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+ minor changes in the paths
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 / access...
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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 genomic...
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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 acceptor...
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2008-06-04 fabio+ fixed index error for negative stand queries of splice...
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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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2008-06-02 fabio+ found string splitting bug
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2008-06-02 fabio+ rewrote some data storage code
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2008-06-02 fabio+ fix starting point for rewrite of data accession...
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2008-06-02 fabio+ added generice parser code
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2008-05-30 fabio+ original reads sequence now has to be reconstructred...
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2008-05-30 fabio+ added missing modules imports
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2008-05-30 fabio+ shell script for the heuristic run
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2008-05-30 fabio+ removed unnecessary numpy dependency
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2008-05-30 fabio+ added modifications of parser to repo
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2008-05-30 fabio+ removed files
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2008-05-30 fabio+ minor changes
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2008-05-30 fabio+ moved sequence access functions to own module
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2008-05-30 fabio+ added dataset generation function to dataset specific...
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2008-05-30 fabio+ moved qpalma dataset generation scripts
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2008-05-30 fabio+ added a script that processes the single lane files...
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2008-05-30 fabio+ added some more scripts from the dataset processing
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2008-05-30 fabio+ added small counting script
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2008-05-26 fabio+ minor changes
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2008-05-21 fabio+ added script which draws the coverage bar plots presented...
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2008-05-21 fabio+ changed data loading procedures
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2008-05-16 fabio+ added missing free for line array
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2008-05-15 fabio+ minor modifications
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2008-05-15 fabio+ modified module in order to act like a database returning...
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2008-05-15 fabio+ coded alternative implementation using a list per...
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2008-05-15 fabio+ fixed seq size bug
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2008-05-15 fabio+ fixed a bug in the sscanf
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2008-05-15 fabio+ removed binaries
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2008-05-15 fabio+ added python module for reads parsing as plain python...
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2008-05-14 fabio+ take into account multiple hits per unique read
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2008-05-14 fabio+ made original reads file location a parameter for...
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2008-05-14 fabio+ First fully working version.
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2008-05-14 fabio+ changed dataset compiler to take the two different...
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2008-05-14 fabio+ first version of a script that uses pythongrid
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2008-05-13 fabio+ added configuration variables to main config file
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2008-05-13 fabio+ sanity checks for the global config file
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2008-05-13 fabio+ adapted training method to use new dataset standard
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2008-05-12 fabio+ changed dataset representation
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2008-05-11 fabio+ removed obsolete code
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2008-05-11 fabio+ removed lot of redundant/old code from the dataset...
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2008-04-22 fabio+ fix changes we made so far
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2008-04-21 fabio+ Aaaarghh found stupid bug in the parser (Case statement...
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2008-04-19 fabio+ support dangling end for unspliced reads in computeSpliceA...
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2008-04-19 fabio+ added faster evaluation function
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2008-04-19 fabio+ fixed some index bugs in the evaluation
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2008-04-18 fabio+ using new parsers now
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2008-04-18 fabio+ changed code for prediction -> easier and faster
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QPalma the short reads alignment project