+ changed check for intial setting of old_w. (matrix != None does not work in cvxopt)
[qpalma.git] / test.conf
index 39e2b0c..9eb7f82 100644 (file)
--- a/test.conf
+++ b/test.conf
@@ -28,9 +28,9 @@ result_dir = /fml/ag-raetsch/home/fabio/tmp/sandbox/first_test
 # These variables store the filename of the raw read data
 #
 
-spliced_reads_fn = /fml/ag-raetsch/home/fabio/tmp/sandbox/map_2nd.vm
+#spliced_reads_fn = /fml/ag-raetsch/home/fabio/tmp/sandbox/map_2nd.vm
 
-unspliced_reads_fn = /fml/ag-raetsch/home/fabio/tmp/sandbox/map.vm
+#unspliced_reads_fn = /fml/ag-raetsch/home/fabio/tmp/sandbox/map.vm
 
 #
 # You can specify how many nodes you want to use via this variable
@@ -38,12 +38,6 @@ unspliced_reads_fn = /fml/ag-raetsch/home/fabio/tmp/sandbox/map.vm
 
 num_splits = 5
 
-#
-# The parameter you want to do prediction with:
-#
-
-prediction_param_fn = /fml/ag-raetsch/home/fabio/tmp/newest_run/alignment/run_enable_quality_scores_+_enable_splice_signals_+_enable_intron_length_+/param_526.pickle
-
 #
 # In order to align short reads QPalma relies on additional information such as
 # splice site score prediction.
@@ -89,7 +83,7 @@ optimizer = CVXOPT
 # The output format can be one of BLAT, ShoRe or mGene
 #
 
-output_format = BLAT
+output_format = blat
 
 #prb_offset = 50
 prb_offset = 64
@@ -125,4 +119,3 @@ min_intron_len          = 20
 min_qual                = -5
 min_svm_score           = 0.0
 print_matrix            = False
-totalQualSuppPoints     = 300