|
87abd3b1
|
Switch .hgignore to .gitignore
|
James Taylor <j****s@j****g>
|
about 11 years ago
|
|
|
277e3b47
|
Switch (back) from distirbute to setuptools.
|
James Taylor <j****s@j****g>
|
about 11 years ago
|
|
|
a14b3d89
|
merge
Merged in ghuls/bx-python/allow_dot_as_strand (pull request #6)
|
James Taylor <j****r@e****u>
|
about 11 years ago
|
|
|
83ebaaa0
|
merge
Merged in brentp/bx-python (pull request #7)
|
James Taylor <j****r@e****u>
|
about 11 years ago
|
|
|
d32e9c9c
|
Fix typo in classifiers list name in setup.py pointed out by Bob Harris.
|
Nate Coraor <n****e@b****u>
|
about 11 years ago
|
|
|
7419905c
|
The bigwig/bigbed stuff is slow. This commit improves the speed by about 2-fold.
|
Brent Pedersen <b****e@g****m>
|
over 11 years ago
|
|
|
c31f1c7b
|
Add LICENSE to MANIFEST.in so it's included in the source distribution.
|
Nate Coraor <n****e@b****u>
|
over 11 years ago
|
|
|
031d6de3
|
Add license (MIT) and classifiers for PyPI.
|
Nate Coraor <n****e@b****u>
|
over 11 years ago
|
|
|
bd1fc6bb
|
Allow '.' as valid value for strand in GenomicInterval.
|
Gert Hulselmans <h****t@g****m>
|
over 11 years ago
|
|
|
1cbcf748
|
Bump version to 0.7.2
|
Nate Coraor <n****e@b****u>
|
over 12 years ago
|
|
|
021bdc38
|
Change raised exceptions from strings to ValueErrors
|
sontek <s****k@g****m>
|
almost 13 years ago
|
|
|
86c569e7
|
tagget final bnmapper version
|
olgert denas <g****s@g****m>
|
about 13 years ago
|
|
|
55a72e3d
|
Added tag bnMapper freeze for changeset 83b6d153f889
|
olgert denas <g****s@g****m>
|
about 13 years ago
|
|
|
d904f793
|
bnMapper documentation
|
gertidenas <g****s@l****t>
|
over 13 years ago
|
|
|
bb535f84
|
bnMapper was ignoring peaks it should have not
|
olgert denas <g****s@g****m>
|
over 13 years ago
|
|
|
fe650826
|
maf_tile_2bit.py: fix chromosome name for 2bit access
|
James Taylor <j****s@j****g>
|
over 13 years ago
|
|
|
4fcdb53e
|
maf_tile_2bit.py: Variant of maf_tile_2.py that fetches reference sequence da...
|
James Taylor <j****s@j****g>
|
over 13 years ago
|
|
|
e4c30d22
|
bpt_file: fix a bug recursing into the BPT, only encountered for files with l...
|
James Taylor <j****s@j****g>
|
over 13 years ago
|
|
|
eb07f566
|
Moving maf_covered_ranges.py util from ESPERR
|
James Taylor <j****s@j****g>
|
over 13 years ago
|
|
|
1e1b88d1
|
Don't fail on missing lzo unless actually used
|
James Taylor <j****s@j****g>
|
over 13 years ago
|
|
|
55923721
|
Run everything through Cython 0.18. Fixed a bug in BinnedBitset when the size...
|
James Taylor <j****s@j****g>
|
over 13 years ago
|
|
|
8c959c74
|
Updating to latest distribute_setup.py
|
James Taylor <j****s@j****g>
|
over 13 years ago
|
|
|
4f5b13ed
|
merge
Merged in eivindgl/bx-python (pull request #2)
|
James Taylor <j****r@e****u>
|
over 13 years ago
|
|
|
9a346f31
|
lrucache.py: remove functools.total_ordering call
|
Matthew Ruffalo <m****o@c****u>
|
over 13 years ago
|
|
|
a95d1d84
|
lrucache.py: remove __future__.generators import
|
Matthew Ruffalo <m****o@c****u>
|
over 13 years ago
|
|
|
07abb4e8
|
BED4 output (bnMapper) had a problem
|
olgert denas <g****s@g****m>
|
almost 14 years ago
|
|
|
09820573
|
progress message / chromosome
|
olgert denas <g****s@g****m>
|
about 14 years ago
|
|
|
efad9652
|
check cached chains are up to date and int chain score
|
olgert denas <g****s@g****m>
|
about 14 years ago
|
|
|
87a59bd4
|
fixed small bugs and added options
|
olgert denas <g****s@g****m>
|
about 14 years ago
|
|
|
e0d40373
|
fixed issue with peaks spanning multiple chains
|
olgert denas <g****s@g****m>
|
about 14 years ago
|
|
|
91763064
|
scripts for chain to EPO (.out) conversion and feature mapping
|
olgert denas <g****s@g****m>
|
about 14 years ago
|
|
|
3554d058
|
Alter bbi_file.pyx ZoomLevel._summary_blocks_in_region to be slightly more ef...
|
Jacob Silterra <j****r@g****m>
|
over 14 years ago
|
|
|
89a5be83
|
fixed BinnedBitSet memory leak
|
eivindgl <e****l@l****t>
|
over 14 years ago
|
|
|
44409d7b
|
If Python 3, use 2to3 distutils builder instead
|
Matthew Ruffalo <m****o@c****u>
|
over 14 years ago
|
|
|
08b4e7c2
|
pstat.py: fix one cmp call, add TODO to another
|
Matthew Ruffalo <m****o@c****u>
|
over 14 years ago
|
|
|
49bb218c
|
Fix more usage of old cmp function
|
Matthew Ruffalo <m****o@c****u>
|
over 14 years ago
|
|
|
5f201eb8
|
phylo.newick: fix old usage of cmp, __cmp__
|
Matthew Ruffalo <m****o@c****u>
|
over 14 years ago
|
|
|
fed28a63
|
intervals/intersection.pyx: replace old 'cmp' usage
|
Matthew Ruffalo <m****o@c****u>
|
over 14 years ago
|
|
|
36a7b90e
|
setup.py: correctly identify Python 3 as >= 2.4 for issue #35
|
Matthew Ruffalo <m****o@c****u>
|
almost 15 years ago
|
|
|
ba63a85b
|
Raise exceptions instead of raw strings for issue #35
|
Matthew Ruffalo <m****o@c****u>
|
almost 15 years ago
|
|
|
5e95d8cd
|
Cythonizing everything with 15.1, fix some deprecations and tests. AlignmentM...
|
James Taylor <j****s@j****g>
|
almost 15 years ago
|
|
|
a7ec8e30
|
BigWig/BigBed: fixed some missing type declerations in the summarization code...
|
James Taylor <j****s@j****g>
|
almost 15 years ago
|
|
|
c8cf0cb2
|
Update .c from .pyx
|
James Taylor <j****s@j****g>
|
almost 15 years ago
|
|
|
c1d60e09
|
BigWig/BigBed: fix a bug where data might not be returned for summary blocks ...
|
James Taylor <j****s@j****g>
|
almost 15 years ago
|
|
|
5c63048d
|
merge
Automated merge with https://bitbucket.org/james_taylor/bx-python
|
James Taylor <j****s@j****g>
|
almost 15 years ago
|
|
|
d0a1d2df
|
Helper for displaying progress bar while iterating
|
James Taylor <j****s@j****g>
|
almost 15 years ago
|
|
|
2030858e
|
Fixes to allow BGZF to compile on Solaris
|
Nate Coraor <n****e@b****u>
|
over 15 years ago
|
|
|
9772345e
|
Add back BGZF tests
|
Kanwei Li <k****i@g****m>
|
over 15 years ago
|
|
|
08dab43b
|
Fix bigBed#query
|
Kanwei Li <k****i@g****m>
|
over 15 years ago
|
|
|
eaf04d4d
|
typo
|
Kanwei Li <k****i@g****m>
|
over 15 years ago
|
|
|
d6b543c9
|
Add manifest to pull in generated C files; eases easy_install/pip installatio...
|
Brad Chapman <c****b@5****m>
|
over 15 years ago
|
|
|
58a6e3ca
|
Support space separated files as backup to tab separation with allow_spaces f...
|
Brad Chapman <c****b@5****m>
|
over 15 years ago
|
|
|
d47dff40
|
Tests now run when PYTHONPATH is not set
|
Kanwei Li <k****i@g****m>
|
over 15 years ago
|
|
|
6b2b0f11
|
Remove bigbed_file.so
|
Kanwei Li <k****i@g****m>
|
over 15 years ago
|
|
|
398a624d
|
Use instanceof() instead of type()
|
Kanwei Li <k****i@g****m>
|
over 15 years ago
|
|
|
aee27b45
|
add bed_extend_to.py, extend each record to a minimum size
|
James Taylor <j****s@j****g>
|
over 15 years ago
|
|
|
020458f8
|
merge
Merge to restore BGZFFile
|
James Taylor <j****s@j****g>
|
over 15 years ago
|
|
|
510858b6
|
Backed out changeset c1e165e97419, bgzf is still useful.
|
James Taylor <j****s@j****g>
|
over 15 years ago
|
|
|
f5097021
|
bigbed support
|
James Taylor <j****s@j****g>
|
over 15 years ago
|
|
|
b2cba0da
|
script for computing signal profiles (from bigwig) around interval centers
|
James Taylor <j****s@j****g>
|
over 15 years ago
|
|
|
91f3433f
|
small bigwig tweaks
|
James Taylor <j****s@j****g>
|
over 15 years ago
|
|
|
9e014f6c
|
Implement support for getting raw data points from bigwig, either in a numpy ...
|
James Taylor <j****s@j****g>
|
over 15 years ago
|
|
|
ddf8579d
|
refactor bigwig support, add more tests
|
James Taylor <j****s@j****g>
|
over 15 years ago
|
|
|
c4872aed
|
Fix 'first line is header' support in tabular.io
|
James Taylor <j****s@j****g>
|
over 15 years ago
|
|
|
67048d4f
|
Remove leading and trailing white space from around chromosome names in Genom...
|
Daniel Blankenberg <d****n@b****u>
|
over 15 years ago
|
|
|
40235b92
|
Fix for fixed step records in bigwig
|
James Taylor <j****s@j****g>
|
over 15 years ago
|
|
|
ed3f7e3e
|
Free tree iterator in clustertree after getting results
|
Kanwei Li <k****i@g****m>
|
over 15 years ago
|
|
|
134a4b11
|
Bump to 0.7.0, fix doc URL
|
Kanwei Li <k****i@g****m>
|
over 15 years ago
|
|
|
0bff1bc7
|
Fix string padding in bbi.bpt_file. Fix edge case when valid_count was less t...
|
Kanwei Li <k****i@g****m>
|
over 15 years ago
|
|
|
0c1bbabe
|
Minor refactorings to bbi
|
Kanwei Li <k****i@g****m>
|
over 15 years ago
|
|
|
3179d769
|
Use deque instead of list comprehension to greatly increase performance
|
Kanwei Li <k****i@g****m>
|
over 15 years ago
|
|
|
f79a4116
|
Rename bx.intervals.random to bx.intervals.random_intervals so it doesn't clo...
|
Kanwei Li <k****i@g****m>
|
over 15 years ago
|
|
|
afc9688c
|
Remove unused bgzf test data
|
Kanwei Li <k****i@g****m>
|
over 15 years ago
|
|
|
b1c61dd9
|
Add BigWig tests and test datasets. Fix error with min and max values being s...
|
Kanwei Li <k****i@g****m>
|
over 15 years ago
|
|
|
b3048e42
|
Make mean, max and min return NaN if no values in the region instead of 0.0. ...
|
Kanwei Li <k****i@g****m>
|
over 15 years ago
|
|
|
70dba296
|
Fully working and correct bigWig reader. Added new 'query' method that is use...
|
Kanwei Li <k****i@g****m>
|
almost 16 years ago
|
|
|
1f5b3403
|
Fixes to bigwig stuff from Bob Harris
|
James Taylor <j****s@j****g>
|
almost 16 years ago
|
|
|
416f03fc
|
BigWigFile subclassing BBIFile, support for creating summaries from 'unzoomed...
|
James Taylor <j****s@j****g>
|
almost 16 years ago
|
|
|
d97314ad
|
BBI Files: Summarization from zoom levels now working. Still need to implement
|
James Taylor <j****s@j****g>
|
almost 16 years ago
|
|
|
6684d029
|
Adding generated C files
|
James Taylor <j****s@j****g>
|
almost 16 years ago
|
|
|
000269df
|
Renaming cir_tree to cirtree_file to be consistent with other packages
|
James Taylor <j****s@j****g>
|
almost 16 years ago
|
|
|
5a2a1341
|
First steps toward bigbed/bigwig reading -- working read-only implementations...
|
James Taylor <j****s@j****g>
|
almost 16 years ago
|
|
|
5d28288c
|
using this small cython directive [1] improves speed by about 5%
|
brentp <b****e@g****m>
|
about 16 years ago
|
|
|
23e18e11
|
Fix small twobit reading bug & add test
|
Kanwei Li <k****i@g****m>
|
about 16 years ago
|
|
|
30538f5f
|
interval index file, make sure start is not > stop. added test.
|
brentp <b****e@g****m>
|
over 16 years ago
|
|
|
afcc3b3a
|
Up version to 0.6.0, release to pypi
|
James Taylor <j****s@j****g>
|
over 16 years ago
|
|
|
41914e4e
|
Added comment in header to clarify that intervals are origin-zero, half-open.
|
Bob Harris <B****s@l****t>
|
over 16 years ago
|
|
|
654610f3
|
Corrected problem in maf_extract_ranges_indexed, which failed when a maf bloc...
|
Bob Harris <B****s@l****t>
|
over 16 years ago
|
|
|
15bd0d82
|
- Changes to array_tree to enable frequencies (how many times a node is visit...
|
Kanwei Li <k****i@g****m>
|
over 16 years ago
|
|
|
5329a5dd
|
add new ez_setup.py
|
brentp <b****e@g****m>
|
over 16 years ago
|
|
|
b5e43a09
|
Note about issue #10
|
James Taylor <j****s@j****g>
|
over 16 years ago
|
|
|
1165ce94
|
Remove bgzf as it's no longer planned to be used
|
Kanwei Li <k****i@g****m>
|
over 16 years ago
|
|
|
3f5e170f
|
add cython generated file to repo
|
brentp <b****e@g****m>
|
over 16 years ago
|
|
|
5b53a809
|
Two fixes for align.tools from Thomas Mailund
|
James Taylor <j****s@j****g>
|
over 16 years ago
|
|
|
13a25d26
|
Make BGZF test a real unittest
|
James Taylor <j****s@j****g>
|
over 16 years ago
|
|
|
5f743c20
|
BGZF support (really simple wrapper to code from samtools)
|
James Taylor <j****s@j****g>
|
over 16 years ago
|
|
|
d46242e8
|
Return empty list for interval operations on empty trees to prevent segfaults...
|
Kanwei Li <k****i@g****m>
|
almost 17 years ago
|
|
|
1ccdc4fc
|
Update array_tree version assert, use cython for cluster
|
Kanwei Li <k****i@g****m>
|
almost 17 years ago
|
|
|
9894e17e
|
Fix interval_index_file test to use max parameter
|
Kanwei Li <k****i@g****m>
|
almost 17 years ago
|
|
|
67616d1d
|
Fix return bug in bits#bitCountRange
|
Kanwei Li <k****i@g****m>
|
almost 17 years ago
|
|