qpalma.git
12 years ago+ changed filter criteria
fabio [Fri, 28 Dec 2007 14:36:15 +0000 (14:36 +0000)]
+ changed filter criteria
+ added some counters to infer why certain reads are excluded
+ disabled smoothness checks for now

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7216 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ loosened filtering criterion
fabio [Sat, 22 Dec 2007 16:14:34 +0000 (16:14 +0000)]
+ loosened filtering criterion
+ fixed memory leaks

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7210 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ found bug which caused ~10 reads of overlap "0"
fabio [Sat, 22 Dec 2007 02:03:57 +0000 (02:03 +0000)]
+ found bug which caused ~10 reads of overlap "0"
TODO
+ still a memory leak -> check all malloc/free occurrences
+ read line skipping can be made faster

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7209 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added missing check for strand orientation
fabio [Fri, 21 Dec 2007 15:44:52 +0000 (15:44 +0000)]
+ added missing check for strand orientation
+ added function remove_ambiguities which is responsible for the differences
between annotation and reads ( the [XY] pairs in the sequence string)

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7207 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added support for writing in result file
fabio [Thu, 20 Dec 2007 16:29:37 +0000 (16:29 +0000)]
+ added support for writing in result file
+ changed number of attributes which are stored in result file

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7200 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ optimized and fixed map file parser
fabio [Thu, 20 Dec 2007 15:05:19 +0000 (15:05 +0000)]
+ optimized and fixed map file parser

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7199 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ compacted parser code
fabio [Thu, 20 Dec 2007 08:18:56 +0000 (08:18 +0000)]
+ compacted parser code
+ found conceptual error

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7191 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ parser works now with mmap and sscanf
fabio [Wed, 19 Dec 2007 16:26:28 +0000 (16:26 +0000)]
+ parser works now with mmap and sscanf
TODO
+ perform some logical checks -> orientation...

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7178 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added processing function for reads
fabio [Wed, 19 Dec 2007 11:43:54 +0000 (11:43 +0000)]
+ added processing function for reads
TODO
- figure out how to use sscanf together with mmap

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7170 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ wrote faster parser / file processing tools in C
fabio [Tue, 18 Dec 2007 14:44:40 +0000 (14:44 +0000)]
+ wrote faster parser / file processing tools in C
TODO
+ finish solexa reads parser

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7164 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added python parsers for gff and solexa / read files
fabio [Mon, 17 Dec 2007 15:11:15 +0000 (15:11 +0000)]
+ added python parsers for gff and solexa / read files

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7156 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ started to add quality scoring function to C code
fabio [Fri, 14 Dec 2007 16:48:46 +0000 (16:48 +0000)]
+ started to add quality scoring function to C code

TODO
- think about apropriate replacement for global vars
- think about how dnaest should be visible to the python layer

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7100 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ started to extend fill_matrix in order to be able to use quality scores
fabio [Thu, 13 Dec 2007 18:51:36 +0000 (18:51 +0000)]
+ started to extend fill_matrix in order to be able to use quality scores
+ started to extend qpalma.py accordingly

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7066 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed a parameter name bug in the exporter script
fabio [Thu, 13 Dec 2007 14:09:29 +0000 (14:09 +0000)]
+ fixed a parameter name bug in the exporter script
+ minor changes to qpalma

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7059 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed a bug in the C++ interface
fabio [Wed, 12 Dec 2007 16:32:22 +0000 (16:32 +0000)]
+ fixed a bug in the C++ interface
+ removed some debugging printfs
+ added first version of an evaluation script
+ added standalone code to svn

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7048 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added small scripts for EST filtering
fabio [Tue, 11 Dec 2007 18:20:07 +0000 (18:20 +0000)]
+ added small scripts for EST filtering

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7018 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added export_param function to export parameters to "palma definition files" (param...
fabio [Mon, 10 Dec 2007 15:00:42 +0000 (15:00 +0000)]
+ added export_param function to export parameters to "palma definition files" (parameter files)
+ added parameter saving function which is called after training
+ fixed some indices for the splice weights

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6978 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed some index bugs
fabio [Mon, 10 Dec 2007 12:14:34 +0000 (12:14 +0000)]
+ fixed some index bugs
+ added debugging output

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6961 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ removed accidently checked in vim swap files
fabio [Fri, 7 Dec 2007 16:56:33 +0000 (16:56 +0000)]
+ removed accidently checked in vim swap files

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6946 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ found index bug in SWIG interface
fabio [Fri, 7 Dec 2007 16:53:09 +0000 (16:53 +0000)]
+ found index bug in SWIG interface
+ added more checks
+ adapted SIQP_CPX solver from the RFP project to work with QPalma
TODO
- check newWeights -> still a +2 offset at some positions

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6945 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ found bug in SWIG interface dna_len vs. dna_len-1 because of '\0' in matlab
fabio [Fri, 7 Dec 2007 13:08:45 +0000 (13:08 +0000)]
+ found bug in SWIG interface dna_len vs. dna_len-1 because of '\0' in matlab

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6941 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ changed interface array_function to array_class
fabio [Thu, 6 Dec 2007 12:04:46 +0000 (12:04 +0000)]
+ changed interface array_function to array_class
+ removed bug in alignmentscores

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6935 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ changed design
fabio [Thu, 6 Dec 2007 12:03:46 +0000 (12:03 +0000)]
+ changed design
+ fixed variable names
+ introduced more auxiliary functions

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6934 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed some index bugs in the weights calculation
fabio [Wed, 5 Dec 2007 17:39:01 +0000 (17:39 +0000)]
+ fixed some index bugs in the weights calculation
+ fixed array bug in SWIG interface

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6931 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ Extended C/C++ interface to return results easily
fabio [Wed, 5 Dec 2007 14:34:37 +0000 (14:34 +0000)]
+ Extended C/C++ interface to return results easily
+ First running version of QPalma SWIG interface
TODO

- still some index issues remain
- add evaluation after wrong alignment generation

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6929 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago- python code is now checked and complete
fabio [Wed, 5 Dec 2007 10:10:18 +0000 (10:10 +0000)]
- python code is now checked and complete
- interface is complete
TODO

- Change logic in the myalign function
- Modify training loop accordingly

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6927 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ removed several index bugs
fabio [Tue, 4 Dec 2007 14:36:29 +0000 (14:36 +0000)]
+ removed several index bugs
+ added checks to compare against matlab version
+ added convenience functions
TODO
- go on with value checks

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6923 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ rewrote C interface for SWIG/Python
fabio [Mon, 3 Dec 2007 12:19:09 +0000 (12:19 +0000)]
+ rewrote C interface for SWIG/Python
+ extended qpalma algorithm
+ added evalutation script for alignments
TODO

- added preprocessing scripts
- create an evaluation score

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6915 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ using correct interface now
fabio [Sun, 2 Dec 2007 20:11:22 +0000 (20:11 +0000)]
+ using correct interface now
+ added some assertions for range checks
+ added two new python scripts translated from the matlab version
TODO
- dimension and range checking for all other structures/array after set_param_palma
- decide between numpy and lists for smaller arrays

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6913 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ created necessary interfaces
fabio [Sat, 1 Dec 2007 00:59:22 +0000 (00:59 +0000)]
+ created necessary interfaces
+ wrote some convenience python functions in set_param_palma

TODO

- complete python training loop

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6906 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added c code from the palma project
fabio [Fri, 30 Nov 2007 15:53:57 +0000 (15:53 +0000)]
+ added c code from the palma project
+ added own version of the swig interface

TODO

- think about wrapper for structs / cells
  user either SWIG constrcuts or native python object

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6902 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added first converted scripts
fabio [Fri, 30 Nov 2007 13:13:42 +0000 (13:13 +0000)]
+ added first converted scripts
+ SpliceAlign computation works

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6888 e1793c9e-67f9-0310-80fc-b846ff1f7b36