v0.1.5

We stopped developing pyranges0 (this repo) in favor of pyranges1.
This may be the last release of pyranges0.

0.0.132

Tagging a "stable" v0 in view of the transition to v1
v0 tagged releases will have long-term documentation in readthedocs

What's Changed

• Spliced subseq2 by @endrebak in #232
• 0.0.112 by @endrebak in #226
• Add subsequence by @marco-mariotti in #240
• Fix gff3 writer by @endrebak in #241
• Changes to make flake8 pass by @endrebak in #242
• Update ghwf by @endrebak in #243
• Fix one-off error for GTF Start coordinates in read_gtf_restricted (read_gtf(full=False)) by @SamBryce-Smith in #260
• Trying to autogenerate book with github actions. by @endrebak in #247
• Allow reading empty attribute GTF by @endrebak in #269
• A small update to remove pd.append() warnings by @aallahyar in #279
• Fixed the replace parameter. by @FabrizioG202 in #270
• added step to reorder bed columns based on order in PyRanges object before writing by @fairliereese in #275
• Linked intervals by @marco-mariotti in #266
• Fix UnboundLocalError for 'null' variable by @mkanai in #264
• Docstring update by @marco-mariotti in #290
• Bug fix on subsequence and spliced_subsequence by @marco-mariotti in #294
• 0.0.121 by @endrebak in #300
• Improve genome bounds by @marco-mariotti in #295
• fixed empty attribute bug in read_gtf when duplicate_attr=True by @fairliereese in #297
• Fix FutureWarning by @y9c in #284
• book: index and tutorial by @marco-mariotti in #318
• Preserve order aallahyar by @endrebak in #319
• hi by @endrebak in #328
• ho by @endrebak in #329
• hi by @endrebak in #330
• hia by @endrebak in #331
• hi by @endrebak in #333
• Update run_hypothesis_tests.yml by @endrebak in #334
• Update run_hypothesis_tests.yml by @endrebak in #335
• Add property tests by @endrebak in #336
• Require fewer property tests on github actions by @endrebak in #337
• Fix tostring2 by @endrebak in #339
• 0.0.128 Fix left join category error #342 by @endrebak in #343
• 342 2 by @endrebak in #344
• New documentation by @marco-mariotti in #347
• RTD bugfix by @marco-mariotti in #350
• Bump urllib3 from 2.0.5 to 2.0.6 in /docs by @dependabot in #352
• Option to automatically rename reserved GTF columns in read_gtf by @fairliereese in #354
• Minor doc edits by @marco-mariotti in #358
• COC by @endrebak in #368
• Del by @endrebak in #369
• Open file fix by @endrebak in #379

New Contributors

• @SamBryce-Smith made their first contribution in #260
• @aallahyar made their first contribution in #279
• @FabrizioG202 made their first contribution in #270
• @fairliereese made their first contribution in #275
• @mkanai made their first contribution in #264
• @y9c made their first contribution in #284
• @dependabot made their first contribution in #352

Full Changelog: 0.0.111...v0

0.0.111

Set min version pyranges (#225)

Co-authored-by: endre bakken stovner <endrebakkenstovner@endres-MacBook-Air.local>

0.0.85

Fix read_gtf.

0.0.79

Fix features.introns (#135)

* Fix features.introns

* Fix introns bump version

* Fix introns bump version

0.0.58

• fix merge print functions
• make pickleable
• add iter as alias for itergrs in pr. namespace
• gr.length() shows nucleotide length (sum of all interval lengths)
• gr.lengths() takes as_dict=False flag to return as vector
• fix slack in join: added columns when joining with itself
• fix print for unstranded pyranges: printed tail and head of first chromosome

0.0.57

0.0.57 (10.10.19): add overlap-flag to tile + bugfixes (#34)

* 0.0.57 (10.10.19): add overlap-flag to tile + bugfixes

- add overlap-flag to tile
- add chain to print-method
- bugfix: printing stranded pyranges sorted output even though sort was false
- bugfix: wrong number hidden cols on very small terminal widths
- bugfix: unstrand did not change underlying dict to chromosomes only
- show number of hidden columns in header
- tests: mismatches in strand between dict and dataframes

* Fix bug in tile overlap

* Fix tests

* Fix tile overlap

* df/as_df returns non-duplicated index

0.0.56

0.0.56 (25.09.19)

• add possibility of 5-end and 3-end in slack being different/none
• add slack to join-method
• add new_position method to take union or intersection of two pairs of Start/End-columns in pyranges