zaeleus/noodles

Issues

• Can support flush method on writer ?

  #269 opened 3 days ago by sharkLoc
  1

• Parsing VCF fails for ID in header

  #241 opened 4 days ago by apraga
  3

• noodles sam successfully read the recording but failed to write it

  #228 opened 4 months ago by natir
  2

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

  #253 opened 2 months ago by Crispy13
  2

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

  #266 opened 14 days ago by tedil
  2

• IUPAC codes in VCF REF field

  #268 opened 14 days ago by ACEnglish
  1

• `gff::AsyncReader` gated by async feature

  #264 opened 24 days ago by tshauck
  2

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

  #262 opened 25 days ago by tshauck
  2

• Reading entries of file into preallocated buffer

  #260 opened a month ago by rickymagner
  3

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

  #259 opened a month ago by tedil
  1

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

  #258 opened a month ago by Crispy13
  2

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

  #257 opened 2 months ago by jch-13
  1

• Unexpected EOF on BCF File

  #255 opened 2 months ago by tshauck
  2

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

  #254 opened 2 months ago by jch-13
  1

• Docs typo

  #252 opened 2 months ago by Crispy13
  2

• Getting raw record lines with lazy records

  #251 opened 2 months ago by rkimoakbioinformatics
  2

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

  #247 opened 2 months ago by zaeleus
  2

• record_buf object to sam::Record object?

  #249 opened 2 months ago by larryns
  2

• util feature

  #248 opened 2 months ago by larryns
  4

• question: how to convert cigar from bytes.

  #233 opened 4 months ago by cauliyang
  4

• bgzf MultiThreadedReader Missing Error Message

  #246 opened 2 months ago by asgray
  2

• Async BGZF readers eagerly evaluate blocks

  #243 opened 3 months ago by mmalenic
  2

• migrating from 0.49 to 0.65: generating invalid BAM files

  #244 opened 3 months ago by jamestwebber
  2

• bgzf/multithreaded_writer: Add builder

  #238 opened 3 months ago by zaeleus
  1

• Why `Flags::PROPERLY_ALIGNED` instead of `Flags::PROPERLY_PAIRED` as name?

  #236 opened 3 months ago by ghuls
  2

• BGZF invalid header really strict

  #237 opened 3 months ago by andypexai
  6

• `Send`-able `Repository`?

  #234 opened 4 months ago by tshauck
  2

• Fixed-length `Character` fields

  #235 opened 4 months ago by holtgrewe
  2

• Installation error

  #231 opened 4 months ago by andyjslee
  2

• Alignment span calculation (bug or misunderstanding)

  #230 opened 4 months ago by rob-p
  4

• noodles bam failled to write record with large mapping position.

  #229 opened 4 months ago by natir
  1

• Seamless parsing of BAM/SAM

  #227 opened 4 months ago by mbhall88
  4

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

  #226 opened 4 months ago by vsbuffalo
  1

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

  #218 opened 5 months ago by bwlang
  5

• Question: different coalescing of bytes for index queries?

  #222 opened 5 months ago by tshauck
  2

• Lazy reading of BAM records requires reading of the header first

  #221 opened 6 months ago by markjschreiber
  1

• Add underlying reader access for CRAM `AsyncReader`

  #220 opened 6 months ago by mmalenic
  1

• Concurrent reading/decompression of BAM files.

  #219 opened 6 months ago by Adoni5
  3

• Build Error on Windows

  #217 opened 7 months ago by tshauck
  1

• csi: tabix header indices are off by one

  #215 opened 7 months ago by zaeleus
  2

• How to index a VCF statically or on the fly

  #214 opened 7 months ago by nh13
  4

• csi/writer: End position of a chunk is using wrong virtual position

  #216 opened 7 months ago by zaeleus
  0

• Nondeterministic TBI index creation

  #213 opened 8 months ago by holtgrewe
  1

• sam/record/data/field/tag: Add const initializer

  #204 opened 9 months ago by zaeleus
  2

• How to extract pileup information from a bam file?

  #205 opened 9 months ago by huangnengCSU
  2

• Should record::data::field::tag::other be public?

  #197 opened 10 months ago by jamestwebber
  7

• Question about number in META Lines

  #203 opened 9 months ago by holtgrewe
  1

• Noodles-vcf generates invalid record error on PEDIGREE header

  #201 opened 9 months ago by xiamaz
  4

• query_unmapped fails

  #200 opened 9 months ago by drtconway
  3

• query sorted bam for unmapped reads

  #198 opened 9 months ago by drtconway
  1