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
#303 - `noodles_util`'s `alignment::io::indexed_reader` does not recognize `set_index`
Issue -
State: open - Opened by jonghwanyoon 5 days ago
#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
#295 - cram/io/writer/builder: Rename Builder::build_with_writer to Builder::build_from_writer
Issue -
State: closed - Opened by zaeleus about 1 month ago
Labels: cram
#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
#275 - Help request: using the noodles async FASTQ writer with async compression without corrupting the output
Issue -
State: closed - Opened by nrminor 3 months ago
- 1 comment
#275 - Help request: using the noodles async FASTQ writer with async compression without corrupting the output
Issue -
State: closed - Opened by nrminor 3 months ago
- 1 comment
#275 - Help request: using the noodles async FASTQ writer with async compression without corrupting the output
Issue -
State: closed - Opened by nrminor 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
- 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
#226 - Documentation is opaque on 0 vs 1 indexing, and whether regions are right-inclusive or not.
Issue -
State: open - Opened by vsbuffalo 8 months ago
- 1 comment
#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