+ changed parameter handling a bit (input files command line args and not inside...
[qpalma.git] / qpalma /
2008-10-22 Fabio+ changed parameter handling a bit (input files command...
2008-10-22 Fabio+ fixed automatic Python path settings in Makefiles
2008-10-21 Fabio+ set proper logging in optimizer code
2008-10-20 Fabio+ restructured test cases
2008-10-15 Fabio+ fixed issue with negative strand in lookup table
2008-10-15 Fabio+ extended manual to describe output file format
2008-10-15 Fabio+ fixed alignment index calculation for negative strand
2008-10-14 Fabio+ fixed minor bugs
2008-10-14 Fabio+ extended test cases
2008-10-13 Fabio+ extended documentation
2008-10-13 Fabio+ fixed some issues with the splice site scores and...
2008-10-10 Fabio+ extended docu
2008-10-08 Fabio+ got rid of some legacy code
2008-10-07 Fabio+ cleaned up directories
2008-10-07 Fabio+ renamed dyn_prog directory
2008-10-02 Fabio+ removed load_genomic dependency
2008-10-02 Fabio+ added palma_utils file
2008-10-02 Fabio+ added sample configuration file
2008-10-01 Fabio+ fixed minor inconsistencies in the code
2008-09-30 Fabio+ combined two scripts that were responsible for genera...
2008-09-29 Fabio+ extended pipeline code
2008-09-22 Fabio+ added some documentary text
2008-09-16 Fabio+ added some text and references to the documentation
2008-09-14 Fabio+ added module to convert pickled predictions to severa...
2008-09-13 Fabiofixed minor inconsistencies in the code (naming of...
2008-09-13 Fabio+ moved file to module directory
2008-09-13 Fabio+ added paths for the dataset generation
2008-09-11 Fabio+ added dataset generation function for training set
2008-09-10 Fabio+ changed dataset compilation to support new framework
2008-09-10 Fabio+ got rid of minor bugs
2008-09-10 Fabio+ changed module hierarchy a bit
2008-09-10 Fabio+ added settings parser module
2008-09-10 Fabio+ added settings parser module
2008-09-10 Fabio+ added configuration file parsing and checking functions
2008-09-09 Fabio+ added settings in the form of a global and a run...
2008-09-01 Fabio+ changed python and c code in order to perform easier...
2008-09-01 Fabio+ removed some obsolete dependencies
2008-09-01 fabio+ minor changes in the paths
2008-08-06 fabio+ minor mods in sequence_utils
2008-08-05 fabio+ higher level cluster tasks interface for qpalma
2008-08-04 fabio+ minor modifications for the prefetching the whole...
2008-08-04 fabio+ minor fixes
2008-07-29 fabio+ changed sequence utils to support more general genomi...
2008-07-10 fabio+ Fixed issue with g being last element of a sequence...
2008-07-09 fabio+ wrapped sequence and score functions in order to...
2008-07-09 fabio+ some bugfixes
2008-06-26 fabio+ moved penalty lookup and compute_doncc to Plif module
2008-06-25 fabio+ removed unnecessary file
2008-06-25 fabio+ cleaning up code base
2008-06-23 fabio+ added proper treatment of reads overlapping into...
2008-06-20 fabio+ added checks to see whether reads lie in the 250nuc...
2008-06-05 fabio+ fixed some bugs in the negative strand lookup table
2008-06-04 fabio+ extended Lookup object to support negative strand
2008-06-04 fabio+ fixed other bug (missing n last entries of the accept...
2008-06-04 fabio+ fixed index error for negative stand queries of splic...
2008-06-03 fabio+ added code for negative strand processing
2008-05-30 fabio+ added missing modules imports
2008-05-30 fabio+ removed unnecessary numpy dependency
2008-05-30 fabio+ added modifications of parser to repo
2008-05-30 fabio+ moved sequence access functions to own module
2008-05-13 fabio+ added configuration variables to main config file
2008-04-22 fabio+ fix changes we made so far
2008-04-21 fabio+ Aaaarghh found stupid bug in the parser (Case stateme...
2008-04-19 fabio+ support dangling end for unspliced reads in computeSp...
2008-04-18 fabio+ optimized parsers
2008-04-18 fabio+ pipeline parse is much faster now,
2008-04-18 fabioadded file
2008-04-18 fabio+ added solver wrapper for cvxopt
2008-04-18 fabioanother module init
2008-04-18 fabiomodule init
2008-04-17 raetschgit-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects...
2008-04-17 raetschgit-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects...
2008-04-17 raetschgit-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects...
2008-04-17 raetschgit-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects...
2008-04-17 raetschgit-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects...
2008-04-17 raetschgit-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects...
2008-04-17 raetschgit-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects...
2008-04-17 raetschgit-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects...
2008-04-17 raetschgit-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects...
2008-04-17 raetschgit-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects...
2008-04-17 raetschgit-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects...
2008-04-17 raetschgit-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects...
2008-04-17 raetschgit-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects...
2008-04-17 raetschgit-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects...
2008-04-17 raetschgit-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects...
2008-04-17 raetschgit-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects...
2008-04-17 raetschgit-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects...
2008-04-17 raetschfirst version of faster heuristic
2008-04-17 fabio+ updated filtering
2008-04-17 fabio+ changes
2008-03-20 fabio+ changes in the main configuration -> no pickled init...
2008-03-12 fabio+ fixed mentioned index bugs of the SpliceAlign of...
2008-03-05 fabio+ removed some obsolete variables
2008-03-05 fabio+ refactored code further
2008-02-11 fabio+ added scripts for model selection on the cluster
2008-02-10 fabio+ changed filter behavior (tendency towards smaller...
2008-02-10 fabio+ fixed a bug in the filtering (forgot to disable remov...
2008-02-08 fabio+ fixed bug in the computeSpliceAlign... function
2008-02-08 fabio+ minor changes to filterReads
2008-02-06 fabio+ resolved an issue with the memory mapping in filterReads
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