marcelm/dnaio

Issues

• SequenceRecord.__getitem__ should support slicing for certain BAM tags.

  #143 opened 23 days ago by rhpvorderman
  0

• SequenceRecord BAM tags should be stored to FASTQ as well

  #142 opened 23 days ago by rhpvorderman
  0

• Extended BAM support

  #129 opened 9 months ago by rhpvorderman
  10

• Chunking for uBAM

  #140 opened 25 days ago by rhpvorderman
  2

• dnaio.exceptions.UnknownFileFormat

  #136 opened 2 months ago by wook2014
  3

• installation from source with `pip install` fails

  #138 opened 2 months ago by boegel
  2

• Update bioconda-recipe to support osx-arm64

  #137 opened 2 months ago by isaacovercast
  1

• _Py_NegativeRefcount error

  #132 opened 7 months ago by bistace
  7

• How to cite dnaio in a manuscript?

  #127 opened 9 months ago by DongzeHE
  2

• Add ubam support

  #109 opened a year ago by rhpvorderman
  11

• SequenceRecord array class

  #77 opened a year ago by marcelm
  6

• Typing warnings from mypy

  #118 opened a year ago by fjossandon
  7

• Add better type hints for dnaio.open()

  #94 opened a year ago by marcelm
  0

• Version 1.0

  #114 opened a year ago by rhpvorderman
  3

• check quality score integrity

  #111 opened a year ago by rhpvorderman
  1

• Add Sequence.id attribute

  #10 opened a year ago by marcelm
  9

• Use a newline index for FastqIter

  #108 opened a year ago by rhpvorderman
  10

• FastqFormatError, while reading in chunks

  #107 opened 2 years ago by arunhpatil
  5

• ResourceWarnings

  #103 opened 2 years ago by marcelm
  3

• compresslevel and open_threads should be arguments in the dnaio.open interface

  #90 opened 2 years ago by rhpvorderman
  0

• Identifying bottlenecks

  #84 opened 2 years ago by rhpvorderman
  4

• Switch single&paired API to single&multiple API.

  #82 opened 2 years ago by rhpvorderman
  2

• Publish documentation on Read The Docs

  #8 opened 2 years ago by marcelm
  4

• Compilation error

  #83 opened 2 years ago by stheil15
  3

• API review

  #56 opened 2 years ago by marcelm
  4

• Three-way is mate comparison

  #78 opened 2 years ago by rhpvorderman
  2

• Does SequenceRecord need to support the buffer protocol?

  #76 opened 3 years ago by rhpvorderman
  2

• API review: an alternative namo for `dnaio.open`?

  #70 opened 3 years ago by marcelm
  2

• Remove BytesSequenceRecord

  #66 opened 3 years ago by rhpvorderman
  2

• reverse complement

  #64 opened 3 years ago by jazberna1
  6

• ascii_check.h should be in its own repo

  #61 opened 3 years ago by rhpvorderman
  6

• ASCII check should be moved to update buffer.

  #59 opened 3 years ago by rhpvorderman
  0

• Move dnaio to its own organization

  #62 opened 3 years ago by marcelm
  2

• Consider renaming Sequence to SequenceRecord

  #36 opened 3 years ago by marcelm
  1

• Implement ASCII check

  #40 opened 3 years ago by rhpvorderman
  0

• Stop shipping Cython-generated .c files

  #50 opened 3 years ago by marcelm
  0

• Possible improvements for paired_fastq_heads

  #24 opened 3 years ago by rhpvorderman
  0

• Error in dnaio

  #6 opened 3 years ago by sprakashUTH
  2

• Two_headers should be a SequenceRecord attribute

  #38 opened 3 years ago by rhpvorderman
  2

• Add Sequence and BytesSequence method for paired-end id comparison

  #35 opened 3 years ago by marcelm
  1

• Profiling of fastq iter method

  #26 opened 3 years ago by rhpvorderman
  3

• fastq_iter should be made a class.

  #31 opened 3 years ago by rhpvorderman
  0

• Fastq_iter improvements

  #25 opened 3 years ago by rhpvorderman
  5

• dnaio.open() should return fewer classes

  #9 opened 3 years ago by marcelm
  0

• Why decode?

  #11 opened 3 years ago by rhpvorderman
  4

• Allow paired-end read id suffixes other than just 1 and 2

  #7 opened 3 years ago by marcelm
  0

• conda install fails for py38 (also prevents cutadapt in py38)

  #4 opened 4 years ago by eaton-lab
  2

• Opening a single empty file using format auto-detect raises OSError.

  #3 opened 4 years ago by DriesSchaumont
  1

• Determining file type from contents rather than name

  #1 opened 5 years ago by nickilott
  1