pybigwig - 0.3.24

Handle cases where the contig order in the header and the data sections differ. This was previously impossible, but apparently not now. Thanks to https://github.com/VonAlphaBisZulu for indicating the root cause and suggesting a fix. This also brings in other unrelated updates from libBigWig, which are mostly not relevant for this python wrapper.

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Published by dpryan79 about 1 year ago

pybigwig - 0.3.23

Build with numpy 2.x, python build with 3.9 instead of 3.7

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Published by WardDeb over 1 year ago

pybigwig - 0.3.22

Try fixing wheels

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Published by dpryan79 almost 3 years ago

pybigwig - 0.3.21

Update wheel creation (issue #140)

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Published by dpryan79 almost 3 years ago

pybigwig - 0.3.20

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Published by dpryan79 almost 3 years ago

pybigwig - 0.3.19

Build and wheel updates courtesy of @EricR86 https://github.com/deeptools/pyBigWig/pull/135

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Published by dpryan79 about 3 years ago

pybigwig - 0.3.18

Fixed issue #111. Now bigWig files with all 0 summary values are not assumed to be empty (instead a header that indicates that the index is at position 0 is assumed to be empty).

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Published by dpryan79 about 5 years ago

pybigwig - 0.3.17

• Fixed #91, wherein there was a memory leak if many files were written in a single python session.
• Fixed #88, so user-friendlier message should instead be printed if one attempts most operations on a file being written.
• Updated some documentation about zoom levels.

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Published by dpryan79 over 6 years ago

pybigwig - 0.3.16

Fixed https://github.com/deeptools/pyBigWig/issues/85

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Published by dpryan79 almost 7 years ago

pybigwig - 0.3.15

Copied over changes from libBigWig dealing with segfaults when accessing remote files.

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Published by dpryan79 almost 7 years ago

pybigwig - 0.3.14

• Fixed issue #81, which caused errors upon installation if curl was absent

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Published by dpryan79 almost 7 years ago

pybigwig - 0.3.13

• Fixed some python 3 builds (PR #76 from @rmsds )
• Started testing for python 3.7 and dropped official support for python 2 (it should work, but I'm no longer testing it).

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Published by dpryan79 about 7 years ago

pybigwig - 0.3.12

• Fixed compilation without curl
• Added at least partial support for pandas (issue #63)

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Published by dpryan79 over 7 years ago

pybigwig - 0.3.11

• Fixed linking on OSX. This led to issues like #58 and was fixed by @gokceneraslan in #60

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Published by dpryan79 almost 8 years ago

pybigwig - 0.3.10

• Fixed issue #54, which was due to incorrectly handling numpy vectors of unicode strings.

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Published by dpryan79 about 8 years ago

pybigwig - 0.3.9

• Fixed a segfault caused by a misplaced reference count decrementation in version 0.3.8 (when numpy is not used).

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Published by dpryan79 about 8 years ago

pybigwig - 0.3.8

• Fixed a memory leak when numpy is used during file creation. Thanks to @pmarks for both finding and patching this.

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Published by dpryan79 about 8 years ago

pybigwig - 0.3.7

• Fixed issue #48. The object-specific functions are no longer exposed at the module level.

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Published by dpryan79 over 8 years ago

pybigwig - 0.3.6

• Fixed issue #45, which only occurs if numpy was not installed at the time pyBigWig was. This will not affect pyBigWig if it's installed with conda install pyBigWig, since numpy is listed as a dependency.

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Published by dpryan79 over 8 years ago

pybigwig - 0.3.5

• Fixed issue #36 and #39 . Now approximately one billion contigs are supported when writing files. The resulting files can be read by IGV now.
• Fixed issue #38. Files with no entries can now be opened.
• You can now use with with pyBigWig (see #35)
• A number of rare issues involving accessing remote files were resolved (#31 and #32)

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Published by dpryan79 over 8 years ago

pybigwig - 0.3.4

pyBigWig can now be installed without support for remote files (this was issue #29). If python can't find curl-config during installation then remote file access will be removed.

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Published by dpryan79 almost 9 years ago

pybigwig - 0.3.3

• Includes libBigWig version 0.3.1, which fixes a potential bug with the creation of bigWig files with only very very (50+ megabase) long intervals. The phenotype of the previous bug was an infinite loop, so if you never got that then you never ran into this bug.

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Published by dpryan79 about 9 years ago

pybigwig - 0.3.1

Fixes compilation on OSX

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Published by dpryan79 over 9 years ago

pybigwig - 0.3.2

Fix compilation when numpy isn't present.

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Published by dpryan79 over 9 years ago

pybigwig - 0.3.0

• If numpy is installed prior to pyBigWig then numpy vectors can be used to create bigWig files. Additionally, the values() function can then output numpy vectors.
• bigBed files can now be read (but not created).

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Published by dpryan79 over 9 years ago

pybigwig -

• (Sorry about the delay on the actual release!) Finally fixed handling of large numbers of contigs. This release just fixed things for two different users, so hopefully this issue is now completely resolved.

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Published by dpryan79 almost 10 years ago

pybigwig - 0.2.7

• Fixed a bug where bigWig files with more than ~256 chromsomes would cause a segmentation fault (issue #14). This involved including libBigWig-0.1.6.

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Published by dpryan79 almost 10 years ago

pybigwig - 0.2.6

• There is now an exact option in the stats() command. This implements the request from #12. The default is False for the sake of speed and backward compatability.
• libBigWig-0.1.5 was also copied over, which slightly increases the precision of one of the mean computations functions (this is related to the bullet point above).

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Published by dpryan79 almost 10 years ago

pybigwig - 0.2.5

Copy over libBigWig 0.1.4, which should fix JBrowse/et al. being able to parse the bigWig files.

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Published by dpryan79 about 10 years ago

pybigwig -

• Fixed a critical issue wherein None, or a list containing None could be returned without the reference indicator first being incremented. This resulted in rare cases of python trying to free None. See fidelram/deepTools#245

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Published by dpryan79 about 10 years ago

pybigwig -

• Copy over libBigWig-0.1.3, which contains additional file creation fixes. Written files now work in IGV as long as you include zoom levels.

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Published by dpryan79 about 10 years ago

pybigwig -

• Copy over libBigWig-0.1.2
• Various file creation bug fixes

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Published by dpryan79 about 10 years ago

pybigwig -

• Allowed the nosetests to run anywhere
• Fixed a python2 -> python3 difference that caused memory issues.

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Published by dpryan79 about 10 years ago

pybigwig -

• Add support for bigWig file creation

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Published by dpryan79 about 10 years ago

pybigwig -

• fixed the download_url
• Removed a NULL return from a void function (initpyBigWig()).

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Published by dpryan79 about 10 years ago

pybigwig -

• Added a Galaxy XML file
• Removed excess Py_INCREF()s
• Free memory once the module is no longer needed

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Published by dpryan79 about 10 years ago

pybigwig -

• Fixed the MANIFEST
• Various compilation fixes, which should fix Galaxy installation

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Published by dpryan79 about 10 years ago

pybigwig -

• Added nose tests
• libBigWig to 1.0.8
• Transitioned to setuptools

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Published by dpryan79 about 10 years ago

pybigwig -

• Added initial python3 support
• Started throwing RuntimeErrors on errors.
• Added initial OSX support

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Published by dpryan79 about 10 years ago