Commits

Author Commit Message Labels Comments Date
Istvan Albert
merged changes from trunk
guru
Skip single sequence containing blocks from CpG masking, which should take care of the index errors being thrown by the script.
James Taylor
Cythonized wiggle reader, added script for converting wiggle to array_tree.
ial...@bigbird
updated to current bx-python trunk
James Taylor
Adding generated C code for array_tree.pyx
James Taylor
Documentation comment for chop
James Taylor
Exclude test modules and privat modules (starting with _) from apidocs
James Taylor
Added sphinx documentation skelaton from Istvan Albert. Modified styles to match bx.mathcs.emory.edu. Added support for sphinx to setup.py. Created a shortcut build_docs to build both API and sphinc documentation.
James Taylor
ArrayTree for storing block-sparse array data with summaries
James Taylor
Convenience class for reading and writing binary data
ial...@bigbird
more removals
ial...@bigbird
actually removed html pages(unlike git won't happen implicitly)
ial...@bigbird
removed html pages, cleaned up REST sources
Istvan Albert
makefile paths updated
Istvan Albert
renamed doc build directory to not match the python build directory
Istvan Albert
image change not detected by sphinx
Istvan Albert
adding files required by sphinx
Istvan Albert
small change to artwork, left unsaved
Istvan Albert
added custom sphinx layout
Istvan Albert
added apidoc generated by epydoc, see makefile on how to run build docs
Istvan Albert
adding a documentation directory, inited sphinx
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.
Brent Pedersen
cleanup in intersection, remove old code, micro optimization checking for is None, rather than bool
Brent Pedersen
make the interval in an IntervalNode public so it can be traversed.
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
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