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2008-06-20	fabio	+ optimized dataset generation/storage	commit \| commitdiff \| tree
2008-06-18	fabio	+ cleaning up scripts directory	commit \| commitdiff \| tree
2008-06-18	fabio	+ added alignment reconstruction function	commit \| commitdiff \| tree
2008-06-16	fabio	+ added two scripts for the psl2gff step	commit \| commitdiff \| tree
2008-06-15	fabio	+ saving alignment information now in array container...	commit \| commitdiff \| tree
2008-06-12	fabio	+ added selection option for alignment format	commit \| commitdiff \| tree
2008-06-11	fabio	+ changed output format of alignment file script to...	commit \| commitdiff \| tree
2008-06-11	fabio	+ minor changes to support transcriptome data	commit \| commitdiff \| tree
2008-06-05	fabio	+ fixed some bugs in the negative strand lookup table	commit \| commitdiff \| tree
2008-06-04	fabio	+ extended Lookup object to support negative strand	commit \| commitdiff \| tree
2008-06-04	fabio	+ fixed other bug (missing n last entries of the acceptor...	commit \| commitdiff \| tree
2008-06-04	fabio	+ fixed index error for negative stand queries of splice...	commit \| commitdiff \| tree
2008-06-03	fabio	+ added code for negative strand processing	commit \| commitdiff \| tree
2008-06-03	fabio	+ added script to parallelize QPalma heuristic on the...	commit \| commitdiff \| tree
2008-06-03	fabio	+ return value is a tuple now containing the original...	commit \| commitdiff \| tree
2008-06-02	fabio	+ added compatiblity to PipelineHeuristic parser	commit \| commitdiff \| tree
2008-06-02	fabio	+ removed stupid temp file	commit \| commitdiff \| tree
2008-06-02	fabio	+ added VECTOR and MAP mode to ParaParser in order...	commit \| commitdiff \| tree
2008-06-02	fabio	+ added some assertions	commit \| commitdiff \| tree
2008-06-02	fabio	+ found string splitting bug	commit \| commitdiff \| tree
2008-06-02	fabio	+ rewrote some data storage code	commit \| commitdiff \| tree
2008-06-02	fabio	+ fix starting point for rewrite of data accession...	commit \| commitdiff \| tree
2008-06-02	fabio	+ added generice parser code	commit \| commitdiff \| tree
2008-05-30	fabio	+ original reads sequence now has to be reconstructred...	commit \| commitdiff \| tree
2008-05-30	fabio	+ added missing modules imports	commit \| commitdiff \| tree
2008-05-30	fabio	+ shell script for the heuristic run	commit \| commitdiff \| tree
2008-05-30	fabio	+ removed unnecessary numpy dependency	commit \| commitdiff \| tree
2008-05-30	fabio	+ added modifications of parser to repo	commit \| commitdiff \| tree
2008-05-30	fabio	+ removed files	commit \| commitdiff \| tree
2008-05-30	fabio	+ minor changes	commit \| commitdiff \| tree
2008-05-30	fabio	+ moved sequence access functions to own module	commit \| commitdiff \| tree
2008-05-30	fabio	+ added dataset generation function to dataset specific...	commit \| commitdiff \| tree
2008-05-30	fabio	+ moved qpalma dataset generation scripts	commit \| commitdiff \| tree
2008-05-30	fabio	+ added a script that processes the single lane files...	commit \| commitdiff \| tree
2008-05-30	fabio	+ added some more scripts from the dataset processing	commit \| commitdiff \| tree
2008-05-30	fabio	+ added small counting script	commit \| commitdiff \| tree
2008-05-26	fabio	+ minor changes	commit \| commitdiff \| tree
2008-05-21	fabio	+ added script which draws the coverage bar plots presented...	commit \| commitdiff \| tree
2008-05-21	fabio	+ changed data loading procedures	commit \| commitdiff \| tree
2008-05-16	fabio	+ added missing free for line array	commit \| commitdiff \| tree
2008-05-15	fabio	+ minor modifications	commit \| commitdiff \| tree
2008-05-15	fabio	+ modified module in order to act like a database returning...	commit \| commitdiff \| tree
2008-05-15	fabio	+ coded alternative implementation using a list per...	commit \| commitdiff \| tree
2008-05-15	fabio	+ fixed seq size bug	commit \| commitdiff \| tree
2008-05-15	fabio	+ fixed a bug in the sscanf	commit \| commitdiff \| tree
2008-05-15	fabio	+ removed binaries	commit \| commitdiff \| tree
2008-05-15	fabio	+ added python module for reads parsing as plain python...	commit \| commitdiff \| tree
2008-05-14	fabio	+ take into account multiple hits per unique read	commit \| commitdiff \| tree
2008-05-14	fabio	+ made original reads file location a parameter for...	commit \| commitdiff \| tree
2008-05-14	fabio	+ First fully working version.	commit \| commitdiff \| tree
2008-05-14	fabio	+ changed dataset compiler to take the two different...	commit \| commitdiff \| tree
2008-05-14	fabio	+ first version of a script that uses pythongrid	commit \| commitdiff \| tree
2008-05-13	fabio	+ added configuration variables to main config file	commit \| commitdiff \| tree
2008-05-13	fabio	+ sanity checks for the global config file	commit \| commitdiff \| tree
2008-05-13	fabio	+ adapted training method to use new dataset standard	commit \| commitdiff \| tree
2008-05-12	fabio	+ changed dataset representation	commit \| commitdiff \| tree
2008-05-11	fabio	+ removed obsolete code	commit \| commitdiff \| tree
2008-05-11	fabio	+ removed lot of redundant/old code from the dataset...	commit \| commitdiff \| tree
2008-04-22	fabio	+ fix changes we made so far	commit \| commitdiff \| tree
2008-04-21	fabio	+ Aaaarghh found stupid bug in the parser (Case statement...	commit \| commitdiff \| tree
2008-04-19	fabio	+ support dangling end for unspliced reads in computeSpliceA...	commit \| commitdiff \| tree
2008-04-19	fabio	+ added faster evaluation function	commit \| commitdiff \| tree
2008-04-19	fabio	+ fixed some index bugs in the evaluation	commit \| commitdiff \| tree
2008-04-18	fabio	+ using new parsers now	commit \| commitdiff \| tree
2008-04-18	fabio	+ changed code for prediction -> easier and faster	commit \| commitdiff \| tree
2008-04-18	fabio	+ optimized parsers	commit \| commitdiff \| tree
2008-04-18	fabio	+ fixed missing newlines in output	commit \| commitdiff \| tree
2008-04-18	fabio	+ changed prediction	commit \| commitdiff \| tree
2008-04-18	fabio	+ pipeline parse is much faster now,	commit \| commitdiff \| tree
2008-04-18	fabio	minor changes of paths	commit \| commitdiff \| tree
2008-04-18	fabio	+ Lookup table checked for pos. strand	commit \| commitdiff \| tree
2008-04-18	fabio	+ added wrapper class for prefetching of genomic sequences...	commit \| commitdiff \| tree
2008-04-18	fabio	+ saving results in two files (spliced/unspliced)	commit \| commitdiff \| tree
2008-04-18	fabio	+ added if statement to create numpy mat for unspliced...	commit \| commitdiff \| tree
2008-04-18	fabio	git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch...	commit \| commitdiff \| tree
2008-04-18	fabio	added file	commit \| commitdiff \| tree
2008-04-18	fabio	missing files	commit \| commitdiff \| tree
2008-04-18	fabio	+ added solver wrapper for cvxopt	commit \| commitdiff \| tree
2008-04-18	fabio	another module init	commit \| commitdiff \| tree
2008-04-18	fabio	module init	commit \| commitdiff \| tree
2008-04-18	fabio	+ a slighlty better way to create a big dataset	commit \| commitdiff \| tree
2008-04-18	fabio	git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch...	commit \| commitdiff \| tree
2008-04-18	fabio	git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch...	commit \| commitdiff \| tree
2008-04-17	fabio	works soso	commit \| commitdiff \| tree
2008-04-17	fabio	git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch...	commit \| commitdiff \| tree
2008-04-17	fabio	+ updated filtering	commit \| commitdiff \| tree
2008-04-17	fabio	+ changes	commit \| commitdiff \| tree
2008-04-17	fabio	+ added small script for the evaluation of the first...	commit \| commitdiff \| tree
2008-04-17	fabio	+ changed alignment output format to be more blat-like	commit \| commitdiff \| tree
2008-04-17	fabio	+ extended alignment script	commit \| commitdiff \| tree
2008-04-16	fabio	+ minor modifications to allow for parallel prediction...	commit \| commitdiff \| tree
2008-04-16	fabio	+ added new format for QPalma alignment output	commit \| commitdiff \| tree
2008-04-16	fabio	+ added field to prediction dict	commit \| commitdiff \| tree
2008-04-14	fabio	+ refined creation of alternative alignments	commit \| commitdiff \| tree
2008-04-14	fabio	+ finished first running version of the spliced/unspliced...	commit \| commitdiff \| tree
2008-04-14	fabio	+ added information on cut positions of spliced reads	commit \| commitdiff \| tree
2008-04-09	fabio	+ added first version of the heuristic for the mapping...	commit \| commitdiff \| tree
2008-04-07	fabio	minor changes in the dataset compilation and the evaluation...	commit \| commitdiff \| tree
2008-03-20	fabio	+ minor changes in qpalma_main to take into accout...	commit \| commitdiff \| tree
2008-03-20	fabio	+ changes in the main configuration -> no pickled init...	commit \| commitdiff \| tree
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QPalma the short reads alignment project

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