Author Commit Message Labels Comments Date
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
Brent Pedersen avatarBrent Pedersen
add cython generated file to repo
James Taylor avatarJames Taylor
Two fixes for align.tools from Thomas Mailund
James Taylor avatarJames Taylor
Make BGZF test a real unittest
James Taylor avatarJames Taylor
BGZF support (really simple wrapper to code from samtools)
Kanwei Li avatarKanwei Li
Return empty list for interval operations on empty trees to prevent segfaults. Fixes #8
Kanwei Li avatarKanwei Li
Update array_tree version assert, use cython for cluster
Kanwei Li avatarKanwei Li
Fix interval_index_file test to use max parameter
Kanwei Li avatarKanwei Li
Fix return bug in bits#bitCountRange
Kanwei Li avatarKanwei Li
Added array_tree tests, bump to version 1
Default avatar guru
Bug fix in gops concatenation: previously it was returning 1 less column from the 2nd dataset in cases where 2nd dataset had more columns than 1st dataset.
Kanwei Li avatarKanwei Li
Make wiggle parsing more resiliant (fix UCSC truncation issues)
James Taylor avatarJames Taylor
Making some ArrayTree attributes public
James Taylor avatarJames Taylor
Working on FileArrayTree, now supports direct access to a complete leaf or single summary
Kanwei Li avatarKanwei Li
Merge. Fixes #9
Kanwei Li avatarKanwei Li
More docs, tabs -> spaces
Kanwei Li avatarKanwei Li
New ClusterTree that fixes a node merging problem in the original, and that uses less memory
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