v1.0.5

News:

1. Added GFFutils arguments as part of LiftOn's arguments. Users can now specify the merge_strategy in gffutils.create_db as 'create_unique', 'merge', 'error', 'warning', or 'replace' to correctly create the database #12
2. Fixed the extraction of reference protein and transcript sequences from the GFFutils database.
3. Fixed errors when using GTF files as input #10

Documentation:

The link to the documentation: http://ccb.jhu.edu/lifton/

PyPi release

LiftOn v1.0.5 is available on PyPi: https://pypi.org/project/lifton/

v1.0.4

News:

1. Add a second pass for gffutils build if gffutils fails to create the db #7.
2. Fix inherited argument error in LiftOn from Liftoff (args.mm2_options += " --end-bonus 5")
3. Update documentation page

Documentation:

The link to the documentation: http://ccb.jhu.edu/lifton/

PyPi release

LiftOn v1.0.4 is available on PyPi: https://pypi.org/project/lifton/

v1.0.3 release

News:

1. Fix the dependency issue in #6. Adding pytest>=7.0.0
2. Update transcript missing error caused by extra copy number counting & update setup.py dependency
3. Update documentation page

Documentation:

The link to the documentation: http://ccb.jhu.edu/lifton/

PyPi release

LiftOn v1.0.3 is available on PyPi: https://pypi.org/project/lifton/

v1.0.2 release

News:

1. Fix the error of KeyError: 'gene_biotype' in #2
2. Add an example running GFF file without 'gene_biotype' : https://github.com/Kuanhao-Chao/LiftOn/blob/main/test/lifton_chr22_example_no_biotype.sh
3. Update documentation page: https://ccb.jhu.edu/lifton/content/feature_counting.html

Documentation:

The link to the documentation: http://ccb.jhu.edu/lifton/

PyPi release

LiftOn v1.0.2 is available on PyPi: https://pypi.org/project/lifton/

v1.0.1 release

News:

1. Correct the coordinate errors of the first/last CDS.
2. Fix the frame of the CDS on the reverse strand.

Documentation:

The link to the documentation: http://ccb.jhu.edu/lifton/

PyPi release

LiftOn v1.0.1 is available on PyPi: https://pypi.org/project/lifton/

v1.0.0 release

This is the initial release of the LiftOn code and documentation.

Documentation:

The link to the documentation: http://ccb.jhu.edu/lifton/

PyPi release

LiftOn v1.0.0 is available on PyPi: https://pypi.org/manage/project/lifton/release/1.0.0/