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CHANGELOG
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CHANGELOG
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1.7 2014-05-13 Jian-Long Huang <jianlong@ntu.edu.tw>
* Fix the bug of adding the matching information.
* Fix the string consumption when scanning matched sequences
for a pattern. The overlapping sites will be retained now.
1.6 2014-04-25 Jian-Long Huang <jianlong@ntu.edu.tw>
* Add the positive set supports information for each
cluster to 'cluster_support.txt'
1.5 2014-03-19 Jian-Long Haung <jianlong@ntu.edu.tw>
* Add positive set support information to
'merged_patterns' file.
1.4 2014-02-27 Jian-Long Huang <jianlong@ntu.edu.tw>
* Enhancement of parsing conservation score file.
When parsing the conservation score (-cs), if
the score is a dash ('-'), that means it's value
is NA and will be omitted.
* Add positive set support information (number
of genes with pattern existence / number of total genes)
to 'clustered_patterns.txt' file.
1.3 2013-12-13 Jian-Long Huang <jianlong@ntu.edu.tw>
* Add new options: -cs and -sc for conservation scoring.
* Fix occupancy scoring.
* Fix the seqid that affect the mi and occupancy scoring.
1.2b 2013-12-13 Jian-Long Huang <jianlong@ntu.edu.tw>
* New option: applying nucleosome occupancy scores (-oc).
* New options for PFM similarity calculation: -ws and -gc.
1.1 2013-12-08 Jian-Long Huang <jianlong@ntu.edu.tw>
* Change the command-line arguments:
(1) -cluster to -nc
(2) -n to -np
* New option: applying sequence mask (-seqmask).
1.0 2013-11-19 Jian-Long Huang <jianlong@ntu.edu.tw>
* Implement basic features.