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 framework code for training modus
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...
2008-09-05 Fabio+ added small parts to docu
2008-09-02 Fabio+ added license text
2008-09-01 Fabio+ got rid of some unneccessary code
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+ added some docu
2008-09-01 Fabio+ added some flags to Makefile args
2008-09-01 fabio+ added documentation
2008-09-01 fabio+ minor changes in the paths
2008-08-21 fabio+ added raw framework of workflow
2008-08-21 fabio+ fixed bug in reads stemming from negative strand
2008-08-14 fabio+ added convenient script
2008-08-11 fabio+ found negative strand bug
2008-08-07 fabio+ fixed bug in position calculation for negative strand
2008-08-06 fabio+ minor mods in sequence_utils
2008-08-06 fabio+ added some testcases
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
2008-07-31 fabio+ fixed quality conversion: According to new specs...
2008-07-31 fabio+ modifications in order to use new data format / acces...
2008-07-31 fabio+ changed PipelinHeuristic to support new data access...
2008-07-29 fabio+ added some testcases for sequence_utils module
2008-07-29 fabio+ adapted Lookup table to new data interface
2008-07-29 fabio+ changed sequence utils to support more general genomi...
2008-07-29 fabio+ fix version before moving to new format
2008-07-10 fabio+ Fixed issue with g being last element of a sequence...
2008-07-10 fabio+ modified Lookup table to work with negative strands
2008-07-09 fabio+ wrapped sequence and score functions in order to...
2008-07-09 fabio+ some bugfixes
2008-07-04 fabio+ interesting version : it crashes but valgrind detects...
2008-07-04 fabio+ recalculating exons boundaries fixed
2008-07-04 fabio+ added reverse complementation to filter reads function
2008-07-03 fabio+ moved tools from training dataset generation to their...
2008-07-03 fabio+ saving changes in the dataset generation
2008-07-02 fabio+ some optimization
2008-06-30 fabio+ pruned a lot of import declarations
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
2008-06-24 fabio+ added small program for intron-position comparison
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...
2008-06-20 fabio+ optimized dataset generation/storage
2008-06-18 fabio+ cleaning up scripts directory
2008-06-18 fabio+ added alignment reconstruction function
2008-06-16 fabio+ added two scripts for the psl2gff step
2008-06-15 fabio+ saving alignment information now in array container...
2008-06-12 fabio+ added selection option for alignment format
2008-06-11 fabio+ changed output format of alignment file script to...
2008-06-11 fabio+ minor changes to support transcriptome data
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
2008-06-03 fabio+ added script to parallelize QPalma heuristic on the...
2008-06-03 fabio+ return value is a tuple now containing the original...
2008-06-02 fabio+ added compatiblity to PipelineHeuristic parser
2008-06-02 fabio+ removed stupid temp file
2008-06-02 fabio+ added VECTOR and MAP mode to ParaParser in order...
2008-06-02 fabio+ added some assertions
2008-06-02 fabio+ found string splitting bug
2008-06-02 fabio+ rewrote some data storage code
2008-06-02 fabio+ fix starting point for rewrite of data accession...
2008-06-02 fabio+ added generice parser code
2008-05-30 fabio+ original reads sequence now has to be reconstructred...
2008-05-30 fabio+ added missing modules imports
2008-05-30 fabio+ shell script for the heuristic run
2008-05-30 fabio+ removed unnecessary numpy dependency
2008-05-30 fabio+ added modifications of parser to repo
2008-05-30 fabio+ removed files
2008-05-30 fabio+ minor changes
2008-05-30 fabio+ moved sequence access functions to own module
2008-05-30 fabio+ added dataset generation function to dataset specific...
2008-05-30 fabio+ moved qpalma dataset generation scripts
2008-05-30 fabio+ added a script that processes the single lane files...
2008-05-30 fabio+ added some more scripts from the dataset processing
2008-05-30 fabio+ added small counting script
2008-05-26 fabio+ minor changes