+ added some flags to Makefile args
[qpalma.git] / scripts /
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
2008-08-11 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
2008-08-05 fabio+ higher level cluster tasks interface for qpalma
2008-08-04 fabio+ minor modifications for the prefetching the whole...
2008-07-31 fabio+ fixed quality conversion: According to new specs...
2008-07-31 fabio+ changed PipelinHeuristic to support new data access...
2008-07-29 fabio+ adapted Lookup table to new data interface
2008-07-29 fabio+ fix version before moving to new format
2008-07-10 fabio+ modified Lookup table to work with negative strands
2008-06-30 fabio+ pruned a lot of import declarations
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
2008-06-03 fabio+ added script to parallelize QPalma heuristic on the...
2008-06-02 fabio+ fix starting point for rewrite of data accession...
2008-05-30 fabio+ shell script for the heuristic run
2008-05-30 fabio+ removed files
2008-05-30 fabio+ minor changes
2008-05-30 fabio+ moved sequence access functions to own module
2008-05-26 fabio+ minor changes
2008-05-21 fabio+ added script which draws the coverage bar plots prese...
2008-05-21 fabio+ changed data loading procedures
2008-05-14 fabio+ take into account multiple hits per unique read
2008-05-14 fabio+ made original reads file location a parameter for...
2008-05-14 fabio+ First fully working version.
2008-05-14 fabio+ changed dataset compiler to take the two different...
2008-05-14 fabio+ first version of a script that uses pythongrid
2008-05-13 fabio+ added configuration variables to main config file
2008-05-13 fabio+ sanity checks for the global config file
2008-05-13 fabio+ adapted training method to use new dataset standard
2008-05-12 fabio+ changed dataset representation
2008-05-11 fabio+ removed obsolete code
2008-05-11 fabio+ removed lot of redundant/old code from the dataset...
2008-04-22 fabio+ fix changes we made so far
2008-04-19 fabio+ added faster evaluation function
2008-04-19 fabio+ fixed some index bugs in the evaluation
2008-04-18 fabio+ using new parsers now
2008-04-18 fabio+ changed code for prediction -> easier and faster
2008-04-18 fabio+ fixed missing newlines in output
2008-04-18 fabio+ changed prediction
2008-04-18 fabiominor changes of paths
2008-04-18 fabio+ Lookup table checked for pos. strand
2008-04-18 fabio+ added wrapper class for prefetching of genomic sequen...
2008-04-18 raetschgit-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects...
2008-04-18 raetschoptimized heuristic
2008-04-18 fabio+ saving results in two files (spliced/unspliced)
2008-04-18 raetschheuristic seems to work well
2008-04-18 fabio+ added if statement to create numpy mat for unspliced...
2008-04-18 fabiogit-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects...
2008-04-18 raetschgit-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects...
2008-04-18 fabio+ a slighlty better way to create a big dataset
2008-04-18 raetschgit-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects...
2008-04-18 fabiogit-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects...
2008-04-18 raetschgit-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects...
2008-04-18 fabiogit-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects...
2008-04-17 fabioworks soso
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 fabiogit-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 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...
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