daler/pybedtools

Issues

• Test suite fails with 1 value error and 8 assertion errors.

  #342 opened 3 years ago
  6

• python3.8 - runtime warning

  #340 opened 4 years ago
  5

• Temporary files usage

  #337 opened 4 years ago
  1

• Errors being thrown after python (3.9.1), pybedtools updates

  #336 opened 3 years ago
  2

• intersect threshold

  #335 opened 4 years ago
  1

• Pandas throws EmptyDataError when bedtools results are empty [bedtool.py, in to_dataframe() line 3688]

  #333 opened 4 years ago
  1

• Pypi version discrepancies.

  #331 opened 4 years ago
  2

• Is it possible to keep column information after intersecting?

  #330 opened 4 years ago
  0

• 0.8.0 tests fail with `No module named 'pybedtools.cbedtools'`

  #329 opened 4 years ago
  1

• Failed to build pybedtools (pip install pybedtools)

  #328 opened 4 years ago
  1

• Merge is not working as expected

  #327 opened 4 years ago
  0

• Intervals when using UCSC genome are wrong (pybedtools is 0-based and doesn't correct for 1-based?)

  #325 opened 4 years ago
  1

• RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode

  #322 opened 5 years ago
  3

• from_dataframe only extracting first character of feature start and end position

  #321 opened 5 years ago
  2

• error reading unicode symbols in the vcf.gz file

  #319 opened 5 years ago
  1

• Automatically try to run cythonize when needed while installing from source

  #317 opened 4 years ago
  6

• import error on bedtools from pybedtools

  #316 opened 5 years ago
  4

• Ideas for the next major release

  #315 opened 5 years ago
  0

• Confusing error for too many pybedtools intersect -b files

  #303 opened 5 years ago
  0

• undefined symbol in cbedtools.so when importing pybedtools

  #302 opened 5 years ago
  5

• get_chromsizes_from_ucsc: allow specification of UCSC host url in mysql query

  #300 opened 5 years ago
  1

• MalformedBedLineError: adding a ':' character to the interval?

  #299 opened 5 years ago
  2

• missing pybedtools.contrib.plotting module

  #298 opened 5 years ago
  1

• pybedtools will not accept mac line endings

  #297 opened 5 years ago
  1

• Bedtools CRAM support

  #296 opened 5 years ago
  0

• 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.

  #294 opened 5 years ago
  2

• `BedTools.introns()` returns malformed intervals

  #293 opened 5 years ago
  1

• Can pybedtools controls the resouces used?

  #292 opened 5 years ago
  1

• saving bed.gz files as bed.gz again

  #291 opened 5 years ago
  2

• Issue with mergeBed collapse function

  #290 opened 5 years ago
  2

• bedtools may have distribution prefix that causes error in version detection

  #288 opened 5 years ago
  1

• Change in license of bedtools

  #286 opened 3 years ago
  0

• intersecting multiple files produces different default output that bedtools

  #285 opened 5 years ago
  4

• Version number on pip fails to parse on import

  #284 opened 5 years ago
  3

• version error using bedtools GitHub master branch

  #283 opened 5 years ago
  2

• "ResourceWarning: unclosed file" when using cat during unittesting in Python 3.7

  #282 opened 5 years ago
  2

• to_dataframe() uses first row as header

  #279 opened 6 years ago
  2

• Error loading Python module when bedtools version has atypical name

  #275 opened 6 years ago
  2

• pandas.read_table will be deprecated

  #273 opened 6 years ago
  0

• Sorted input out of order

  #272 opened 5 years ago
  2

• Change 4 GPL 2.0-licensed files to GPL 2.0 or later?

  #271 opened 3 years ago
  1

• Module Error

  #270 opened 6 years ago
  2

• saving file

  #268 opened 6 years ago
  1

• Equivalent option of -wa and -wb in pybedtools

  #267 opened 6 years ago
  1

• Using the intersect options

  #266 opened 6 years ago
  4

• Using Windows, can't install pybedtools with conda, pip or development version

  #263 opened 6 years ago
  2

• Error: install a newer version of bedtools

  #262 opened 6 years ago
  1

• Test failures with Bedtools 2.26.0

  #261 opened 6 years ago
  2

• Test failures with bedtools 2.27.1

  #260 opened 6 years ago
  1

• pip install pybedtools does not work with Mac OS X Mojave and Anaconda 5.3 (Python 3.7)

  #259 opened 6 years ago
  7