Commits

Author Commit Message Labels Comments Date
Kanwei Li
Bump to 0.7.0, fix doc URL
Kanwei Li
Fix string padding in bbi.bpt_file. Fix edge case when valid_count was less than 1, causing a division by zero
Kanwei Li
Minor refactorings to bbi
Kanwei Li
Use deque instead of list comprehension to greatly increase performance
Kanwei Li
Rename bx.intervals.random to bx.intervals.random_intervals so it doesn't clobber python namespace. This fixes unit test for intersection_tests.py and all tests are green now.
Kanwei Li
Remove unused bgzf test data
Kanwei Li
Add BigWig tests and test datasets. Fix error with min and max values being switched. Fix issue with fetching from full.
Kanwei Li
Make mean, max and min return NaN if no values in the region instead of 0.0. Move bigWig specific code back to bigwig_file.pyx. More error checking
Kanwei Li
Fully working and correct bigWig reader. Added new 'query' method that is used to return 'summary_size' number of dictionaries containing the mean, max, min, coverage, and std_dev.
James Taylor
Fixes to bigwig stuff from Bob Harris
James Taylor
BigWigFile subclassing BBIFile, support for creating summaries from 'unzoomed' data points.
James Taylor
BBI Files: Summarization from zoom levels now working. Still need to implement
James Taylor
Adding generated C files
James Taylor
Renaming cir_tree to cirtree_file to be consistent with other packages
James Taylor
First steps toward bigbed/bigwig reading -- working read-only implementations of bPlusTree and cirTree, bbiFile can find and parse summaries
Brent Pedersen
using this small cython directive [1] improves speed by about 5%
Kanwei Li
Fix small twobit reading bug & add test
Brent Pedersen
interval index file, make sure start is not > stop. added test.
James Taylor
Up version to 0.6.0, release to pypi
Bob Harris
Added comment in header to clarify that intervals are origin-zero, half-open.
Bob Harris
Corrected problem in maf_extract_ranges_indexed, which failed when a maf block contains more than one line with the desired reference sequence. The failure manifested as an abort, from the range error test in coord_to_col() in align/core.py. The correction is two-fold. First, we add a test in the script co that coord_to_col is not called with an empty interval. Second, we change the script to loop over *all* interesting reference intervals, rather than the first.
Kanwei Li
- Changes to array_tree to enable frequencies (how many times a node is visited, and also option to disable leaf nodes to save space
Brent Pedersen
add new ez_setup.py
James Taylor
Note about issue #10
Kanwei Li
Remove bgzf as it's no longer planned to be used
Brent Pedersen
add cython generated file to repo
James Taylor
Two fixes for align.tools from Thomas Mailund
James Taylor
Make BGZF test a real unittest
James Taylor
BGZF support (really simple wrapper to code from samtools)
Kanwei Li
Return empty list for interval operations on empty trees to prevent segfaults. Fixes #8
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