Change default parameters to better ones

iprada · Aug 15, 2019 · 69c10f7 · 69c10f7
1 parent 56cac9d
commit 69c10f7
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Showing 2 changed files with 9 additions and 8 deletions.
diff --git a/circlemap/__version__.py b/circlemap/__version__.py
@@ -0,0 +1 @@
+__version__ = '1.1.0'
diff --git a/circlemap/circle_map.py b/circlemap/circle_map.py
@@ -391,8 +391,8 @@ def args_realigner(self):
                                            default=0.99)
 
             alignment_options.add_argument('-m', '--min_sc', type=float, metavar='',
-                                           help="Minimum soft-clipped length to attempt the realignment. Default: 6",
-                                           default=6)
+                                           help="Minimum soft-clipped length to attempt the realignment. Default: 5",
+                                           default=5)
 
             alignment_options.add_argument('-g', '--gap_open', type=int, metavar='',
                                            help="Gap open penalty in the position specific scoring matrix. Default: 5",
@@ -434,8 +434,8 @@ def args_realigner(self):
             # Interval options
 
             interval.add_argument('-f', '--merge_fraction', type=float, metavar='',
-                                  help="Merge intervals reciprocally overlapping by a fraction. Default 0.95",
-                                  default=0.95)
+                                  help="Merge intervals reciprocally overlapping by a fraction. Default 0.99",
+                                  default=0.99)
 
             interval.add_argument('-P', '--interval_probability', type=float, metavar='',
                                   help="Skip edges of the graph with a probability below the threshold. Default: 0.01",
@@ -510,8 +510,8 @@ def args_realigner(self):
                                            default=0.99)
 
             alignment_options.add_argument('-m', '--min_sc', type=float, metavar='',
-                                           help="Minimum soft-clipped length to attempt the realignment. Default: 6",
-                                           default=6)
+                                           help="Minimum soft-clipped length to attempt the realignment. Default: 5",
+                                           default=5)
 
             alignment_options.add_argument('-g', '--gap_open', type=int, metavar='',
                                            help="Gap open penalty in the position specific scoring matrix. Default: 5",
@@ -552,8 +552,8 @@ def args_realigner(self):
             # Interval options
 
             interval.add_argument('-f', '--merge_fraction', type=float, metavar='',
-                                  help="Merge intervals reciprocally overlapping by a fraction. Default 0.95",
-                                  default=0.95)
+                                  help="Merge intervals reciprocally overlapping by a fraction. Default 0.99",
+                                  default=0.99)
 
             interval.add_argument('-P', '--interval_probability', type=float, metavar='',
                                   help="Skip edges of the graph with a probability below the threshold. Default: 0.01",