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+ changed check for intial setting of old_w. (matrix != None does not work in cvxopt)
[qpalma.git]
/
tools
/
2008-10-15
Fabio
+ fixed alignment index calculation for negative strand
tree
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commitdiff
2008-10-14
Fabio
+ extended test cases
tree
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commitdiff
2008-10-13
Fabio
+ extended documentation
tree
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commitdiff
2008-09-01
fabio
+ minor changes in the paths
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commitdiff
2008-08-14
fabio
+ added convenient script
tree
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commitdiff
2008-08-11
fabio
+ found negative strand bug
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commitdiff
2008-08-07
fabio
+ fixed bug in position calculation for negative strand
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commitdiff
2008-07-31
fabio
+ fixed quality conversion: According to new specs...
tree
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commitdiff
2008-07-31
fabio
+ modifications in order to use new data format / acces...
tree
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commitdiff
2008-07-04
fabio
+ interesting version : it crashes but valgrind detects...
tree
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commitdiff
2008-07-04
fabio
+ recalculating exons boundaries fixed
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commitdiff
2008-07-04
fabio
+ added reverse complementation to filter reads function
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commitdiff
2008-07-03
fabio
+ moved tools from training dataset generation to their...
tree
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commitdiff
2008-07-03
fabio
+ saving changes in the dataset generation
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commitdiff
2008-07-02
fabio
+ some optimization
tree
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commitdiff
2008-06-24
fabio
+ added small program for intron-position comparison
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commitdiff
2008-06-20
fabio
+ optimized dataset generation/storage
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commitdiff
2008-05-30
fabio
+ original reads sequence now has to be reconstructred...
tree
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commitdiff
2008-05-30
fabio
+ added dataset generation function to dataset specific...
tree
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commitdiff
2008-05-30
fabio
+ moved qpalma dataset generation scripts
tree
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commitdiff
2008-05-30
fabio
+ added a script that processes the single lane files...
tree
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commitdiff
2008-05-30
fabio
+ added some more scripts from the dataset processing
tree
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commitdiff
2008-05-30
fabio
+ added small counting script
tree
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commitdiff
2008-04-22
fabio
+ fix changes we made so far
tree
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commitdiff
2008-04-17
fabio
+ updated filtering
tree
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commitdiff
2008-03-06
fabio
+ fixed index of reads in filterReads
tree
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commitdiff
2008-03-05
fabio
+ refactored code further
tree
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commitdiff
2008-02-11
fabio
+ added scripts for model selection on the cluster
tree
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commitdiff
2008-02-10
fabio
+ changed filter behavior (tendency towards smaller...
tree
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commitdiff
2008-02-10
fabio
+ fixed a bug in the filtering (forgot to disable remov...
tree
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commitdiff
2008-02-09
fabio
+ fixed bug in the combination of reads with deletions
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commitdiff
2008-02-09
fabio
+ fixed bug in the filtering function (if read offset...
tree
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commitdiff
2008-02-09
fabio
+ extended filtering to take indels [A-] resp. [-A...
tree
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commitdiff
2008-02-08
fabio
+ minor changes to filterReads
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commitdiff
2008-02-07
fabio
+ fixed uninitialised values
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commitdiff
2008-02-07
fabio
+ new version of the filterReads program
tree
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commitdiff
2008-02-07
fabio
+ some fixes of the filterReads and parser functions
tree
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commitdiff
2008-02-06
fabio
+ resolved an issue with the memory mapping in filterReads
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commitdiff
2008-02-06
fabio
+ rearranged code
tree
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commitdiff
2008-02-05
fabio
+ extended dataset compilation function
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commitdiff
2008-02-04
fabio
+ minor changes
tree
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commitdiff
2008-02-04
fabio
+ modified filtering of reads
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commitdiff
2008-02-02
fabio
+ added read structure for new parser
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commitdiff
2008-01-28
fabio
+ removed duplicated code
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commitdiff
2008-01-25
fabio
+ fix development stage before doing some refactoring
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commitdiff
2008-01-25
fabio
+ added exons read boundary output to filterReads output
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commitdiff
2008-01-23
fabio
+ added splicesite scores to training
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commitdiff
2008-01-23
fabio
+ minor mods
tree
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commitdiff
2008-01-23
fabio
+ changed output in the filterReads
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commitdiff
2008-01-23
fabio
+ restored functionality
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commitdiff
2008-01-23
fabio
+ some changes concerning filter params
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commitdiff
2008-01-23
fabio
+ small changes
tree
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commitdiff
2008-01-22
fabio
+ solved some issues with the data generation
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commitdiff
2008-01-22
ong
an example shows how to integrate into qpalma
tree
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commitdiff
2008-01-21
ong
First try at splice site scores. Not yet integrated.
tree
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commitdiff
2008-01-16
ong
used the last value of quality plifs to fill out the...
tree
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commitdiff
2008-01-16
fabio
+ fixed matchmatrix for the quality case to be a 1x6...
tree
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commitdiff
2008-01-16
ong
plot the parameter vector in a useful way
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commitdiff
2008-01-09
fabio
+ added fasta parser for TAIR7 sequences
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commitdiff
2008-01-09
fabio
+ restored old filtering functionality -> reads have...
tree
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commitdiff
2008-01-07
fabio
+ changed reads combination in order to allow for overl...
tree
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commitdiff
2007-12-28
fabio
+ changed filter criteria
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commitdiff
2007-12-22
fabio
+ loosened filtering criterion
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commitdiff
2007-12-22
fabio
+ found bug which caused ~10 reads of overlap "0"
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commitdiff
2007-12-21
fabio
+ added missing check for strand orientation
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commitdiff
2007-12-20
fabio
+ added support for writing in result file
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commitdiff
2007-12-20
fabio
+ optimized and fixed map file parser
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commitdiff
2007-12-20
fabio
+ compacted parser code
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commitdiff
2007-12-19
fabio
+ parser works now with mmap and sscanf
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commitdiff
2007-12-19
fabio
+ added processing function for reads
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commitdiff
2007-12-18
fabio
+ wrote faster parser / file processing tools in C
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commitdiff
2007-12-17
fabio
+ added python parsers for gff and solexa / read files
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commitdiff
2007-12-12
fabio
+ fixed a bug in the C++ interface
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commitdiff
2007-12-11
fabio
+ added small scripts for EST filtering
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commitdiff
2007-12-10
fabio
+ fixed some index bugs
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commitdiff
2007-12-04
fabio
+ removed several index bugs
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commitdiff
2007-12-03
fabio
+ rewrote C interface for SWIG/Python
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commitdiff