zaeleus/noodles issues and pull requests

#271 - BED name column limit

Issue - State: closed - Opened by ghuls 16 days ago - 1 comment
Labels: bed

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

Pull Request - State: closed - Opened by ghuls 16 days ago - 1 comment
Labels: bed

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

Pull Request - State: closed - Opened by ghuls 16 days ago - 1 comment
Labels: bed

#269 - Can support flush method on writer ?

Issue - State: closed - Opened by sharkLoc 24 days ago - 3 comments
Labels: enhancement, fasta

#269 - Can support flush method on writer ?

Issue - State: closed - Opened by sharkLoc 24 days ago - 3 comments
Labels: enhancement, fasta

#269 - Can support flush method on writer ?

Issue - State: closed - Opened by sharkLoc 24 days ago - 3 comments
Labels: enhancement, fasta

#268 - IUPAC codes in VCF REF field

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

#267 - fix: error on sequence complement

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

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

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

#265 - add queried reader

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

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

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

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

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

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

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

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

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

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

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

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

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

#260 - Reading entries of file into preallocated buffer

Issue - State: closed - Opened by rickymagner about 2 months ago - 3 comments
Labels: bam

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

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

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

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

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

Issue - State: closed - Opened by jch-13 2 months ago - 1 comment
Labels: sam

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

Issue - State: closed - Opened by jch-13 2 months ago - 1 comment
Labels: sam

#255 - Unexpected EOF on BCF File

Issue - State: closed - Opened by tshauck 2 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 2 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 2 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 2 months ago - 1 comment
Labels: bug, bam

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

Issue - State: closed - Opened by Crispy13 3 months ago - 2 comments

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

Issue - State: closed - Opened by Crispy13 3 months ago - 2 comments
Labels: sam

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

Issue - State: closed - Opened by Crispy13 3 months ago - 2 comments

#252 - Docs typo

Issue - State: closed - Opened by Crispy13 3 months ago - 2 comments
Labels: bam

#251 - Getting raw record lines with lazy records

Issue - State: closed - Opened by rkimoakbioinformatics 3 months ago - 2 comments
Labels: vcf

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

Issue - State: closed - Opened by larryns 3 months ago - 2 comments
Labels: sam

#248 - util feature

Issue - State: closed - Opened by larryns 3 months ago - 4 comments
Labels: util

#248 - util feature

Issue - State: closed - Opened by larryns 3 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 3 months ago - 2 comments
Labels: sam

#246 - bgzf MultiThreadedReader Missing Error Message

Issue - State: closed - Opened by asgray 3 months ago - 2 comments
Labels: bgzf

#245 - Add new BAM example for full PG entry

Pull Request - State: closed - Opened by jamestwebber 4 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 4 months ago - 2 comments
Labels: bug, bam

#243 - Async BGZF readers eagerly evaluate blocks

Issue - State: closed - Opened by mmalenic 4 months ago - 2 comments
Labels: bgzf

#241 - Parsing VCF fails for ID in header

Issue - State: closed - Opened by apraga 4 months ago - 3 comments
Labels: vcf

#238 - bgzf/multithreaded_writer: Add builder

Issue - State: closed - Opened by zaeleus 4 months ago - 1 comment
Labels: enhancement, bgzf

#238 - bgzf/multithreaded_writer: Add builder

Issue - State: closed - Opened by zaeleus 4 months ago - 1 comment
Labels: enhancement, bgzf

#237 - BGZF invalid header really strict

Issue - State: closed - Opened by andypexai 4 months ago - 6 comments
Labels: bgzf

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

Issue - State: closed - Opened by ghuls 4 months ago - 2 comments
Labels: sam

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

Issue - State: closed - Opened by ghuls 4 months ago - 2 comments
Labels: sam

#235 - Fixed-length `Character` fields

Issue - State: open - Opened by holtgrewe 4 months ago - 2 comments
Labels: vcf, bcf

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

Issue - State: closed - Opened by tshauck 4 months ago - 2 comments
Labels: bug, fasta

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

Issue - State: closed - Opened by cauliyang 5 months ago - 4 comments
Labels: enhancement, sam

#231 - Installation error

Issue - State: closed - Opened by andyjslee 5 months ago - 2 comments

#230 - Alignment span calculation (bug or misunderstanding)

Issue - State: closed - Opened by rob-p 5 months ago - 4 comments
Labels: bug, bam

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

Issue - State: closed - Opened by natir 5 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 5 months ago - 2 comments
Labels: sam

#227 - Seamless parsing of BAM/SAM

Issue - State: closed - Opened by mbhall88 5 months 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 5 months ago - 1 comment

#224 - fix: lazy vcf overreading into next record

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

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

Pull Request - State: closed - Opened by tshauck 5 months ago - 1 comment
Labels: vcf

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

Issue - State: closed - Opened by tshauck 6 months ago - 2 comments
Labels: csi

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

Issue - State: closed - Opened by markjschreiber 6 months ago - 1 comment

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

Issue - State: closed - Opened by mmalenic 7 months ago - 1 comment
Labels: enhancement

#219 - Concurrent reading/decompression of BAM files.

Issue - State: closed - Opened by Adoni5 7 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 7 months ago - 5 comments
Labels: bam, bgzf

#217 - Build Error on Windows

Issue - State: closed - Opened by tshauck 8 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 8 months ago
Labels: bug, csi

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

Issue - State: closed - Opened by zaeleus 8 months ago - 2 comments
Labels: bug, csi

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

Issue - State: open - Opened by nh13 8 months ago - 4 comments
Labels: enhancement, vcf

#213 - Nondeterministic TBI index creation

Issue - State: closed - Opened by holtgrewe 8 months ago - 1 comment
Labels: enhancement, csi

#213 - Nondeterministic TBI index creation

Issue - State: closed - Opened by holtgrewe 8 months ago - 1 comment
Labels: enhancement, csi

#211 - fix: add get_ref/get_mut/into_inner for noodles-vcf

Pull Request - State: closed - Opened by holtgrewe 8 months ago - 4 comments
Labels: vcf

#211 - fix: add get_ref/get_mut/into_inner for noodles-vcf

Pull Request - State: closed - Opened by holtgrewe 8 months ago - 4 comments
Labels: vcf

#206 - Add reserve method to Cigar for use in `get_cigar`

Pull Request - State: closed - Opened by tshauck 9 months ago - 6 comments
Labels: bam

#205 - How to extract pileup information from a bam file?

Issue - State: closed - Opened by huangnengCSU 9 months ago - 2 comments
Labels: bam, sam

#205 - How to extract pileup information from a bam file?

Issue - State: closed - Opened by huangnengCSU 9 months ago - 2 comments
Labels: bam, sam

#205 - How to extract pileup information from a bam file?

Issue - State: closed - Opened by huangnengCSU 9 months ago - 2 comments
Labels: bam, sam

#204 - sam/record/data/field/tag: Add const initializer

Issue - State: closed - Opened by zaeleus 10 months ago - 2 comments
Labels: enhancement, sam

#204 - sam/record/data/field/tag: Add const initializer

Issue - State: closed - Opened by zaeleus 10 months ago - 2 comments
Labels: enhancement, sam

#203 - Question about number in META Lines

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

#203 - Question about number in META Lines

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

#202 - vcf/header/parser: Allow for v4.2 PEDIGREE format fields

Pull Request - State: closed - Opened by xiamaz 10 months ago

#202 - vcf/header/parser: Allow for v4.2 PEDIGREE format fields

Pull Request - State: closed - Opened by xiamaz 10 months ago

#201 - Noodles-vcf generates invalid record error on PEDIGREE header

Issue - State: closed - Opened by xiamaz 10 months ago - 4 comments
Labels: enhancement, vcf

#200 - query_unmapped fails

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

#199 - feat: add lazy record reader to vcf async reader

Pull Request - State: closed - Opened by tshauck 10 months ago - 1 comment
Labels: vcf

#199 - feat: add lazy record reader to vcf async reader

Pull Request - State: closed - Opened by tshauck 10 months ago - 1 comment
Labels: vcf

#199 - feat: add lazy record reader to vcf async reader

Pull Request - State: closed - Opened by tshauck 10 months ago - 1 comment
Labels: vcf

#199 - feat: add lazy record reader to vcf async reader

Pull Request - State: closed - Opened by tshauck 10 months ago - 1 comment
Labels: vcf

#199 - feat: add lazy record reader to vcf async reader

Pull Request - State: closed - Opened by tshauck 10 months ago - 1 comment
Labels: vcf