qpalma.git
12 years ago+ a slighlty better way to create a big dataset
fabio [Fri, 18 Apr 2008 08:58:03 +0000 (08:58 +0000)]
+ a slighlty better way to create a big dataset

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8655 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8654 e1793c9e...
raetsch [Fri, 18 Apr 2008 08:57:22 +0000 (08:57 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8654 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8653 e1793c9e...
fabio [Fri, 18 Apr 2008 08:47:29 +0000 (08:47 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8653 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8652 e1793c9e...
raetsch [Fri, 18 Apr 2008 08:41:10 +0000 (08:41 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8652 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8651 e1793c9e...
fabio [Fri, 18 Apr 2008 08:33:30 +0000 (08:33 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8651 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agoworks soso
fabio [Thu, 17 Apr 2008 22:28:15 +0000 (22:28 +0000)]
works soso

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8650 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8649 e1793c9e...
raetsch [Thu, 17 Apr 2008 22:01:31 +0000 (22:01 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8649 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8648 e1793c9e...
raetsch [Thu, 17 Apr 2008 22:00:19 +0000 (22:00 +0000)]
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raetsch [Thu, 17 Apr 2008 21:58:46 +0000 (21:58 +0000)]
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raetsch [Thu, 17 Apr 2008 21:58:24 +0000 (21:58 +0000)]
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raetsch [Thu, 17 Apr 2008 21:52:35 +0000 (21:52 +0000)]
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raetsch [Thu, 17 Apr 2008 21:49:09 +0000 (21:49 +0000)]
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raetsch [Thu, 17 Apr 2008 21:43:04 +0000 (21:43 +0000)]
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raetsch [Thu, 17 Apr 2008 21:42:28 +0000 (21:42 +0000)]
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fabio [Thu, 17 Apr 2008 21:42:19 +0000 (21:42 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8641 e1793c9e-67f9-0310-80fc-b846ff1f7b36

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raetsch [Thu, 17 Apr 2008 21:34:58 +0000 (21:34 +0000)]
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raetsch [Thu, 17 Apr 2008 21:33:27 +0000 (21:33 +0000)]
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raetsch [Thu, 17 Apr 2008 21:32:00 +0000 (21:32 +0000)]
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raetsch [Thu, 17 Apr 2008 21:29:07 +0000 (21:29 +0000)]
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raetsch [Thu, 17 Apr 2008 21:27:28 +0000 (21:27 +0000)]
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12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8635 e1793c9e...
raetsch [Thu, 17 Apr 2008 21:24:17 +0000 (21:24 +0000)]
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raetsch [Thu, 17 Apr 2008 21:23:37 +0000 (21:23 +0000)]
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raetsch [Thu, 17 Apr 2008 21:22:59 +0000 (21:22 +0000)]
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raetsch [Thu, 17 Apr 2008 21:09:50 +0000 (21:09 +0000)]
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raetsch [Thu, 17 Apr 2008 21:05:14 +0000 (21:05 +0000)]
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raetsch [Thu, 17 Apr 2008 21:04:53 +0000 (21:04 +0000)]
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raetsch [Thu, 17 Apr 2008 21:03:55 +0000 (21:03 +0000)]
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raetsch [Thu, 17 Apr 2008 21:01:18 +0000 (21:01 +0000)]
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12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8627 e1793c9e...
raetsch [Thu, 17 Apr 2008 21:00:57 +0000 (21:00 +0000)]
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12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8626 e1793c9e...
raetsch [Thu, 17 Apr 2008 20:56:40 +0000 (20:56 +0000)]
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12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8625 e1793c9e...
raetsch [Thu, 17 Apr 2008 20:46:45 +0000 (20:46 +0000)]
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12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8624 e1793c9e...
raetsch [Thu, 17 Apr 2008 20:44:25 +0000 (20:44 +0000)]
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12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8623 e1793c9e...
raetsch [Thu, 17 Apr 2008 20:43:00 +0000 (20:43 +0000)]
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raetsch [Thu, 17 Apr 2008 20:40:28 +0000 (20:40 +0000)]
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raetsch [Thu, 17 Apr 2008 20:38:58 +0000 (20:38 +0000)]
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raetsch [Thu, 17 Apr 2008 20:38:27 +0000 (20:38 +0000)]
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12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8619 e1793c9e...
raetsch [Thu, 17 Apr 2008 20:24:43 +0000 (20:24 +0000)]
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raetsch [Thu, 17 Apr 2008 20:23:56 +0000 (20:23 +0000)]
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12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8617 e1793c9e...
raetsch [Thu, 17 Apr 2008 20:22:55 +0000 (20:22 +0000)]
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12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8616 e1793c9e...
raetsch [Thu, 17 Apr 2008 20:21:22 +0000 (20:21 +0000)]
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12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8615 e1793c9e...
raetsch [Thu, 17 Apr 2008 20:21:07 +0000 (20:21 +0000)]
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raetsch [Thu, 17 Apr 2008 20:08:17 +0000 (20:08 +0000)]
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raetsch [Thu, 17 Apr 2008 20:06:51 +0000 (20:06 +0000)]
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12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8612 e1793c9e...
raetsch [Thu, 17 Apr 2008 20:06:25 +0000 (20:06 +0000)]
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12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8611 e1793c9e...
raetsch [Thu, 17 Apr 2008 20:05:44 +0000 (20:05 +0000)]
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raetsch [Thu, 17 Apr 2008 20:04:20 +0000 (20:04 +0000)]
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12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8609 e1793c9e...
raetsch [Thu, 17 Apr 2008 20:03:42 +0000 (20:03 +0000)]
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12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8608 e1793c9e...
raetsch [Thu, 17 Apr 2008 20:03:11 +0000 (20:03 +0000)]
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12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8607 e1793c9e...
raetsch [Thu, 17 Apr 2008 19:44:14 +0000 (19:44 +0000)]
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raetsch [Thu, 17 Apr 2008 19:43:29 +0000 (19:43 +0000)]
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12 years agounspliced should work
raetsch [Thu, 17 Apr 2008 19:41:13 +0000 (19:41 +0000)]
unspliced should work

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12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8604 e1793c9e...
raetsch [Thu, 17 Apr 2008 19:38:50 +0000 (19:38 +0000)]
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raetsch [Thu, 17 Apr 2008 19:37:58 +0000 (19:37 +0000)]
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raetsch [Thu, 17 Apr 2008 19:37:31 +0000 (19:37 +0000)]
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raetsch [Thu, 17 Apr 2008 19:36:40 +0000 (19:36 +0000)]
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12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8600 e1793c9e...
raetsch [Thu, 17 Apr 2008 19:36:17 +0000 (19:36 +0000)]
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12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8599 e1793c9e...
raetsch [Thu, 17 Apr 2008 19:34:52 +0000 (19:34 +0000)]
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12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8598 e1793c9e...
raetsch [Thu, 17 Apr 2008 19:27:34 +0000 (19:27 +0000)]
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raetsch [Thu, 17 Apr 2008 19:26:10 +0000 (19:26 +0000)]
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raetsch [Thu, 17 Apr 2008 19:25:04 +0000 (19:25 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8596 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8595 e1793c9e...
raetsch [Thu, 17 Apr 2008 19:23:55 +0000 (19:23 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8595 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8594 e1793c9e...
raetsch [Thu, 17 Apr 2008 19:22:59 +0000 (19:22 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8594 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8593 e1793c9e...
raetsch [Thu, 17 Apr 2008 19:22:29 +0000 (19:22 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8593 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8592 e1793c9e...
raetsch [Thu, 17 Apr 2008 19:21:49 +0000 (19:21 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8592 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8591 e1793c9e...
raetsch [Thu, 17 Apr 2008 19:18:56 +0000 (19:18 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8591 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8590 e1793c9e...
raetsch [Thu, 17 Apr 2008 19:16:29 +0000 (19:16 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8590 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8589 e1793c9e...
raetsch [Thu, 17 Apr 2008 19:14:47 +0000 (19:14 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8589 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agofirst version of faster heuristic
raetsch [Thu, 17 Apr 2008 19:10:14 +0000 (19:10 +0000)]
first version of faster heuristic

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8588 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ updated filtering
fabio [Thu, 17 Apr 2008 18:34:18 +0000 (18:34 +0000)]
+ updated filtering
+ some minor changes in parsers and data processing

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8587 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ changes
fabio [Thu, 17 Apr 2008 18:33:36 +0000 (18:33 +0000)]
+ changes

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8586 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added small script for the evaluation of the first vmatch round
fabio [Thu, 17 Apr 2008 14:26:06 +0000 (14:26 +0000)]
+ added small script for the evaluation of the first vmatch round

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8573 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ changed alignment output format to be more blat-like
fabio [Thu, 17 Apr 2008 09:54:19 +0000 (09:54 +0000)]
+ changed alignment output format to be more blat-like
+ performed prediction to see whether changes are correct

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8561 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ extended alignment script
fabio [Thu, 17 Apr 2008 08:28:42 +0000 (08:28 +0000)]
+ extended alignment script
+ modified evalutation script in order to produce error_vs_pos table

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8558 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ minor modifications to allow for parallel prediction of large datasets
fabio [Wed, 16 Apr 2008 22:31:23 +0000 (22:31 +0000)]
+ minor modifications to allow for parallel prediction of large datasets

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8556 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added new format for QPalma alignment output
fabio [Wed, 16 Apr 2008 15:27:47 +0000 (15:27 +0000)]
+ added new format for QPalma alignment output
+ still experimenting with the heuristic parameters

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8554 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added field to prediction dict
fabio [Wed, 16 Apr 2008 13:08:38 +0000 (13:08 +0000)]
+ added field to prediction dict
+ extended pipeline heuristic
+ added small script to create alignment file out of alignment objects

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8549 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ refined creation of alternative alignments
fabio [Mon, 14 Apr 2008 14:41:32 +0000 (14:41 +0000)]
+ refined creation of alternative alignments

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8519 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ finished first running version of the spliced/unspliced heuristic
fabio [Mon, 14 Apr 2008 12:28:38 +0000 (12:28 +0000)]
+ finished first running version of the spliced/unspliced heuristic
+ removed dead code from the data generation script
TODO
- generation of alternative alignments in the heuristic may not be optimal

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8516 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added information on cut positions of spliced reads
fabio [Mon, 14 Apr 2008 07:43:24 +0000 (07:43 +0000)]
+ added information on cut positions of spliced reads

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8511 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added first version of the heuristic for the mapping pipeline.
fabio [Wed, 9 Apr 2008 13:39:43 +0000 (13:39 +0000)]
+ added first version of the heuristic for the mapping pipeline.

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8426 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agominor changes in the dataset compilation and the evaluation scripts
fabio [Mon, 7 Apr 2008 09:07:09 +0000 (09:07 +0000)]
minor changes in the dataset compilation and the evaluation scripts

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8396 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ minor changes in qpalma_main to take into accout that jobs may be rescheduled
fabio [Thu, 20 Mar 2008 21:37:04 +0000 (21:37 +0000)]
+ minor changes in qpalma_main to take into accout that jobs may be rescheduled
via exit(99)
+ added switch to run objects to disable support point for disabled intron
length model runs
+ minor changes to the evaluation function

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8224 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ changes in the main configuration -> no pickled init vector necessary anymore
fabio [Thu, 20 Mar 2008 21:31:28 +0000 (21:31 +0000)]
+ changes in the main configuration -> no pickled init vector necessary anymore
+ added switch inside solver to disable optimization for intron length model
   (set corresponding values to 0.0)

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8223 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added function to create tex table from results
fabio [Thu, 20 Mar 2008 10:52:04 +0000 (10:52 +0000)]
+ added function to create tex table from results

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8221 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ minor changes in Evaluation an soap remapping wrapper
fabio [Thu, 20 Mar 2008 01:17:42 +0000 (01:17 +0000)]
+ minor changes in Evaluation an soap remapping wrapper

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8219 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added script to automatically perform alignment using SOAP 1.07
fabio [Wed, 19 Mar 2008 17:02:17 +0000 (17:02 +0000)]
+ added script to automatically perform alignment using SOAP 1.07
+ added parser for the SOAP 1.07 result format

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8213 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added splice site score exception to training/prediction
fabio [Tue, 18 Mar 2008 14:37:07 +0000 (14:37 +0000)]
+ added splice site score exception to training/prediction
+ refactored evaluation script count the number of score comparisons correctly

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8197 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ removed duplicated code
fabio [Mon, 17 Mar 2008 13:08:41 +0000 (13:08 +0000)]
+ removed duplicated code
+ found bug in the evaluation -> wrong position calculation for chr 6 and 7

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8172 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ training works,
fabio [Fri, 14 Mar 2008 17:29:26 +0000 (17:29 +0000)]
+ training works,
+ prediction however has still some issues with the correct dna sequence

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8160 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed mentioned index bugs of the SpliceAlign of the ground truth
fabio [Wed, 12 Mar 2008 14:28:24 +0000 (14:28 +0000)]
+ fixed mentioned index bugs of the SpliceAlign of the ground truth

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8134 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed nasty index bugs in the when creating the label of the ground truth
fabio [Wed, 12 Mar 2008 14:27:48 +0000 (14:27 +0000)]
+ fixed nasty index bugs in the when creating the label of the ground truth
+ computeWeights is now happy -> follow the convention acceptor scores are
located at the 'g' of 'ag'

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8133 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ now using the new interval query interface
fabio [Tue, 11 Mar 2008 14:18:53 +0000 (14:18 +0000)]
+ now using the new interval query interface
+ checked code up to splice scores
+ code runs with splice scores disabled

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8126 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed bug in the index calculation of donor/acceptor scores
fabio [Mon, 10 Mar 2008 16:02:55 +0000 (16:02 +0000)]
+ fixed bug in the index calculation of donor/acceptor scores
+ extended check script

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8111 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ changed training method to work with new dataset format
fabio [Fri, 7 Mar 2008 17:47:42 +0000 (17:47 +0000)]
+ changed training method to work with new dataset format
+ minor changes

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8103 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ refactored compile dataset -> removed remaining redundancies in dataset object
fabio [Thu, 6 Mar 2008 17:34:53 +0000 (17:34 +0000)]
+ refactored compile dataset -> removed remaining redundancies in dataset object
+ added sanity check for data

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8085 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed index of reads in filterReads
fabio [Thu, 6 Mar 2008 17:00:55 +0000 (17:00 +0000)]
+ fixed index of reads in filterReads
+ added script to check for valid splice sites defined by gff files

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8083 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ removed some obsolete variables
fabio [Wed, 5 Mar 2008 16:10:31 +0000 (16:10 +0000)]
+ removed some obsolete variables

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8042 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ refactored code further
fabio [Wed, 5 Mar 2008 16:09:21 +0000 (16:09 +0000)]
+ refactored code further
+ evaluation script and job submission works now
TODO
+ check indices for those sites found by vmatch which are arbitrary off the
original ones

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8041 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added small app to ease profiling
fabio [Wed, 5 Mar 2008 13:16:59 +0000 (13:16 +0000)]
+ added small app to ease profiling

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8036 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ extended scripts
fabio [Thu, 28 Feb 2008 13:18:32 +0000 (13:18 +0000)]
+ extended scripts
+ added function to parse map.vm files from vmatch

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7976 e1793c9e-67f9-0310-80fc-b846ff1f7b36