Commits

Author Commit Message Labels Comments Date
James Taylor
Making some ArrayTree attributes public
James Taylor
Working on FileArrayTree, now supports direct access to a complete leaf or single summary
Kanwei Li
Merge. Fixes #9
Kanwei Li
More docs, tabs -> spaces
Kanwei Li
New ClusterTree that fixes a node merging problem in the original, and that uses less memory
James Taylor
ArrayTree now supports more than one aray per file (using CDB). Also, some minor documentation work
James Taylor
Basic support for writing and reading dictionaries connected to files in CDB format. Should be completely compatible with DJB's files as long as written in little endian. However, this is setup to be embedded in a larger file (e.g. to provide an index from chromosome names to offsets where chromosome indexes are stored in interval_index_file. This would be more efficient if there are a large number of chromosomes [contigs]).
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.
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
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 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).
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