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qpalma.git
2009-01-26
Fabio
+ changed check for intial setting of old_w. (matrix...
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2008-10-23
Fabio
+ update makefiles to fetch automatically valid Python...
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2008-10-22
Fabio
+ changed parameter handling a bit (input files command...
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2008-10-22
Fabio
+ fixed automatic Python path settings in Makefiles
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2008-10-21
Fabio
+ set proper logging in optimizer code
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2008-10-20
Fabio
+ restructured test cases
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2008-10-15
Fabio
+ fixed issue with negative strand in lookup table
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2008-10-15
Fabio
+ extended manual to describe output file format
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2008-10-15
Fabio
+ fixed alignment index calculation for negative strand
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2008-10-14
Fabio
+ fixed minor bugs
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2008-10-14
Fabio
+ extended test cases
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2008-10-13
Fabio
+ extended documentation
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2008-10-13
Fabio
+ fixed some issues with the splice site scores and...
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2008-10-10
Fabio
+ extended docu
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2008-10-08
Fabio
+ got rid of some legacy code
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2008-10-07
Fabio
+ cleaned up directories
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2008-10-07
Fabio
+ renamed dyn_prog directory
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2008-10-02
Fabio
+ removed load_genomic dependency
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2008-10-02
Fabio
+ added palma_utils file
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2008-10-02
Fabio
+ added sample configuration file
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2008-10-01
Fabio
+ fixed minor inconsistencies in the code
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2008-09-30
Fabio
+ combined two scripts that were responsible for genera...
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2008-09-29
Fabio
+ extended pipeline code
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2008-09-22
Fabio
+ added some documentary text
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2008-09-16
Fabio
+ added some text and references to the documentation
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2008-09-14
Fabio
+ added module to convert pickled predictions to severa...
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2008-09-13
Fabio
fixed minor inconsistencies in the code (naming of...
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2008-09-13
Fabio
+ moved file to module directory
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2008-09-13
Fabio
+ added framework code for training modus
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2008-09-13
Fabio
+ added paths for the dataset generation
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2008-09-11
Fabio
+ added dataset generation function for training set
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2008-09-10
Fabio
+ changed dataset compilation to support new framework
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2008-09-10
Fabio
+ got rid of minor bugs
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2008-09-10
Fabio
+ changed module hierarchy a bit
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2008-09-10
Fabio
+ added settings parser module
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2008-09-10
Fabio
+ added settings parser module
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2008-09-10
Fabio
+ added configuration file parsing and checking functions
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2008-09-09
Fabio
+ added settings in the form of a global and a run...
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2008-09-05
Fabio
+ added small parts to docu
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2008-09-02
Fabio
+ added license text
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2008-09-01
Fabio
+ got rid of some unneccessary code
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2008-09-01
Fabio
+ changed python and c code in order to perform easier...
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2008-09-01
Fabio
+ removed some obsolete dependencies
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2008-09-01
Fabio
+ added some docu
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2008-09-01
Fabio
+ added some flags to Makefile args
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2008-09-01
fabio
+ added documentation
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2008-09-01
fabio
+ minor changes in the paths
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2008-08-21
fabio
+ added raw framework of workflow
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2008-08-21
fabio
+ fixed bug in reads stemming from negative strand
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2008-08-14
fabio
+ added convenient script
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2008-08-11
fabio
+ found negative strand bug
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2008-08-07
fabio
+ fixed bug in position calculation for negative strand
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2008-08-06
fabio
+ minor mods in sequence_utils
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2008-08-06
fabio
+ added some testcases
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2008-08-05
fabio
+ higher level cluster tasks interface for qpalma
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2008-08-04
fabio
+ minor modifications for the prefetching the whole...
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2008-08-04
fabio
+ minor fixes
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2008-07-31
fabio
+ fixed quality conversion: According to new specs...
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2008-07-31
fabio
+ modifications in order to use new data format / acces...
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2008-07-31
fabio
+ changed PipelinHeuristic to support new data access...
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2008-07-29
fabio
+ added some testcases for sequence_utils module
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2008-07-29
fabio
+ adapted Lookup table to new data interface
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2008-07-29
fabio
+ changed sequence utils to support more general genomi...
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2008-07-29
fabio
+ fix version before moving to new format
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2008-07-10
fabio
+ Fixed issue with g being last element of a sequence...
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2008-07-10
fabio
+ modified Lookup table to work with negative strands
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2008-07-09
fabio
+ wrapped sequence and score functions in order to...
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2008-07-09
fabio
+ some bugfixes
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2008-07-04
fabio
+ interesting version : it crashes but valgrind detects...
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2008-07-04
fabio
+ recalculating exons boundaries fixed
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2008-07-04
fabio
+ added reverse complementation to filter reads function
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2008-07-03
fabio
+ moved tools from training dataset generation to their...
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2008-07-03
fabio
+ saving changes in the dataset generation
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2008-07-02
fabio
+ some optimization
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2008-06-30
fabio
+ pruned a lot of import declarations
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2008-06-26
fabio
+ moved penalty lookup and compute_doncc to Plif module
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2008-06-25
fabio
+ removed unnecessary file
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2008-06-25
fabio
+ cleaning up code base
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2008-06-24
fabio
+ added small program for intron-position comparison
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2008-06-23
fabio
+ added proper treatment of reads overlapping into...
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2008-06-20
fabio
+ added checks to see whether reads lie in the 250nuc...
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2008-06-20
fabio
+ optimized dataset generation/storage
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2008-06-18
fabio
+ cleaning up scripts directory
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2008-06-18
fabio
+ added alignment reconstruction function
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2008-06-16
fabio
+ added two scripts for the psl2gff step
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2008-06-15
fabio
+ saving alignment information now in array container...
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2008-06-12
fabio
+ added selection option for alignment format
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2008-06-11
fabio
+ changed output format of alignment file script to...
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2008-06-11
fabio
+ minor changes to support transcriptome data
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2008-06-05
fabio
+ fixed some bugs in the negative strand lookup table
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2008-06-04
fabio
+ extended Lookup object to support negative strand
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2008-06-04
fabio
+ fixed other bug (missing n last entries of the accept...
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2008-06-04
fabio
+ fixed index error for negative stand queries of splic...
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2008-06-03
fabio
+ added code for negative strand processing
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2008-06-03
fabio
+ added script to parallelize QPalma heuristic on the...
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2008-06-03
fabio
+ return value is a tuple now containing the original...
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2008-06-02
fabio
+ added compatiblity to PipelineHeuristic parser
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2008-06-02
fabio
+ removed stupid temp file
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2008-06-02
fabio
+ added VECTOR and MAP mode to ParaParser in order...
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2008-06-02
fabio
+ added some assertions
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