Ecosyste.ms: Issues

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

GitHub / biocore-ntnu/pyranges issues and pull requests

#310 - Add a tox file to ease testing and linting

Issue - State: open - Opened by endrebak over 1 year ago
Labels: enhancement

#309 - Add typing with mypy.

Issue - State: open - Opened by endrebak over 1 year ago
Labels: enhancement

#307 - Cannot convert non-finite values (NA or inf) to integer

Issue - State: closed - Opened by seven1112233 over 1 year ago - 10 comments

#306 - Remove CPU-flag?

Issue - State: open - Opened by endrebak over 1 year ago

#304 - added a `preserve_order` flag to `pr.join()`

Pull Request - State: open - Opened by aallahyar over 1 year ago - 2 comments

#303 - Row-order after df1.join(df2, how="right")

Issue - State: open - Opened by aallahyar over 1 year ago - 2 comments

#302 - Remove support for int32 chromosome starts/ends?

Issue - State: open - Opened by endrebak over 1 year ago

#301 - Cython wants us to stop executing setup.py

Issue - State: open - Opened by endrebak over 1 year ago - 1 comment
Labels: enhancement

#300 - 0.0.121

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

#299 - Incompatibility with pandas 2.0

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

#298 - Overlap function met error using multi-cpus

Issue - State: open - Opened by ttbond over 1 year ago - 2 comments

#297 - fixed empty attribute bug in read_gtf when duplicate_attr=True

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

#296 - Inconsistent handling of bookended intervals

Issue - State: open - Opened by marco-mariotti over 1 year ago - 2 comments

#295 - Improve genome bounds

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

#294 - Bug fix on subsequence and spliced_subsequence

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

#293 - subsequence has inconsistent behavior with strand argument

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

#292 - Cannot read GTF: expected 2 values got 1

Issue - State: open - Opened by almart7 almost 2 years ago - 3 comments

#291 - Boolean columns in original data frame in join

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

#290 - Docstring update

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

#289 - overlap() return an empty object

Issue - State: closed - Opened by axol0tl almost 2 years ago - 2 comments

#288 - [Feature request] Incorporate inplace parameter in drop() method

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

#287 - NumPy `bool` attribute error

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

#286 - Feature request: wrap panda dataframe methods

Issue - State: open - Opened by marco-mariotti almost 2 years ago - 2 comments

#285 - Ranges disappear when get out of bounds on the 5' end in spliced_subsequence

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

#284 - Fix FutureWarning

Pull Request - State: closed - Opened by y9c almost 2 years ago - 1 comment

#283 - pyranges could not be installed on Python 3.11 due to pyrle dependency failed.

Issue - State: open - Opened by y9c almost 2 years ago - 5 comments

#282 - nearest and k_nearest not reporting ties

Issue - State: open - Opened by ASintsova about 2 years ago - 1 comment

#281 - to_gff3 URL escape

Issue - State: open - Opened by tonytony99 about 2 years ago

#280 - window and tile methods doe not work on Windows

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

#279 - A small update to remove pd.append() warnings

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

#278 - pathlib support?

Issue - State: open - Opened by ivirshup about 2 years ago - 1 comment

#277 - Importing pyranges

Issue - State: open - Opened by Sayyam-Shah about 2 years ago - 1 comment

#276 - please help me with this issue raised on stack overflow

Issue - State: open - Opened by GH-MStamboulian over 2 years ago - 1 comment

#275 - added step to reorder bed columns based on order in PyRanges object before writing

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

#274 - `to_bed` reorders bed columns

Issue - State: open - Opened by fairliereese over 2 years ago - 1 comment

#273 - How do I exlucde some ranges

Issue - State: open - Opened by silvewheat over 2 years ago

#272 - `pr.read_gtf` returns error if some GTF records end with a semicolon

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

#271 - Error when using python 3.9

Issue - State: open - Opened by MyhFe over 2 years ago - 1 comment

#270 - Fixed the replace parameter.

Pull Request - State: closed - Opened by FabrizioG202 over 2 years ago - 1 comment

#269 - Allow reading empty attribute GTF

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

#268 - GTF reader

Issue - State: open - Opened by yzJiang9 over 2 years ago - 3 comments

#267 - Replace parameter is ignored in PyRanges.sample

Issue - State: closed - Opened by FabrizioG202 over 2 years ago - 3 comments

#266 - Linked intervals

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

#265 - conda bamread not supported

Issue - State: open - Opened by marco-mariotti over 2 years ago

#264 - Fix UnboundLocalError for 'null' variable

Pull Request - State: closed - Opened by mkanai over 2 years ago - 5 comments

#263 - fixes: #262; nearest without overlapping chromosomes

Pull Request - State: closed - Opened by Maarten-vd-Sande over 2 years ago - 6 comments

#261 - introns() function in pyranges/genomicfeatures.py uses `inplace=True`

Issue - State: open - Opened by DongzeHE over 2 years ago - 5 comments

#259 - PyRanges.join() and match columns as well as genomic range

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

#258 - Deprecation of ```np.long`` in NumPy 1.20 in .merge() method

Issue - State: open - Opened by homonecloco almost 3 years ago - 17 comments

#257 - Controlling strand handling wrt input and operations?

Issue - State: open - Opened by alexpreynolds almost 3 years ago - 1 comment

#256 - [Feature request] Publish prebuilt wheels

Issue - State: open - Opened by jwarwick-delfi almost 3 years ago - 3 comments
Labels: enhancement

#254 - read_gtf error if attribute value is empty string (i.e. <key> "";)

Issue - State: closed - Opened by SamBryce-Smith almost 3 years ago - 3 comments

#253 - Add github action to tag releases

Issue - State: open - Opened by endrebak almost 3 years ago

#252 - Add duplicated_position method

Issue - State: open - Opened by endrebak almost 3 years ago

#251 - Merge metadata rows with separator value

Issue - State: open - Opened by endrebak almost 3 years ago

#250 - Run docstring-tests when pushing to repo

Issue - State: open - Opened by endrebak almost 3 years ago

#249 - gr.insert(df, 0) gives incorrect result

Issue - State: open - Opened by endrebak almost 3 years ago

#248 - Remove self contained overlaps

Issue - State: open - Opened by PedroBarbosa almost 3 years ago - 9 comments

#247 - Trying to autogenerate book with github actions.

Pull Request - State: closed - Opened by endrebak almost 3 years ago

#246 - Add build badge from github actions

Issue - State: open - Opened by endrebak almost 3 years ago

#245 - test

Pull Request - State: closed - Opened by endrebak almost 3 years ago

#244 - Test if travis still there

Pull Request - State: closed - Opened by endrebak almost 3 years ago

#243 - Update ghwf

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

#242 - Changes to make flake8 pass

Pull Request - State: closed - Opened by endrebak almost 3 years ago

#241 - Fix gff3 writer

Pull Request - State: closed - Opened by endrebak almost 3 years ago

#240 - Add subsequence

Pull Request - State: closed - Opened by marco-mariotti almost 3 years ago

#239 - Conda: Cannot install under python 3.10

Issue - State: open - Opened by tlkaufmann almost 3 years ago - 11 comments

#238 - Add subsequence

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

#237 - Create python-package-conda.yml

Pull Request - State: closed - Opened by endrebak almost 3 years ago - 2 comments

#236 - Allow for Python 3.9 also

Issue - State: open - Opened by endrebak almost 3 years ago

#235 - Add subsequence

Pull Request - State: closed - Opened by marco-mariotti almost 3 years ago - 5 comments

#234 - Request for tutorial for beginners

Issue - State: closed - Opened by mnshgl0110 almost 3 years ago - 7 comments

#233 - Spliced subseq3

Pull Request - State: open - Opened by endrebak about 3 years ago

#232 - Spliced subseq2

Pull Request - State: closed - Opened by endrebak about 3 years ago

#231 - to_gff3 output not readable by read_gff3

Issue - State: closed - Opened by augustboyle about 3 years ago - 5 comments

#230 - join method ValueError

Issue - State: open - Opened by ilyes495 about 3 years ago - 6 comments

#229 - added spliced_subsequence

Pull Request - State: closed - Opened by marco-mariotti about 3 years ago - 4 comments

#227 - Please consider to tag github releases

Issue - State: open - Opened by nileshpatra about 3 years ago - 2 comments

#226 - 0.0.112

Pull Request - State: closed - Opened by endrebak about 3 years ago

#225 - Set min version NCLS

Pull Request - State: closed - Opened by endrebak about 3 years ago

#224 - pyranges Subtract does not work in pyranges v0.0.110

Issue - State: closed - Opened by mikecormier about 3 years ago - 5 comments

#223 - 0.0.110

Pull Request - State: closed - Opened by endrebak about 3 years ago

#222 - Fix subtract

Pull Request - State: closed - Opened by endrebak about 3 years ago

#221 - overlap(invert=True) not working as expected

Issue - State: closed - Opened by endrebak about 3 years ago - 1 comment

#220 - Subtract over 1024 pyranges gives weird results

Issue - State: closed - Opened by MateuszChilinski about 3 years ago - 18 comments

#219 - 108 hotfix

Pull Request - State: closed - Opened by endrebak about 3 years ago

#218 - SyntaxError originating from a typo in pyranges.readers

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

#217 - 107

Pull Request - State: closed - Opened by endrebak about 3 years ago

#215 - Suffix is not applied to Strand when joining unstranded and stranded ranges

Issue - State: closed - Opened by alecchap about 3 years ago - 7 comments

#214 - `copy` drops rows when Strand is `nan`

Issue - State: open - Opened by alecchap about 3 years ago - 8 comments

#213 - Joining with slack creates extra columns in the original PyRanges object

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

#211 - Can't read BAM file

Issue - State: closed - Opened by dcizin over 3 years ago - 1 comment

#196 - travis-ci.org not triggering

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

#170 - const int32_t' but got 'long' when joining two bed files

Issue - State: open - Opened by akmorrow13 almost 4 years ago - 14 comments