Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / deeptools/pyBigWig issues and pull requests

#151 - pyBigWig.c: fix build failure with gcc 14.

Pull Request - State: open - Opened by emollier 4 months ago

#150 - get np2 compatible

Pull Request - State: closed - Opened by WardDeb 5 months ago

#147 - 'zsh: segmentation fault '

Issue - State: closed - Opened by violacimatti 7 months ago - 1 comment

#146 - Stats Sum Not Working as Expected

Issue - State: closed - Opened by atancoder 9 months ago

#144 - Issue Downloading pyBigWig

Issue - State: closed - Opened by tdb7dgr 11 months ago - 1 comment

#143 - Support for python >=3.11

Issue - State: open - Opened by CodingKaiser 12 months ago - 1 comment

#142 - addHeader does not support multiple calls

Issue - State: open - Opened by rlowe-altoslabs over 1 year ago - 1 comment

#141 - Installing through pip not working

Issue - State: closed - Opened by callum-b over 1 year ago - 9 comments

#140 - Add wheel to pypi upload in github actions

Pull Request - State: closed - Opened by EricR86 over 1 year ago - 3 comments

#139 - Add MANIFEST.in

Pull Request - State: closed - Opened by dpryan79 over 1 year ago - 1 comment

#138 - pip installation broken

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

#137 - Bump to 0.3.19

Pull Request - State: closed - Opened by dpryan79 over 1 year ago

#136 - fix tests

Pull Request - State: closed - Opened by dpryan79 over 1 year ago

#135 - Updated build and wheel distribution for pyBigWig

Pull Request - State: closed - Opened by EricR86 over 1 year ago - 4 comments

#134 - Implement #133

Pull Request - State: closed - Opened by dpryan79 about 2 years ago - 2 comments

#132 - Writing a nan value should leave a gap

Issue - State: open - Opened by rcasero about 2 years ago - 7 comments

#131 - pyBigWig fails to find numpy installation when installing from PyPI

Issue - State: closed - Opened by EricR86 about 2 years ago - 5 comments

#130 - library import error

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

#129 - Create a BedGraph file using addEntries() throws segmentation fault

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

#128 - numpy support broken in 0.3.18?

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

#127 - support for osx-arm64

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

#126 - Cannot add entries of value type int, but only float

Issue - State: open - Opened by XikunZhang over 2 years ago - 2 comments

#125 - Document performance considerations?

Issue - State: open - Opened by alexlenail over 2 years ago - 4 comments

#124 - RuntimeError: Invalid interval bounds

Issue - State: closed - Opened by Ankita-1211 over 2 years ago

#123 - Suppress logging/error messages

Issue - State: open - Opened by EricR86 over 2 years ago - 2 comments

#122 - BigBed interval problem

Issue - State: open - Opened by jtd032 almost 3 years ago - 7 comments

#121 - Update README.md

Pull Request - State: closed - Opened by BaselAbujamous almost 3 years ago - 1 comment

#120 - Error Installing pyBigWig

Issue - State: closed - Opened by pzhang312 about 3 years ago - 11 comments

#119 - 1-based BigWig file as input

Issue - State: closed - Opened by dshan25 about 3 years ago - 2 comments

#118 - Open bw file for appending?

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

#117 - [bwGetOverlappingIntervalsCore] Got an error

Issue - State: closed - Opened by wuzhaoqi1015 over 3 years ago - 3 comments

#116 - Remove unused "dev" stats option.

Pull Request - State: closed - Opened by nathancfox over 3 years ago - 2 comments

#115 - Update the pyBigWig.bigWigFile.stats docstring.

Pull Request - State: closed - Opened by nathancfox over 3 years ago

#113 - Write bigwig to BytesIO object

Issue - State: closed - Opened by joachimwolff over 3 years ago - 4 comments

#112 - Fix issue #111, handle empty files AND those with empty summaries.

Pull Request - State: closed - Opened by dpryan79 over 3 years ago

#111 - File with incorrect header information read as empty

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

#110 - error raised when start and end positions are identical.

Issue - State: closed - Opened by fardokhtsadat almost 4 years ago - 1 comment

#109 - Problem installing pyBigWig

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

#108 - Add poweron architecture ppc64le to travis build

Pull Request - State: closed - Opened by asellappen about 4 years ago

#107 - Support for GCP bucket access?

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

#104 - What is "None" bigwig signal values mean from pyBigWig bw.stats?

Issue - State: closed - Opened by kac2053 over 4 years ago - 1 comment

#103 - Python 3.8 support

Issue - State: closed - Opened by joachimwolff over 4 years ago - 2 comments

#102 - [bug/feature] easier installation and better cross-platform compatibility

Issue - State: closed - Opened by shouldsee over 4 years ago - 6 comments

#101 - Change chromosome names.

Issue - State: closed - Opened by amv33576 over 4 years ago - 1 comment

#100 - "Empty" values in "manually" constructed bigwig file.

Issue - State: closed - Opened by blaiseli almost 5 years ago - 3 comments

#98 - How to install pyBigWig in windows?

Issue - State: closed - Opened by burcakotlu almost 5 years ago - 2 comments

#97 - pyBwGetChroms does not work any more with a BigWig that has headers

Issue - State: closed - Opened by blaiseli about 5 years ago - 4 comments

#96 - get the list of all possible stats

Issue - State: open - Opened by lldelisle about 5 years ago - 2 comments

#95 - pybigwig.values produced negative values

Issue - State: closed - Opened by BenxiaHu about 5 years ago - 1 comment

#94 - Add numpy support for bw.stats()

Pull Request - State: closed - Opened by nvictus about 5 years ago - 2 comments

#93 - Can there be overlapping intervals in bigWig files?

Issue - State: closed - Opened by burcakotlu about 5 years ago - 7 comments

#92 - PyUnicode_AsASCIIString returns a new object that needs to be DECREF'd

Pull Request - State: closed - Opened by dpryan79 over 5 years ago - 1 comment

#91 - Is memory released on bw.close() ?

Issue - State: closed - Opened by PanosFirmpas over 5 years ago - 6 comments

#90 - Writing a bigwig file in python3 is extremely slow compared to python2

Issue - State: closed - Opened by Young-Sook over 5 years ago - 1 comment

#89 - IGV fails to read bigWigs generated by pyBigWig

Issue - State: closed - Opened by pbenner over 5 years ago - 4 comments

#88 - Segfault when trying to access a non-existing header

Issue - State: closed - Opened by pbenner over 5 years ago - 1 comment

#87 - bump to 0.3.16

Pull Request - State: closed - Opened by dpryan79 over 5 years ago

#86 - Fix #85

Pull Request - State: closed - Opened by dpryan79 over 5 years ago

#85 - Reading bigWig files sometimes fails: Uninitialized bwRTree_t->root variable

Issue - State: closed - Opened by pbenner over 5 years ago - 2 comments

#84 - Declare versioned dependency on libBigWig instead of copying

Issue - State: closed - Opened by smoe over 5 years ago - 2 comments

#83 - Copy over changes from libBigWig

Pull Request - State: closed - Opened by dpryan79 over 5 years ago

#82 - Create wheels?

Issue - State: closed - Opened by endrebak over 5 years ago - 2 comments

#81 - Does not compile without curl

Issue - State: closed - Opened by jbedo over 5 years ago - 11 comments

#80 - pyBigWig does not install through install_requires for python package

Issue - State: closed - Opened by msbentsen over 5 years ago - 9 comments

#79 - Hi, I tried all the way to install pybigwig, but all failed

Issue - State: closed - Opened by Urheen over 5 years ago - 1 comment

#78 - ImportError: ndefined symbol: PyInt_Check

Issue - State: closed - Opened by nlapalu over 5 years ago - 4 comments

#77 - Bump to 0.3.13, drop support for python2.

Pull Request - State: closed - Opened by dpryan79 almost 6 years ago

#76 - Fix the build with Python 3 and an external curl

Pull Request - State: closed - Opened by rmsds almost 6 years ago - 1 comment

#75 - Error: Mismatch in the magic number

Issue - State: closed - Opened by alexpreynolds almost 6 years ago - 2 comments

#74 - Parallelizing pyBigWig.values()

Issue - State: closed - Opened by nicolazilio almost 6 years ago - 5 comments

#73 - libcurl3/4 issue on Ubuntu machine

Issue - State: closed - Opened by oristaszewski almost 6 years ago - 1 comment

#72 - Fix #71

Pull Request - State: closed - Opened by dpryan79 about 6 years ago

#71 - Incorrect check of malloc result

Issue - State: closed - Opened by victzh about 6 years ago - 1 comment

#69 - pyBigWig using 30+ cores

Issue - State: closed - Opened by goodez about 6 years ago - 5 comments

#68 - Throw an error on long chromosomes

Issue - State: closed - Opened by dpryan79 about 6 years ago - 1 comment

#67 - Try to properly fix #29

Pull Request - State: closed - Opened by dpryan79 about 6 years ago

#66 - Fix #63

Pull Request - State: closed - Opened by dpryan79 about 6 years ago

#65 - y chromosome in Female error

Issue - State: closed - Opened by judithhariprakash over 6 years ago

#64 - pyBigWig can't open Path objects

Issue - State: closed - Opened by gpratt over 6 years ago - 1 comment

#63 - RuntimeError: You must supply at least a chromosome!

Issue - State: closed - Opened by iamjli over 6 years ago - 6 comments

#62 - Write out bw track color?

Issue - State: closed - Opened by ShanSabri over 6 years ago - 1 comment

#61 - Test OSX fix with continuum conda and release a bugfix version

Issue - State: closed - Opened by dpryan79 over 6 years ago - 1 comment

#60 - Do not link to libpython on Mac

Pull Request - State: closed - Opened by gokceneraslan over 6 years ago - 2 comments

#59 - Unable to open bigBed files

Issue - State: closed - Opened by adelq over 6 years ago - 3 comments

#58 - Segmentation fault: 11 on MacOS High Sierra 10.13.3

Issue - State: closed - Opened by daquang almost 7 years ago - 9 comments

#57 - Sum stats type

Pull Request - State: closed - Opened by dpryan79 almost 7 years ago

#56 - addEntries

Issue - State: closed - Opened by andyjslee almost 7 years ago - 4 comments

#55 - Fix BigWig creation with numpy

Pull Request - State: closed - Opened by dpryan79 almost 7 years ago

#54 - can't create a bigwig file

Issue - State: closed - Opened by rfarouni almost 7 years ago - 7 comments
Labels: bug

#53 - fix leak of objects extracted from numpy string arrays

Pull Request - State: closed - Opened by pmarks almost 7 years ago - 3 comments

#52 - type="sum" for bw.stats()

Issue - State: closed - Opened by tturowski almost 7 years ago - 3 comments