daler/pybedtools issues and pull requests

#416 - better detection of Path for Python 3.13

Pull Request - State: closed - Opened by daler 12 days ago

#415 - Update docs

Pull Request - State: closed - Opened by daler 12 days ago

#414 - Issues with installing through conda

Issue - State: open - Opened by jchan3188 about 1 month ago - 1 comment

#413 - Test failures on 3.13 test_pathlib

Issue - State: closed - Opened by stefanor 2 months ago - 1 comment

#412 - No obvious link to GitHub from docs

Issue - State: closed - Opened by stefanor 2 months ago - 1 comment

#411 - What overlap fraction is used in cleaned_intersect?

Issue - State: closed - Opened by kako-f 3 months ago - 1 comment

#410 - Recent issue with input bed that only have 3 columns

Issue - State: open - Opened by xuebingjie1990 4 months ago - 1 comment

#409 - total_coverage giving a incorrect value

Issue - State: closed - Opened by duartemolha 5 months ago - 1 comment

#408 - pybedtools.bedtool.Bedtool.sort()

Issue - State: open - Opened by Accompany0313 7 months ago - 1 comment

#407 - Add support for csi index

Pull Request - State: open - Opened by liyao001 7 months ago - 2 comments

#406 - Testing a fix for an issue with pathlib

Pull Request - State: closed - Opened by dbolser 8 months ago - 4 comments

#405 - Inconsistent behaviour when using files from `pathlib.PosixPath` with BedTool functions...

Issue - State: closed - Opened by dbolser 8 months ago

#404 - V0.10.0rc

Pull Request - State: closed - Opened by daler 8 months ago

#403 - Issue while doing pip install pybedtools

Issue - State: closed - Opened by sungwookm 9 months ago - 3 comments

#402 - how to mask gap regions for randomization?

Issue - State: closed - Opened by yangsui0122 9 months ago - 1 comment

#401 - Has pybedtools considered packaging bedtools?

Issue - State: closed - Opened by pettyalex 10 months ago - 3 comments

#400 - Len modifying the Bedtools after a filter

Issue - State: closed - Opened by andreforesight 11 months ago - 2 comments

#399 - fix(bedFile): remove register for ISO C++17

Pull Request - State: closed - Opened by cameronraysmith 11 months ago - 1 comment

#398 - Unable to install pybedtools==0.9.1 in Python3.10

Issue - State: closed - Opened by romunov 12 months ago - 4 comments

#397 - intersect with multiple -b arguments not working with -sorted

Issue - State: closed - Opened by eboileau 12 months ago - 1 comment

#396 - "fastaFromBed" error

Issue - State: closed - Opened by franjmt about 1 year ago - 2 comments

#395 - pybedtools multi_bam_coverage assistance

Issue - State: closed - Opened by erinyoung about 1 year ago - 2 comments

#394 - fix: remove six dependency

Pull Request - State: closed - Opened by valentynbez about 1 year ago - 3 comments

#393 - Cythonizing files requires `language_level=2` to be set in cythonize()

Issue - State: closed - Opened by lbeltrame over 1 year ago - 4 comments

#392 - bedtools intersect reported incorrect interval intersection

Issue - State: closed - Opened by leon945945 over 1 year ago - 3 comments

#391 - remove historical py27 support

Issue - State: closed - Opened by daler over 1 year ago - 1 comment

#390 - Cannot create a BedTool object from list of regions that uses np.int64 coordinates

Issue - State: closed - Opened by aksarkar over 1 year ago

#389 - pybedtools intersect error

Issue - State: closed - Opened by katelynmullen over 1 year ago - 2 comments

#388 - Add support for polars dataframes

Pull Request - State: open - Opened by DevangThakkar over 1 year ago - 1 comment

#387 - build failure under python 3.11

Issue - State: closed - Opened by kbipinkumar over 1 year ago - 6 comments

#386 - Add minimal pyproject.toml

Pull Request - State: closed - Opened by afg1 over 1 year ago - 1 comment

#385 - to_dataframe() creates 0th row with generic names in nucleotide_content

Issue - State: closed - Opened by mheskett over 1 year ago - 2 comments

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

Issue - State: closed - Opened by benrhodes26 over 1 year ago - 8 comments

#383 - Support Python 3.10 and 3.11

Issue - State: closed - Opened by woutervh over 1 year ago - 1 comment

#382 - Fixes #381 closes all .tmp files opened by .save_seqs

Pull Request - State: closed - Opened by PeterRobots almost 2 years ago

#381 - pybedtools.bedtool.BedTool.save_seqs leaves open .tmp files

Issue - State: closed - Opened by PeterRobots almost 2 years ago

#380 - Add genome arguments to BedTool.sort()

Pull Request - State: closed - Opened by mgperry almost 2 years ago - 1 comment

#379 - Could NOT find Arrow (missing: ARROW_INCLUDE_DIR ARROW_LIB_DIR

Issue - State: closed - Opened by StephanDrukewitz almost 2 years ago - 2 comments

#378 - IndexError with groupby

Issue - State: closed - Opened by wbvguo almost 2 years ago - 1 comment

#377 - 'generator raised StopIteration' error when running 'randomstats' with multiple processes

Issue - State: open - Opened by tparket almost 2 years ago - 4 comments

#376 - Support for Polars Dataframe needed

Issue - State: open - Opened by YuanfengZhang about 2 years ago - 2 comments

#375 - Missing arm64 MacOS wheel packages

Issue - State: closed - Opened by Kentalot about 2 years ago - 4 comments

#374 - Updating setup.py for GPL->MIT relicense

Pull Request - State: closed - Opened by hyandell about 2 years ago - 1 comment

#373 - setup.py needs updating for License change

Issue - State: closed - Opened by hyandell about 2 years ago

#372 - Cannot pass argument to pybedtools.sort()

Issue - State: closed - Opened by mpj5142 about 2 years ago - 1 comment

#371 - pybedtools from conda use version 2.26 not 2.3

Issue - State: closed - Opened by udiland about 2 years ago - 3 comments

#370 - Bed identified as SAM

Issue - State: closed - Opened by dprat over 2 years ago - 1 comment

#369 - pipenv install trouble

Issue - State: closed - Opened by cmatKhan over 2 years ago - 3 comments

#368 - target branch for v0.9.1

Pull Request - State: closed - Opened by daler over 2 years ago

#367 - allow plotting of lengths of intervals

Pull Request - State: closed - Opened by yunfeiguo over 2 years ago - 2 comments

#366 - allow customization of dpi

Pull Request - State: closed - Opened by yunfeiguo over 2 years ago

#365 - `IndexError: list index out of range` with narrowPeak file

Issue - State: closed - Opened by csestili over 2 years ago - 1 comment

#364 - Customized header

Issue - State: closed - Opened by mike-molnar over 2 years ago - 2 comments

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

Issue - State: closed - Opened by semenko almost 3 years ago - 2 comments

#362 - numpy.int64 has no attribute isdigit

Issue - State: closed - Opened by urrik98 almost 3 years ago - 4 comments