zaeleus/noodles

Issues

• Accept U as a base type and convert to T for BAM.

  #306 opened 21 days ago by jkbonfield
  0

• "invalid start positions" when reading unmapped cram

  #305 opened a month ago by HadrienG
  2

• VCF Sample columns

  #304 opened a month ago by ACEnglish
  1

• `noodles_util`'s `alignment::io::indexed_reader` does not recognize `set_index`

  #303 opened 2 months ago by jonghwanyoon
  1

• Error parsing vcf data from ncbi

  #302 opened 2 months ago by puli1027
  3

• Should writing Strings to INFO be escaped

  #300 opened 2 months ago by holtgrewe
  2

• GTF parser fails when textual attributes contain semicolons

  #299 opened 3 months ago by kaizhang
  1

• Unified async alignment reader/writer

  #286 opened 3 months ago by mbhall88
  3

• How to write custom bam records

  #274 opened 5 months ago by SteampunkIslande
  4

• How to get tags

  #297 opened 3 months ago by Liripo
  0

• cram/io/writer/builder: Rename Builder::build_with_writer to Builder::build_from_writer

  #295 opened 3 months ago by zaeleus
  0

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

  #294 opened 3 months ago by zaeleus
  0

• cram/async/io/writer: Add alignment record writer

  #293 opened 3 months ago by zaeleus
  0

• util/alignment/async: Add async indexed reader

  #296 opened 3 months ago by zaeleus
  0

• gtf parse error

  #291 opened 3 months ago by qingyun039
  1

• Convenience methods for SAM records

  #289 opened 3 months ago by mbhall88
  2

• QualityScore conversion from fastq

  #277 opened 4 months ago by d-cameron
  2

• Support fastq comments/attributes/metadata

  #287 opened 4 months ago by d-cameron
  3

• Create test SAM data

  #278 opened 4 months ago by mbhall88
  2

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

  #283 opened 4 months ago by zaeleus
  3

• templeate_length() for long reads

  #285 opened 4 months ago by Psy-Fer
  2

• Trait bounds changes in noodles_sam 0.62.0

  #282 opened 4 months ago by mbhall88
  1

• Explicitly state the indexing of alignment start and end

  #281 opened 4 months ago by mbhall88
  1

• Performance question

  #279 opened 4 months ago by anderspitman
  0

• Help request: using the noodles async FASTQ writer with async compression without corrupting the output

  #275 opened 5 months ago by nrminor
  1

• bgzf/async/reader: Add seeking to an uncompressed position

  #273 opened 5 months ago by zaeleus
  0

• BED name column limit

  #271 opened 5 months ago by ghuls
  1

• Can support flush method on writer ?

  #269 opened 5 months ago by sharkLoc
  3

• Parsing VCF fails for ID in header

  #241 opened 6 months ago by apraga
  3

• About method names of `noodles_sam::alignment::record::Flags`

  #253 opened 7 months ago by Crispy13
  2

• BCF and VCF `record_bufs` return different `RecordBuf`s

  #266 opened 6 months ago by tedil
  2

• IUPAC codes in VCF REF field

  #268 opened 6 months ago by ACEnglish
  1

• `gff::AsyncReader` gated by async feature

  #264 opened 6 months ago by tshauck
  2

• Add Async GFF Reader and/or expose lazy record from string?

  #262 opened 6 months ago by tshauck
  2

• Reading entries of file into preallocated buffer

  #260 opened 6 months ago by rickymagner
  3

• Missing newlines in `header::record::write_other` when writing collections

  #259 opened 6 months ago by tedil
  1

• How to set tag with value in noodles::bam?

  #258 opened 7 months ago by Crispy13
  2

• `sam::header::programs` module is private

  #257 opened 7 months ago by jch-13
  1

• Unexpected EOF on BCF File

  #255 opened 7 months ago by tshauck
  2

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

  #254 opened 7 months ago by jch-13
  1

• Docs typo

  #252 opened 8 months ago by Crispy13
  2

• Getting raw record lines with lazy records

  #251 opened 8 months ago by rkimoakbioinformatics
  2

• sam/io/writer/record: Increase visibility of SAM record CIGAR string serializer

  #247 opened 8 months ago by zaeleus
  2

• record_buf object to sam::Record object?

  #249 opened 8 months ago by larryns
  2

• util feature

  #248 opened 8 months ago by larryns
  4

• bgzf MultiThreadedReader Missing Error Message

  #246 opened 8 months ago by asgray
  2

• Async BGZF readers eagerly evaluate blocks

  #243 opened 8 months ago by mmalenic
  2

• migrating from 0.49 to 0.65: generating invalid BAM files

  #244 opened 8 months ago by jamestwebber
  2

• bgzf/multithreaded_writer: Add builder

  #238 opened 9 months ago by zaeleus
  1

• BGZF invalid header really strict

  #237 opened 9 months ago by andypexai
  6