CHANGELOG.md

1.1.10 (2016-7-14)

Bugfixes:

• case-sensitivity issue for fusion fix step

Improvements:

• use smaller test data

1.1.9 (2016-6-7)

Improvements:

• offer more deployment methods (PyPI, bioconda, Docker and Galaxy Tool). Thanks @bgruening and @anatskiy for their helps!

1.1.8 (2016-4-21)

Improvements:

• add test codes

1.1.7 (2016-1-28)

Improvements:

• add pysam version checking at running time

1.1.6 (2016-1-22)

Improvements:

• add exon/intron index information

1.1.5 (2016-1-20)

Improvements:

• use setuptools instead of distutils in setup.py, fix #11

1.1.4 (2016-1-16)

Improvements:

• check pysam version at running time
• index fa file automatically if it has not been indexed
• integrate interval.py into it

1.1.3 (2015-7-31)

Bugfixes:

• bug that removes fusion junction reads aligned to first/last exons

Improvements:

• support pysam 0.8.2

1.1.2 (2015-6-18)

Improvements:

• add script fetch_ref.py

1.1.1 (2015-3-13)

Improvements:

• adjust some misleading labels

1.1.0 (2015-2-3)

Bugfixes:

• bug that causes a crash when parsing ciRNA junctions

Improvements:

• support aligner STAR

1.0.6 (2014-12-11)

Bugfixes:

• bug that prints redundant circular RNA information

1.0.5 (2014-11-23)

Improvements:

• add option '--no-fix' to not use fix step

1.0.4 (2014-10-24)

Improvements:

• add option '--tmp' to keep temporary files
• change option '--output' from output file name to output file prefix

1.0.3 (2014-10-11)

Improvements:

• remove redundant source codes
• modify source codes according to PEP8

1.0.2 (2014-09-15)

Bugfixes:

• bug that ignores mismatches of fusion junction reads near the first or last exon
• bug that removes fusion junction reads due to align to a random isoform

1.0.0 (2014-09-12)

Features:

• first release for CIRCexplorer
• all the source codes were derived from the CELL paper and reorganized for general usage