jdidion/atropos

Issues

• cython is required at build time but not install time

  #138 opened a year ago by tillea
  1

• Python 3.12 build errors due to SafeConfigParser removal

  #135 opened a year ago by vpa1977
  2

• Test python 3.10 compatibility

  #133 opened a year ago by jdidion
  0

• Move CI to github actions

  #134 opened 2 years ago by jdidion
  0

• Install Error

  #132 opened 2 years ago by JChristopherEllis
  1

• defaults not listed in cli docs

  #130 opened 3 years ago by nick-youngblut
  0

• detect: --max-reads default

  #129 opened 3 years ago by nick-youngblut
  1

• Can atropos remove 5' adapter variants that are incomplete from the tail?

  #128 opened 3 years ago by lokapal
  5

• error while running the detect command

  #127 opened 4 years ago by manasakaringula
  2

• Atropos generated empty gzip files are not proper gzip file

  #124 opened 4 years ago by jganbat-fn
  3

• Bioconda atropos package tied to python 3.6

  #123 opened 4 years ago by gabeng
  1

• Atropos trim multi thread stuck in infinite loop on empty files.

  #122 opened 4 years ago by jganbat-fn
  2

• Cutadapt version

  #121 opened 4 years ago by Citteny
  1

• N-prefixes / wildcards before an adapter sequence leads to shortening *all* reads at the 3'-end ?

  #110 opened 4 years ago by plijnzaad
  3

• multiqc support?

  #118 opened 4 years ago by plijnzaad
  2

• Implement non-internal adapters

  #119 opened 4 years ago by jdidion
  0

• TypeError: 'CountingDict' object is not callable when using --metrics

  #117 opened 4 years ago by plijnzaad
  2

• atropos crashes all the time

  #91 opened 4 years ago by antonkulaga
  1

• atropos --version exits with stack trace and error status

  #114 opened 4 years ago by plijnzaad
  1

• Bundle adapters file with atropos wheel

  #116 opened 4 years ago by jdidion
  1

• TypeError: can only concatenate tuple (not "list") to tuple

  #112 opened 4 years ago by plijnzaad
  1

• sequencing_adapters.fa : 404 not found

  #111 opened 4 years ago by plijnzaad
  1

• atropos --version prints errors and exits with error status

  #113 opened 4 years ago by plijnzaad
  1

• request: with --output-format sam , add @PG and @CO header lines to output

  #105 opened 5 years ago by plijnzaad
  2

• --output-sam sets all SAM flags to 0

  #104 opened 5 years ago by plijnzaad
  1

• --output-format sam discards all SAM tags !?

  #103 opened 5 years ago by plijnzaad
  2

• TypeError: Object of type 'ProgressBarType' is not JSON serializable

  #102 opened 5 years ago by plijnzaad
  1

• --output-format sam inserts extra header lines every batch-size output lines ?!

  #101 opened 5 years ago by plijnzaad
  4

• Trimmed fastq ordering is not deterministic

  #106 opened 5 years ago by annamerk
  2

• atropos qc multithreads not working ?

  #100 opened 5 years ago by aathbt
  5

• atropos qc not handling single-end reads ?

  #97 opened 5 years ago by aathbt
  3

• Add support for output to BAM

  #95 opened 5 years ago by plijnzaad
  10

• Add configuration option to choose which library to use for reading BAM

  #99 opened 5 years ago by jdidion
  0

• bam (but not sam) reader crashes on '@CO' line in header

  #96 opened 5 years ago by plijnzaad
  6

• Update sequencing_adapters.fa

  #92 opened 5 years ago by amizeranschi
  0

• Dockerfile is missing pip `wheel` package

  #89 opened 5 years ago by nkrumm
  1

• Dockerfile for atropos-paper fails to build due to required apt-get upgrade interactivity

  #90 opened 5 years ago by nkrumm
  1

• Push latest version to DockerHub

  #93 opened 5 years ago by jdidion
  1

• Error when using BAM file as input

  #86 opened 5 years ago by llvisser
  10

• Segmentation Fault After Closing SequenceReader

  #88 opened 5 years ago by jessrosenfield
  7

• Add option to overwrite reads with nextseq low quality

  #82 opened 6 years ago by jessrosenfield
  1

• Replace pysam with bamnostic

  #83 opened 5 years ago by jdidion
  1

• gzip error code -9, different than issue #62?

  #78 opened 6 years ago by pkMyt1
  2

• atropos detect output

  #85 opened 5 years ago by nservant
  1

• atropos does not work with python 3.8 because of clock module

  #87 opened 5 years ago by kingralph80
  2

• Question about adapter removal and length filtering

  #84 opened 5 years ago by ElDeveloper
  2

• Atropos does not output read 2 fastq provided by `-p` argument in paired end mode

  #81 opened 6 years ago by jessrosenfield
  2

• IndexError: list index out of range

  #80 opened 6 years ago by aistBMRG
  2

• trim nextera adapters

  #77 opened 6 years ago by lmanchon
  3

• -i example should use negative value to trim end of read

  #79 opened 6 years ago by yangruialex
  1