels: enhancement, vcf

#340 - feature building flate-2 without zlib-rs

Issue - State: open - Opened by govinda-kamath about 2 months ago - 3 comments
Labels: enhancement, bgzf

#339 - colon is percent encoded in INFO

Issue - State: open - Opened by d-cameron about 2 months ago
Labels: vcf

#338 - feat: `len()` and `iter()` implementations for quality scores

Pull Request - State: closed - Opened by theJasonFan 2 months ago - 1 comment
Labels: bam, sam

#337 - vcf/record/info: Avoid parsing skipped fields

Pull Request - State: closed - Opened by QuartzLibrary 3 months ago - 1 comment
Labels: vcf

#336 - BGZF: block data checksum mismatch

Issue - State: closed - Opened by Turakar 3 months ago - 3 comments
Labels: bug, bgzf

#334 - Question: noodles_util and try_from_variant_record

Issue - State: closed - Opened by holtjma 4 months ago - 3 comments
Labels: enhancement, vcf

#333 - Refget: Handle non-successful status codes

Pull Request - State: closed - Opened by juliangehring 5 months ago - 1 comment
Labels: refget

#332 - Refget: Handling of non-successful status codes

Issue - State: closed - Opened by juliangehring 5 months ago
Labels: refget

#331 - Switch to more performant, 100% Rust zlib

Pull Request - State: closed - Opened by brainstorm 5 months ago - 2 comments
Labels: bgzf

#330 - BED Writer uses Position which disallows 0 index

Issue - State: closed - Opened by Chris7 5 months ago - 2 comments
Labels: bed

#329 - Consider making the cram `read_header` future `Send`

Issue - State: closed - Opened by mmalenic 5 months ago - 1 comment
Labels: cram

#328 - Missing genotypes from BCF file

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

#326 - Cloud object storage support

Issue - State: closed - Opened by mwiewior 5 months ago - 3 comments

#325 - Question / bug: Indexing a VCF file with no records

Issue - State: closed - Opened by holtjma 6 months ago - 2 comments
Labels: bug, csi

#324 - gbff reader?

Issue - State: closed - Opened by djugei 6 months ago - 3 comments

#323 - make csi::io::indexed_records pub for access to ::record::Record

Pull Request - State: closed - Opened by brentp 6 months ago - 1 comment
Labels: csi

#321 - GTF attributes has no iter method (but GFF does)

Issue - State: closed - Opened by rob-p 6 months ago - 2 comments
Labels: bug, gtf

#320 - Question: ergonomic BAM indexing functionality

Issue - State: closed - Opened by holtjma 6 months ago - 2 comments
Labels: enhancement, bam

#319 - tabix header - InvalidReferenceSequenceNames(ExpectedEof)

Issue - State: closed - Opened by cademirch 6 months ago - 4 comments
Labels: bug, tabix

#317 - deserializing records from htsget stream

Issue - State: closed - Opened by cmdoret 6 months ago
Labels: cram, htsget

#316 - How to get a value of a attribute from gtf file by using the key

Issue - State: closed - Opened by zhengxinchang 6 months ago - 1 comment
Labels: enhancement, gtf

#315 - Minimum rust version not correct for bam.

Issue - State: closed - Opened by TyberiusPrime 7 months ago - 1 comment
Labels: bug

#314 - VCF header error

Issue - State: open - Opened by drtconway 7 months ago - 5 comments
Labels: enhancement, vcf

#309 - How to convert Cigar to its string representation?

Issue - State: closed - Opened by kaizhang 8 months ago
Labels: sam

#308 - InvalidVersion error

Issue - State: closed - Opened by ACEnglish 9 months ago - 2 comments
Labels: vcf

#307 - Repeated BAM tag field: `OX`

Issue - State: closed - Opened by wjwei-handsome 9 months ago - 1 comment
Labels: bug, sam

#306 - Accept U as a base type and convert to T for BAM.

Issue - State: open - Opened by jkbonfield 9 months ago
Labels: bam

#305 - "invalid start positions" when reading unmapped cram

Issue - State: closed - Opened by HadrienG 9 months ago - 2 comments
Labels: bug, cram

#304 - VCF Sample columns

Issue - State: closed - Opened by ACEnglish 10 months ago - 1 comment
Labels: vcf

#303 - `noodles_util`'s `alignment::io::indexed_reader` does not recognize `set_index`

Issue - State: closed - Opened by jonghwanyoon 10 months ago - 1 comment
Labels: bug, util

#302 - Error parsing vcf data from ncbi

Issue - State: closed - Opened by MoutainPL 10 months ago - 3 comments
Labels: vcf

#300 - Should writing Strings to INFO be escaped

Issue - State: closed - Opened by holtgrewe 11 months ago - 2 comments
Labels: bug, vcf

#299 - GTF parser fails when textual attributes contain semicolons

Issue - State: closed - Opened by kaizhang 11 months ago - 1 comment
Labels: bug, gtf

#297 - How to get tags

Issue - State: closed - Opened by Liripo 11 months ago

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

Issue - State: open - Opened by zaeleus 11 months ago
Labels: enhancement, util

#295 - cram/io/writer/builder: Rename Builder::build_with_writer to Builder::build_from_writer

Issue - State: closed - Opened by zaeleus 11 months ago
Labels: cram

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

Issue - State: closed - Opened by zaeleus 11 months ago
Labels: enhancement, cram

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

Issue - State: closed - Opened by zaeleus 11 months ago
Labels: enhancement, cram

#292 - Add async alignment writer

Pull Request - State: closed - Opened by mbhall88 11 months ago - 2 comments
Labels: util

#291 - gtf parse error

Issue - State: closed - Opened by qingyun039 11 months 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 11 months ago - 1 comment
Labels: bam

#289 - Convenience methods for SAM records

Issue - State: closed - Opened by mbhall88 12 months ago - 2 comments
Labels: sam

#288 - Add async alignment reader

Pull Request - State: closed - Opened by mbhall88 12 months ago - 2 comments
Labels: util

#287 - Support fastq comments/attributes/metadata

Issue - State: closed - Opened by d-cameron 12 months ago - 3 comments
Labels: enhancement, fastq

#286 - Unified async alignment reader/writer

Issue - State: closed - Opened by mbhall88 about 1 year ago - 3 comments
Labels: util

#285 - templeate_length() for long reads

Issue - State: closed - Opened by Psy-Fer about 1 year 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 about 1 year ago - 3 comments
Labels: bam, cram, sam

#282 - Trait bounds changes in noodles_sam 0.62.0

Issue - State: closed - Opened by mbhall88 about 1 year ago - 1 comment

#279 - Performance question

Issue - State: closed - Opened by anderspitman about 1 year ago

#278 - Create test SAM data

Issue - State: closed - Opened by mbhall88 about 1 year ago - 2 comments
Labels: enhancement, sam

#277 - QualityScore conversion from fastq

Issue - State: closed - Opened by d-cameron about 1 year ago - 2 comments
Labels: fastq

#275 - Help request: using the noodles async FASTQ writer with async compression without corrupting the output

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

#274 - How to write custom bam records

Issue - State: closed - Opened by SteampunkIslande about 1 year ago - 4 comments

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

Issue - State: closed - Opened by zaeleus about 1 year ago
Labels: enhancement, bgzf

#271 - BED name column limit

Issue - State: closed - Opened by ghuls about 1 year ago - 1 comment
Labels: bed

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

Pull Request - State: closed - Opened by ghuls about 1 year ago - 1 comment
Labels: bed

#269 - Can support flush method on writer ?

Issue - State: closed - Opened by sharkLoc about 1 year ago - 3 comments
Labels: enhancement, fasta

#268 - IUPAC codes in VCF REF field

Issue - State: closed - Opened by ACEnglish about 1 year ago - 1 comment
Labels: vcf

#267 - fix: error on sequence complement

Pull Request - State: closed - Opened by sharkLoc about 1 year ago - 1 comment
Labels: fasta

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

Issue - State: closed - Opened by tedil about 1 year ago - 2 comments
Labels: bug, bcf

#265 - add queried reader

Pull Request - State: open - Opened by Crispy13 about 1 year ago

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

Issue - State: closed - Opened by tshauck about 1 year ago - 2 comments
Labels: bug

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

Issue - State: closed - Opened by tshauck about 1 year ago - 2 comments
Labels: enhancement, gff

#260 - Reading entries of file into preallocated buffer

Issue - State: closed - Opened by rickymagner about 1 year ago - 3 comments
Labels: bam

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

Issue - State: closed - Opened by tedil about 1 year ago - 1 comment
Labels: bug, vcf

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

Issue - State: closed - Opened by Crispy13 about 1 year ago - 2 comments
Labels: bam, sam

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

Issue - State: closed - Opened by jch-13 over 1 year ago - 1 comment
Labels: sam

#255 - Unexpected EOF on BCF File

Issue - State: closed - Opened by tshauck over 1 year 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 over 1 year ago - 1 comment
Labels: bug, bam

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

Issue - State: closed - Opened by Crispy13 over 1 year ago - 2 comments
Labels: sam

#252 - Docs typo

Issue - State: closed - Opened by Crispy13 over 1 year ago - 2 comments
Labels: bam

#251 - Getting raw record lines with lazy records

Issue - State: closed - Opened by rkimoakbioinformatics over 1 year ago - 2 comments
Labels: vcf

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

Issue - State: closed - Opened by larryns over 1 year ago - 2 comments
Labels: sam

#248 - util feature

Issue - State: closed - Opened by larryns over 1 year ago - 4 comments
Labels: util

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

Issue - State: closed - Opened by zaeleus over 1 year ago - 2 comments
Labels: sam

#246 - bgzf MultiThreadedReader Missing Error Message

Issue - State: closed - Opened by asgray over 1 year ago - 2 comments
Labels: bgzf

#245 - Add new BAM example for full PG entry

Pull Request - State: closed - Opened by jamestwebber over 1 year ago - 2 comments
Labels: bam, sam

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

Issue - State: closed - Opened by jamestwebber over 1 year ago - 2 comments
Labels: bug, bam

#243 - Async BGZF readers eagerly evaluate blocks

Issue - State: closed - Opened by mmalenic over 1 year ago - 2 comments
Labels: bgzf

#241 - Parsing VCF fails for ID in header

Issue - State: closed - Opened by apraga over 1 year ago - 3 comments
Labels: vcf

#238 - bgzf/multithreaded_writer: Add builder

Issue - State: closed - Opened by zaeleus over 1 year ago - 1 comment
Labels: enhancement, bgzf

#237 - BGZF invalid header really strict

Issue - State: closed - Opened by andypexai over 1 year ago - 6 comments
Labels: bgzf

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

Issue - State: closed - Opened by ghuls over 1 year ago - 2 comments
Labels: sam

#235 - Fixed-length `Character` fields

Issue - State: open - Opened by holtgrewe over 1 year ago - 2 comments
Labels: vcf, bcf

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

Issue - State: closed - Opened by tshauck over 1 year ago - 2 comments
Labels: bug, fasta

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

Issue - State: closed - Opened by cauliyang over 1 year ago - 4 comments
Labels: enhancement, sam

#231 - Installation error

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

#230 - Alignment span calculation (bug or misunderstanding)

Issue - State: closed - Opened by rob-p over 1 year ago - 4 comments
Labels: bug, bam

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

Issue - State: closed - Opened by natir over 1 year ago - 1 comment
Labels: bug, bam

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

Issue - State: closed - Opened by natir over 1 year ago - 2 comments
Labels: sam

#227 - Seamless parsing of BAM/SAM

Issue - State: closed - Opened by mbhall88 over 1 year ago - 4 comments

#226 - Documentation is opaque on 0 vs 1 indexing, and whether regions are right-inclusive or not.

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

#224 - fix: lazy vcf overreading into next record

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

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

Pull Request - State: closed - Opened by tshauck over 1 year ago - 1 comment
Labels: vcf

GitHub / zaeleus/noodles issues and pull requests