james_taylor / bx-python / changesets — bitbucket.org

james_taylor / bx-python

Tools for manipulating biological data, particularly multiple sequence alignments

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Changesets

2010-03-15

commit 498:	f74aec067563
parent 497:	1da5d71c115b

0 12 2

- Changes to array_tree to enable frequencies (how many times a node is visited, and also option to disable leaf nodes to save space - New api allows different readers to be used to create array_trees - New basic BED reader - Rename arrays/IntervalReader to arrays/WiggleReader - More tests for array_tree - Fix unit test for align/tools/thread - Fix typos defaulttip

2010-03-04

commit 497:	1da5d71c115b
parent 496:	ebf9a4b352d3

0 2 0

add new ez_setup.py

2010-01-25

commit 496:	ebf9a4b352d3
parent 495:	c1e165e97419

0 1 0

Note about issue

2010-01-11

commit 495:	c1e165e97419
parent 494:	c3c187a94f1c

6 2 0

Remove bgzf as it's no longer planned to be used

2010-01-10

commit 494:	c3c187a94f1c
parent 493:	ef5880615754

0 0 1

add cython generated file to repo from pyx added in rev:fe3d5ebe56f5

2009-12-10

commit 493:	ef5880615754
parent 492:	4d265fa04efd

0 2 0

Two fixes for align.tools from Thomas Mailund

2009-12-01

commit 492:	4d265fa04efd
parent 491:	fe3d5ebe56f5

0 1 0

Make BGZF test a real unittest

commit 491:	fe3d5ebe56f5
parent 490:	3b9d30e47619

0 1 7

BGZF support (really simple wrapper to code from samtools)

2009-11-18

commit 490:	3b9d30e47619
parent 489:	3d4efd893ef7

0 3 0

Return empty list for interval operations on empty trees to prevent segfaults. Fixes

commit 489:	3d4efd893ef7
parent 488:	1b92e62b224a

0 3 0

Update array_tree version assert, use cython for cluster

2009-11-17

commit 488:	1b92e62b224a
parent 487:	146668db6920

0 1 0

Fix interval_index_file test to use max parameter

2009-11-13

commit 487:	146668db6920
parent 486:	557f4b71d878

0 2 0

Fix return bug in bits#bitCountRange

2009-11-12

commit 486:	557f4b71d878
parent 485:	94999d421cbb

0 2 1

Added array_tree tests, bump to version 1

2009-10-02

commit 485:	94999d421cbb
parent 484:	760d1227cbff

0 1 0

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.

2009-09-30

commit 484:	760d1227cbff
parent 483:	206f183871f8

0 5 0

Make wiggle parsing more resiliant (fix UCSC truncation issues)