Commits

Author Commit Message Labels Comments Date
James Taylor
Convenience class for reading and writing binary data
James Taylor
Add chrom to intersection.Interval since it is used in a few places (wrongly)
James Taylor
Cython intersection.pyx -> intersection.c
guru
Modified CpG masking tool - added the option to mask nonCpG sites. Also added unit tests for CpG masking tool.
pch...@saturn.nhgri.nih.gov
Make sure that import from __future__ is the first import; python requires this.
pch...@saturn.nhgri.nih.gov
Ignore track line in BED files
pch...@saturn.nhgri.nih.gov
Merge changes from bx-python-central
pch...@saturn.nhgri.nih.gov
Define functions in bx.misc to transparently open gzip or bzip2 compressed files, in addition to regular uncompressed files. The functions override builtin open() and/or file() functions, thereby requiring minimal changes to scripts. Imported this new function definition into all modules that call open() in main code.
Brent Pedersen
cleanup in intersection, remove old code, micro optimization checking for is None, rather than bool fix spelling of my name. :-)
Brent Pedersen
make the interval in an IntervalNode public so it can be traversed. add traverse() method to IntervalTree add some tests for up/downstream.
James Taylor
More documentation on the different between intervalnode and intervaltree.
James Taylor
Another cleanup pass on intersecter interfaces. Simplified interval node, added wrapper class IntervalTree that includes and expands on the old intersecter (that name is still definied for backward compat). Upstream/downstream methods moved out to the wrapper, the nodes only know about left/right queries based on a single position, variants are all in the wrapper.
James Taylor
Make sure pyx doctests are run by setup.py test. Turn off detailed errors (never seems to expand the right part)
James Taylor
IntervalNode can now contain any value, not just Intervals. This eliminates the need for WrapperInterval and makes the behavior more like the old implementation. The Intersecter API should be unchanged.
James Taylor
Adding generated C code for intersection.pyx
James Taylor
Adding an hgignore file
James Taylor
Rebuilding all generated (.pyx) code with Cython 10.3. Fixed a few bugs and ambiguities, everything should still be valid under Pyrex as well.
James Taylor
Fix issue #2 again.
James Taylor
Backed out changeset a72875307f4b Accidently included generated code.
James Taylor
Fix issue #2 (size problem in interval io).
James Taylor
Patch from Istvan Albert <iua1@psu.edu> to fix some windows compilation issues in bitsets and to disable some modules that currently don't compile in windows.
James Taylor
Tests for new Intersecter
James Taylor
Integrate Cython version of quicksect from Brent Pederson. This replaces the old intersection package with a much faster and more functional version. API compatibility should be maintained
Nate Coraor
Require python_lzo in seeklzop.
Guru Ananda
Small modification to join operation, which should fix the new bug observed today.
Guru Ananda
Modified intervals join function to include minimum-overlap value.
Bob Harris
fixed slicing for -strand reference again; last time I did not get it right; have also added self-test this time
Bob Harris
many fixes related to negative strand components
Bob Harris
changed error message
Guru Ananda
Modified BitSetSafeReaderWrapper to use chr, start, end and strand columns from the input dataset, instead of using standard values.
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