BAMnostic - v1.1.8

Changed relative path of bamnostic.AlignmentFile index file lookup to absolute path.

Scientific Software - Peer-reviewed - Python
Published by betteridiot over 4 years ago

BAMnostic - v1.1.7

Thanks to some community contributions, minor quality of life improvements have been added: * 1-length sequences created as artifacts from some platforms can now be handled correctly (@giesselmann) * Any unnamed sequence is now given a default .reference_name attribute of "*" (@OliverVoogd)

Scientific Software - Peer-reviewed - Python
Published by betteridiot about 5 years ago

BAMnostic - v1.1.6

Appveyor does not support Pytest on Python 3.9. Will debug later

Scientific Software - Peer-reviewed - Python
Published by betteridiot over 5 years ago

BAMnostic - v1.1.5

Includes versioning for Python 3.7-3.9

Scientific Software - Peer-reviewed - Python
Published by betteridiot over 5 years ago

BAMnostic - v1.1.4

Scientific Software - Peer-reviewed - Python
Published by betteridiot almost 7 years ago

BAMnostic - v1.1.2

There was a typo in v1.1.1- that affected how bamnostic.bam.Bam would process BAI files that was missing n_no_coor at the end of it. Up till now, bamnostic would set these to None. But in places where bamnostic.bam.Bam referenced this (bamnostic.bam.Bam._init_index and the bamnostic.bam.Bam.unmapped property) it couldn't add (+) the mapped and unmapped reads to n_no_coord. This would result in an error since a mathematical operation between an integer and NoneType doesn't work.

Scientific Software - Peer-reviewed - Python
Published by betteridiot almost 7 years ago

BAMnostic - v1.1.1rc1

Minor repo fixes compared to v1.1.1

Scientific Software - Peer-reviewed - Python
Published by betteridiot almost 7 years ago

BAMnostic - v1.1.1

Scientific Software - Peer-reviewed - Python
Published by betteridiot almost 7 years ago

BAMnostic - v1.1.0

Scientific Software - Peer-reviewed - Python
Published by betteridiot almost 7 years ago

BAMnostic - v1.0.11

Scientific Software - Peer-reviewed - Python
Published by betteridiot almost 7 years ago

BAMnostic - v1.0.10

Scientific Software - Peer-reviewed - Python
Published by betteridiot about 7 years ago

BAMnostic - v1.0.9

Scientific Software - Peer-reviewed - Python
Published by betteridiot about 7 years ago

BAMnostic - v1.0.8

Scientific Software - Peer-reviewed - Python
Published by betteridiot about 7 years ago

BAMnostic - v1.0.7

Fixes flawed implementation regarding long-read BAM files. Also, fixed subsequent Python 2.7 related regression errors.

Scientific Software - Peer-reviewed - Python
Published by betteridiot over 7 years ago

BAMnostic - v1.0.4

Minor fix to a warning invocation.

Scientific Software - Peer-reviewed - Python
Published by betteridiot over 7 years ago

BAMnostic - v1.0.3

Scientific Software - Peer-reviewed - Python
Published by betteridiot over 7 years ago

BAMnostic - v1.0.1

Fixes lack of preservation of literal contig names.

Scientific Software - Peer-reviewed - Python
Published by betteridiot over 7 years ago

BAMnostic - v1.0.0

Scientific Software - Peer-reviewed - Python
Published by betteridiot over 7 years ago

BAMnostic - v0.9.2

Versioning should match PyPI and conda soon

Scientific Software - Peer-reviewed - Python
Published by betteridiot over 7 years ago

BAMnostic - v0.9.1rc4

Complete re-write of the bamnostic.utils.LruDict so that is is version and runtime compatible

Scientific Software - Peer-reviewed - Python
Published by betteridiot over 7 years ago

BAMnostic - v0.9.1rc3

Fixes the recursion error that py27 observes when dealing with bamnostic.utils.LruDict.

I wrote and override for OrderedDict.move_to_end so that it works in both 2.7 and 3.x.

Scientific Software - Peer-reviewed - Python
Published by betteridiot over 7 years ago

BAMnostic - v0.9.1

Addresses DeprecationWarning causes by array.array behavior in Python 3.x when fromstring() is called.

Scientific Software - Peer-reviewed - Python
Published by betteridiot over 7 years ago

BAMnostic - v0.9.0

Scientific Software - Peer-reviewed - Python
Published by betteridiot over 7 years ago

BAMnostic - 0.8.11

Minor changes to 0.8.10, and micro subversion incremented to reflect conda-forge and pypi versioning

Scientific Software - Peer-reviewed - Python
Published by betteridiot almost 8 years ago

BAMnostic - 0.8.10c1

Contains minor corrections to v0.8.10

Scientific Software - Peer-reviewed - Python
Published by betteridiot almost 8 years ago

BAMnostic - 0.8.9

Scientific Software - Peer-reviewed - Python
Published by betteridiot almost 8 years ago

BAMnostic - bamnostic 0.8.7b2

Scientific Software - Peer-reviewed - Python
Published by betteridiot almost 8 years ago