Author Commit Message Labels Comments Date
James Taylor avatarJames Taylor
refactor bigwig support, add more tests
James Taylor avatarJames Taylor
Fix 'first line is header' support in tabular.io
Daniel Blankenberg avatarDaniel Blankenberg
Remove leading and trailing white space from around chromosome names in GenomicInterval class.
James Taylor avatarJames Taylor
Fix for fixed step records in bigwig
Kanwei Li avatarKanwei Li
Free tree iterator in clustertree after getting results
Kanwei Li avatarKanwei Li
Bump to 0.7.0, fix doc URL
Kanwei Li avatarKanwei 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 avatarKanwei Li
Minor refactorings to bbi
Kanwei Li avatarKanwei Li
Use deque instead of list comprehension to greatly increase performance
Kanwei Li avatarKanwei 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 avatarKanwei Li
Remove unused bgzf test data
Kanwei Li avatarKanwei Li
Add BigWig tests and test datasets. Fix error with min and max values being switched. Fix issue with fetching from full.
Kanwei Li avatarKanwei 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 avatarKanwei 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 avatarJames Taylor
Fixes to bigwig stuff from Bob Harris
James Taylor avatarJames Taylor
BigWigFile subclassing BBIFile, support for creating summaries from 'unzoomed' data points.
James Taylor avatarJames Taylor
BBI Files: Summarization from zoom levels now working. Still need to implement
James Taylor avatarJames Taylor
Adding generated C files
James Taylor avatarJames Taylor
Renaming cir_tree to cirtree_file to be consistent with other packages
James Taylor avatarJames Taylor
First steps toward bigbed/bigwig reading -- working read-only implementations of bPlusTree and cirTree, bbiFile can find and parse summaries
Brent Pedersen avatarBrent Pedersen
using this small cython directive [1] improves speed by about 5%
Kanwei Li avatarKanwei Li
Fix small twobit reading bug & add test
Brent Pedersen avatarBrent Pedersen
interval index file, make sure start is not > stop. added test.
James Taylor avatarJames Taylor
Up version to 0.6.0, release to pypi
Default avatar Bob Harris
Added comment in header to clarify that intervals are origin-zero, half-open.
Default avatar 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 avatarKanwei 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 avatarBrent Pedersen
add new ez_setup.py
James Taylor avatarJames Taylor
Note about issue #10
Kanwei Li avatarKanwei Li
Remove bgzf as it's no longer planned to be used
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