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James Taylor
Merged in ghuls/bx-python/allow_dot_as_strand (pull request #6) Allow '.' as valid value for strand in GenomicInterval.
Gert Hulselmans
Allow '.' as valid value for strand in GenomicInterval. Before this commit, only '+' and '-' where accepted as valid values for strand in GenomicInterval. This gives problems with some valid BigBed files that have '.' as strand info, like '.broadPeak.bigbed' and '.narrowPeak.bigBed' files from the ENCODE project (https://www.encodeproject.org). By allowing '.' as valid value from strand in GenomicInterval, those BigBed files can be correctly opened ('…
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allow_dot_as_strand
James Taylor
Merged in brentp/bx-python (pull request #7) speed up bigbed/bigwig by about 2-fold.
Brent Pedersen
The bigwig/bigbed stuff is slow. This commit improves the speed by about 2-fold. It is still slow, but more improvements would require larger design changes. Previously, where chunks of data were read as, for example: read_uint32() read_uint32() read_uint32() this changes that to read all 3 values in a single pass. I also removed some dead code. See: https://gist.github.com/brentp/c9b24554cff4bab0a0bc for the test of validity and the timing. The md5sums before and after for a whole-genome bigwig and bigbed are identical. Output looks like…
Nate Coraor
Fix typo in classifiers list name in setup.py pointed out by Bob Harris.
Nate Coraor
Add LICENSE to MANIFEST.in so it's included in the source distribution.
Nate Coraor
Add license (MIT) and classifiers for PyPI.
Nate Coraor
Bump version to 0.7.2
sontek
Change raised exceptions from strings to ValueErrors
olgert denas
tagget final bnmapper version
olgert denas
Added tag bnMapper freeze for changeset 83b6d153f889
gertidenas
bnMapper documentation
Tags
bnMapper freeze
olgert denas
bnMapper was ignoring peaks it should have not
Comments 1
James Taylor
maf_tile_2bit.py: fix chromosome name for 2bit access
James Taylor
maf_tile_2bit.py: Variant of maf_tile_2.py that fetches reference sequence data from twoBit format files
James Taylor
bpt_file: fix a bug recursing into the BPT, only encountered for files with large numbers of keys (e.g. scaffolds)
James Taylor
Moving maf_covered_ranges.py util from ESPERR
James Taylor
Don't fail on missing lzo unless actually used
James Taylor
Run everything through Cython 0.18. Fixed a bug in BinnedBitset when the size is larger than the max size, all tests passing
James Taylor
Updating to latest distribute_setup.py
James Taylor
Merged in eivindgl/bx-python (pull request #2) fixed BinnedBitSet memory leak
eivindgl
fixed BinnedBitSet memory leak
mruffalo
lrucache.py: remove functools.total_ordering call This isn't present in Python 2.4, so replace it with a manual total ordering by implementing the rest of the __comparison__ methods.
mruffalo
lrucache.py: remove __future__.generators import Python 2.4 is now the minimum version, and generators don't require a __future__ import now.
olgert denas
BED4 output (bnMapper) had a problem
olgert denas
progress message / chromosome
olgert denas
check cached chains are up to date and int chain score
olgert denas
fixed small bugs and added options
olgert denas
fixed issue with peaks spanning multiple chains
olgert denas
scripts for chain to EPO (.out) conversion and feature mapping
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