+ extended documentation
[qpalma.git] / tools /
2008-10-13 Fabio+ extended documentation
2008-09-01 fabio+ minor changes in the paths
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
2008-07-31 fabio+ fixed quality conversion: According to new specs...
2008-07-31 fabio+ modifications in order to use new data format / acces...
2008-07-04 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
2008-06-24 fabio+ added small program for intron-position comparison
2008-06-20 fabio+ optimized dataset generation/storage
2008-05-30 fabio+ original reads sequence now has to be reconstructred...
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
2008-04-22 fabio+ fix changes we made so far
2008-04-17 fabio+ updated filtering
2008-03-06 fabio+ fixed index of reads in filterReads
2008-03-05 fabio+ refactored code further
2008-02-11 fabio+ added scripts for model selection on the cluster
2008-02-10 fabio+ changed filter behavior (tendency towards smaller...
2008-02-10 fabio+ fixed a bug in the filtering (forgot to disable remov...
2008-02-09 fabio+ fixed bug in the combination of reads with deletions
2008-02-09 fabio+ fixed bug in the filtering function (if read offset...
2008-02-09 fabio+ extended filtering to take indels [A-] resp. [-A...
2008-02-08 fabio+ minor changes to filterReads
2008-02-07 fabio+ fixed uninitialised values
2008-02-07 fabio+ new version of the filterReads program
2008-02-07 fabio+ some fixes of the filterReads and parser functions
2008-02-06 fabio+ resolved an issue with the memory mapping in filterReads
2008-02-06 fabio+ rearranged code
2008-02-05 fabio+ extended dataset compilation function
2008-02-04 fabio+ minor changes
2008-02-04 fabio+ modified filtering of reads
2008-02-02 fabio+ added read structure for new parser
2008-01-28 fabio+ removed duplicated code
2008-01-25 fabio+ fix development stage before doing some refactoring
2008-01-25 fabio+ added exons read boundary output to filterReads output
2008-01-23 fabio+ added splicesite scores to training
2008-01-23 fabio+ minor mods
2008-01-23 fabio+ changed output in the filterReads
2008-01-23 fabio+ restored functionality
2008-01-23 fabio+ some changes concerning filter params
2008-01-23 fabio+ small changes
2008-01-22 fabio+ solved some issues with the data generation
2008-01-22 ongan example shows how to integrate into qpalma
2008-01-21 ongFirst try at splice site scores. Not yet integrated.
2008-01-16 ongused the last value of quality plifs to fill out the...
2008-01-16 fabio+ fixed matchmatrix for the quality case to be a 1x6...
2008-01-16 ongplot the parameter vector in a useful way
2008-01-09 fabio+ added fasta parser for TAIR7 sequences
2008-01-09 fabio+ restored old filtering functionality -> reads have...
2008-01-07 fabio+ changed reads combination in order to allow for overl...
2007-12-28 fabio+ changed filter criteria
2007-12-22 fabio+ loosened filtering criterion
2007-12-22 fabio+ found bug which caused ~10 reads of overlap "0"
2007-12-21 fabio+ added missing check for strand orientation
2007-12-20 fabio+ added support for writing in result file
2007-12-20 fabio+ optimized and fixed map file parser
2007-12-20 fabio+ compacted parser code
2007-12-19 fabio+ parser works now with mmap and sscanf
2007-12-19 fabio+ added processing function for reads
2007-12-18 fabio+ wrote faster parser / file processing tools in C
2007-12-17 fabio+ added python parsers for gff and solexa / read files
2007-12-12 fabio+ fixed a bug in the C++ interface
2007-12-11 fabio+ added small scripts for EST filtering
2007-12-10 fabio+ fixed some index bugs
2007-12-04 fabio+ removed several index bugs
2007-12-03 fabio+ rewrote C interface for SWIG/Python