Mercurial > repos > artbio > lumpy_sv

changeset 5:6ae3a402b9af draft default tip

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv commit e1bfc70a74f12ef8182d9afa0b3ab69d620fb3a8"
author artbio
date Sun, 24 May 2020 18:48:46 -0400
parents 093bb151a0a8
children
files lumpy.xml pairend_distro.py
diffstat 2 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/lumpy.xml	Mon May 11 19:51:38 2020 -0400
+++ b/lumpy.xml	Sun May 24 18:48:46 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="lumpy" name="lumpy-sv" version="1.2.1">
+<tool id="lumpy" name="lumpy-sv" version="1.2.2">
     <description>find structural variants</description>
     <requirements>
         <requirement type="package" version="0.2.13">lumpy-sv</requirement>
--- a/pairend_distro.py	Mon May 11 19:51:38 2020 -0400
+++ b/pairend_distro.py	Sun May 24 18:48:46 2020 -0400
@@ -81,7 +81,7 @@
 min_elements = 1000
 if len(L) < min_elements:
     sys.stderr.write("Warning: only %s elements in distribution (min: %s)\n" %
-                     (len(L), min_elements))
+                     (str(len(L)), str(min_elements)))
     mean = "NA"
     stdev = "NA"
 
@@ -94,8 +94,8 @@
     L = L[L < upper_cutoff]
     new_len = len(L)
     removed = c - new_len
-    sys.stderr.write("Removed %d outliers with isize >= %d\n" %
-                     (removed, upper_cutoff))
+    sys.stderr.write("Removed %s outliers with isize >= %s\n" %
+                     (str(removed), str(upper_cutoff)))
     c = new_len
 
     mean = np.mean(L)