1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
|
# Release notes
## [Upcoming release](https://github.com/open2c/bioframe/compare/v0.8.0...HEAD)
## v0.8.0
Date: 2025-04-08
API changes:
* bigtools engine for bigwig and bigbed.
* run length functions `mark_runs` and `compress_runs`.
Maintenance:
* Numpy 2.x support.
## v0.7.2
Date: 2024-06-19
API changes:
* `read_alignment` function introduced in v0.7.0 has been pluralized to `read_alignments`
Maintenance:
* Skip `read_alignments` tests on big-endian architectures by @nvictus in https://github.com/open2c/bioframe/pull/216
**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.7.1...v0.7.2
## v0.7.1
Date: 2024-06-17
Maintenance:
* Refactor join arrayops and intidx internals by @nvictus in https://github.com/open2c/bioframe/pull/204
* NumPy 2.0 was released. Pin `numpy < 2` until we migrate.
**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.7.0...v0.7.1
## v0.7.0
Date: 2024-05-20
API changes:
* Add `to_bed` function to validate and write standard BED files @gamazeps in https://github.com/open2c/bioframe/pull/203
* `read_bam` deprecated in favor of `read_alignments` @gamazeps in https://github.com/open2c/bioframe/pull/206
Documentation:
* Add "bioframe for bedtools users" guide to docs by @gamazeps in https://github.com/open2c/bioframe/pull/198
Bug fixes:
* Fix contig name and JSON issues in read_bam implementation by @gamazeps in https://github.com/open2c/bioframe/pull/206
New Contributors:
* @gamazeps made their first contribution in https://github.com/open2c/bioframe/pull/203
**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.6.4...v0.7.0
## v0.6.4
Date: 2024-04-06
Maintenance:
* Migrate from setuptools `pkg_resources` to `importlib.resources` by @nvictus in https://github.com/open2c/bioframe/pull/194
* Use `importlib.metadata` for versioning by @nvictus in https://github.com/open2c/bioframe/pull/195
Bug fixes:
* Overlap point segment patch #183 by @smitkadvani in https://github.com/open2c/bioframe/pull/184
* #167: Replaced np.int with int as the attribute is deprecated by numpy by @harshit148 in https://github.com/open2c/bioframe/pull/192
New Contributors:
* @harshit148 made a first contribution in https://github.com/open2c/bioframe/pull/192
**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.6.3...v0.6.4
## v0.6.3
Date: 2024-03-11
Fixes:
* Prevent dropout from `closest` in some cases of left intervals with no neighbors by @agalitsyna in https://github.com/open2c/bioframe/pull/185
* Fix overlap returning float indexes causing failing tests (numpy v1.22.4, pandas v1.5.2) by @agalitsyna in https://github.com/open2c/bioframe/pull/185
**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.6.2...v0.6.3
## v0.6.2
Date: 2024-02-08
Changes:
* cols and df_view_col passed to downstream functions by @smitkadvani in https://github.com/open2c/bioframe/pull/182
Fixes:
* Update to new UCSC hgdownload url by @golobor and @nvictus in https://github.com/open2c/bioframe/pull/187
**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.6.1...v0.6.2
## v0.6.1
Date: 2024-01-08
API changes:
Default behavior of `ensure_nullable` option in `overlap` was modified to minimize the possibility of regressions in libraries that depend on legacy behavior.
* The new option was renamed `ensure_int` and is `True` by default. It ensures that output coordinate columns are always returned with an integer dtype, as was the case in prior versions. This is achieved by converting columns having non-nullable NumPy dtypes to Pandas nullable ones in the specific case where the result of an **outer join** generates missing values; otherwise, column dtypes are preserved unchanged in the output.
* Unlike previous minor versions of bioframe, the nullable dtype chosen will have the **same underlying type** as the corresponding column from the input (i.e, an input dataframe using `np.uint32` start coordinates may yield a `pd.UInt32` start column in the output).
* This behavior can be turned off by setting `ensure_int` to `False`, in which case outer joins on dataframes using NumPy dtypes may produce floating point output columns when missing values are introduced (stored as `NaN`), following the native casting behavior of such columns.
**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.6.0...v0.6.1
## v0.6.0
Date: 2024-01-04
API changes:
* `overlap`: In previous versions, output coordinate columns were always converted to Pandas "nullable" `Int64` dtype before returning outer join results. In the interest of flexibility, memory efficiency, and least surprise, the coordinate columns returned in the output dataframe now preserve dtype from the input dataframes, following native type casting rules if missing data are introduced. We introduce the `ensure_nullable` argument to force Pandas nullable dtypes in the output coordinates. See the [docs](https://bioframe.readthedocs.io/en/latest/api-intervalops.html#bioframe.ops.overlap) for more details. (#178)
Bug fixes:
* Fixed `coverage` with custom `cols1` (#170)
Documentation:
* Added contributing guidelines and NumFOCUS affiliation.
* Updated README and added CITATION.cff file.
* Updated performance benchmarks.
**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.5.1...v0.6.0
## v0.5.1
Date: 2023-11-08
Bug fixes:
* Series are treated like dict in `make_chromarms`
**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.5.0...v0.5.1
## v0.5.0
Date: 2023-10-05
API changes:
* New builtin curated genome assembly database (metadata, chromsizes, cytobands):
* `bioframe.list_assemblies()`
* `bioframe.assembly_info()`
* New UCSC RGB color converter utility #158
* Options added to `pair_by_distance`
Bug fixes:
* Make expand throw an error if both pad and scale are passed (#148)
* Fixes to bioframe.select query interval semantics (#147)
Maintenance:
* Migrate to hatch build system and pyproject.toml
* Various refactorings
**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.4.1...v0.5.0
## v0.4.1
Date: 2023-04-22
Bug fixes:
* Fix bug introduced in the last release in `select` and `select_*` query interval semantics. Results of select are now consistent with the query interval being interpreted as half-open, closed on the left.
**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.4.0...v0.4.1
## v0.4.0
Date: 2023-03-23
API changes:
* New strand-aware directionality options for `closest()` via `direction_col` #129.
* New index-based range query selectors on single bioframes to complement `select()` #128:
* `select_mask()` returns boolean indices corresponding to intervals that overlap the query region
* `select_indices()` returns integer indices corresponding to intervals that overlap the query region
* `select_labels()` returns pandas label indices corresponding to intervals that overlap the query region
Bug fixes:
* Import fixes in sandbox
* Relax bioframe validator to permit using same column as start and end (e.g. point variants).
**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.3.3...v0.4.0
## v0.3.3
Date: 2022-02-28
Bug fixes:
* fixed a couple functions returning an error instance instead of raising
* fetch_mrna link fixed
**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.3.2...v0.3.3
## v0.3.2
Date: 2022-02-01
Bug fixes:
* fixed error in is_contained
* tutorial updates
**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.3.1...v0.3.2
## v0.3.1
Date: 2021-11-15
API changes:
* `bioframe.sort_bedframe` does not append columns or modify their dtypes.
**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.3.0...v0.3.1
## v0.3.0
Date: 2021-08-31
Conceptual changes:
* we formulated strict definitions for genomic intervals, dataframes, and
their various properties. All bioframe functions are expected to follow
to these definitions tightly.
API changes:
* reorganize modules:
* ops - operations on genomic interval dataframes
* extras - miscellaneous operations, most involving
genomic sequences and gene annotations
* vis - visualizations of genomic interval dataframes
* core.arrops - operations on genomic interval arrays
* core.checks - tests for definitions of genomic interval dataframes
* core.construction - construction and sanitation of genomic interval dataframes
* core.specs - specifications for the implementation of genomic intervals in pandas.dataframes
(i.e. column names, datatypes, etc)
* core.stringops - operations on genomic interval strings
* io.fileops - I/O on common file formats for genomic data
* io.schemas - schemas for standard tabular formats for genomic data storage
* io.resources - interfaces to popular online genomic data resources
* new functions: extras.pair_by_distance, ops.sort_bedframe, ops.assign_view,
dataframe constructors
* existing functions:
* expand: take negative values and fractional values
* overlap: change default suffixes, keep_order=True
* subtract: add return_index and keep_order
* enable pd.NA for missing values, typecasting
New data:
* add schemas for bedpe, gap, UCSCmRNA, pgsnp
* add tables with curated detailed genome assembly information
Bugfixes:
* None?..
Miscellaneous:
* speed up frac_gc is faster now
* drop support for Python 3.6, add support for 3.9
**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.2.0...v0.3.0
## v0.2.0
Date: 2020-12-02
API changes:
* `read_chromsizes` and `fetch_chromsizes`: add new `as_bed` parameter.
* `read_chromsizes` and `fetch_chromsizes`: revert to filtering chromosome names by default, but clearly expose `filter_chroms` kwarg.
Bug fixes:
* Fixed `bioframe.split`
* Restored `frac_genome_coverage`
**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.1.0...v0.2.0
## v0.1.0
Date: 2020-09-23
First beta release.
What's new:
* New extensive dataframe genomic interval arithmetic toolsuite.
* Improved region handling and region querying functions.
* [Documentation!](https://bioframe.readthedocs.io/)
Maintenance:
* Dropped Python 2 support
* Refactoring of various genome operations and resources.
* Improved testing and linting
**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.0.12...v0.1.0
|
