daler/pybedtools

Issues

• Test failures on 3.13 test_pathlib

  #413 opened 2 months ago by stefanor
  1

• No obvious link to GitHub from docs

  #412 opened 2 months ago by stefanor
  1

• Issues with installing through conda

  #414 opened 3 months ago by jchan3188
  1

• What overlap fraction is used in cleaned_intersect?

  #411 opened 2 months ago by kako-f
  1

• Recent issue with input bed that only have 3 columns

  #410 opened 5 months ago by xuebingjie1990
  1

• total_coverage giving a incorrect value

  #409 opened 2 months ago by duartemolha
  1

• pybedtools.bedtool.Bedtool.sort()

  #408 opened 8 months ago by Accompany0313
  1

• IndexError with groupby

  #378 opened 2 years ago by wbvguo
  1

• Unable to install pybedtools==0.9.1 in Python3.10

  #398 opened 9 months ago by romunov
  4

• Has pybedtools considered packaging bedtools?

  #401 opened 9 months ago by pettyalex
  3

• remove historical py27 support

  #391 opened 9 months ago by daler
  1

• Inconsistent behaviour when using files from `pathlib.PosixPath` with BedTool functions...

  #405 opened 9 months ago by dbolser
  0

• bedtools intersect reported incorrect interval intersection

  #392 opened 9 months ago by leon945945
  3

• "fastaFromBed" error

  #396 opened 9 months ago by franjmt
  2

• how to mask gap regions for randomization?

  #402 opened 9 months ago by yangsui0122
  1

• Issue while doing pip install pybedtools

  #403 opened 9 months ago by sungwookm
  3

• Len modifying the Bedtools after a filter

  #400 opened 10 months ago by andreforesight
  2

• intersect with multiple -b arguments not working with -sorted

  #397 opened a year ago by eboileau
  1

• pybedtools multi_bam_coverage assistance

  #395 opened a year ago by erinyoung
  2

• Cythonizing files requires `language_level=2` to be set in cythonize()

  #393 opened a year ago by lbeltrame
  4

• "python setup.py bdist_wheel did not run successfully" when pip installing with python v3.11

  #384 opened a year ago by benrhodes26
  8

• BEDtools can handle more than 510 files at a time

  #354 opened a year ago by leeleavitt
  1

• Cannot create a BedTool object from list of regions that uses np.int64 coordinates

  #390 opened a year ago by aksarkar
  0

• pybedtools.bedtool.BedTool.save_seqs leaves open .tmp files

  #381 opened a year ago by PeterRobots
  0

• 'generator raised StopIteration' error when running 'randomstats' with multiple processes

  #377 opened 2 years ago by tparket
  4

• build failure under python 3.11

  #387 opened 2 years ago by kbipinkumar
  6

• pybedtools intersect error

  #389 opened 2 years ago by katelynmullen
  2

• to_dataframe() creates 0th row with generic names in nucleotide_content

  #385 opened 2 years ago by mheskett
  2

• Missing arm64 MacOS wheel packages

  #375 opened 2 years ago by Kentalot
  4

• setup.py needs updating for License change

  #373 opened 2 years ago by hyandell
  0

• Cannot pass argument to pybedtools.sort()

  #372 opened 2 years ago by mpj5142
  1

• Bed identified as SAM

  #370 opened 2 years ago by dprat
  1

• numpy.int64 has no attribute isdigit

  #362 opened 3 years ago by urrik98
  4

• Support Python 3.10 and 3.11

  #383 opened 2 years ago by woutervh
  1

• Could NOT find Arrow (missing: ARROW_INCLUDE_DIR ARROW_LIB_DIR

  #379 opened 2 years ago by StephanDrukewitz
  2

• Support for Polars Dataframe needed

  #376 opened 2 years ago by YuanfengZhang
  2

• pybedtools from conda use version 2.26 not 2.3

  #371 opened 2 years ago by udiland
  3

• Handling of wide pseudo-bed files (pseudo-bed files interpreted as .sam)?

  #363 opened 3 years ago by semenko
  2

• pipenv install trouble

  #369 opened 2 years ago by cmatKhan
  3

• `IndexError: list index out of range` with narrowPeak file

  #365 opened 3 years ago by csestili
  1

• Customized header

  #364 opened 3 years ago by mike-molnar
  2

• NotImplementedError: "intersectBed" does not appear to be installed or on the path, so this method is disabled. Please install a more recent version of BEDTools and re-import to use this method.

  #361 opened 3 years ago by stanleyjs
  7

• POS-field in VCF files and intervals derived from them

  #355 opened 3 years ago by DRL
  1

• Issue with the initialization of otherfileds in Interval

  #348 opened 3 years ago by Shrulik
  0

• unexpected behavior due to bedtools bug, might better considering put the "-a" options to ahead in _cmds

  #345 opened 3 years ago by xubeisi
  0

• module 'pybedtools' has no attribute 'featurefuncs'

  #346 opened 3 years ago by quantumdot
  1

• remove_invalid not removing entries with start and stop negative

  #343 opened 3 years ago by blaiseli
  6

• Loss of tag-value pairs in GFF attribute field with duplicated tags after accessing interval.attrs

  #352 opened 3 years ago by ijhoskins
  4

• NotImplementedError: "intersectBed" does not appear to be installed or on the path, so this method is disabled. Please install a more recent version of BEDTools and re-import to use this method

  #347 opened 3 years ago by starboyvarun
  0

• Error When Running Shuffle

  #344 opened 4 years ago by Jome0169
  1