# HG changeset patch
# User peterjc
# Date 1496758716 14400
# Node ID 86455d19abb80e0a9db044e07c7c7791c9732b88
# Parent  f27732bbfafafe6e4f52e3829def9d79662e78c8
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats commit 79bbb921cb5aa953f0323accd6c8c293c6e486cf-dirty

diff -r f27732bbfafa -r 86455d19abb8 tools/coverage_stats/README.rst
--- a/tools/coverage_stats/README.rst	Fri May 19 06:19:37 2017 -0400
+++ b/tools/coverage_stats/README.rst	Tue Jun 06 10:18:36 2017 -0400
@@ -65,6 +65,7 @@
         - Report total length and overall mean coverage in stdout.
         - Use ``<command detect_errors="aggressive">`` (internal change only).
         - Single quote command line arguments (internal change only).
+v0.0.6  - Python 3 compatibility fix.
 ======= ======================================================================
 
 
diff -r f27732bbfafa -r 86455d19abb8 tools/coverage_stats/coverage_stats.py
--- a/tools/coverage_stats/coverage_stats.py	Fri May 19 06:19:37 2017 -0400
+++ b/tools/coverage_stats/coverage_stats.py	Tue Jun 06 10:18:36 2017 -0400
@@ -24,7 +24,7 @@
 
 if "-v" in sys.argv or "--version" in sys.argv:
     # Galaxy seems to invert the order of the two lines
-    print("BAM coverage statistics v0.0.5")
+    print("BAM coverage statistics v0.0.6")
     cmd = "samtools 2>&1 | grep -i ^Version"
     sys.exit(os.system(cmd))
 
@@ -85,6 +85,7 @@
 def samtools_depth_opt_available():
     """Determine if samtools depth supports maximum coverage argument."""
     child = subprocess.Popen(["samtools", "depth"],
+                             universal_newlines=True,
                              stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
     # Combined stdout/stderr in case samtools is ever inconsistent
     output, tmp = child.communicate()
diff -r f27732bbfafa -r 86455d19abb8 tools/coverage_stats/coverage_stats.xml
--- a/tools/coverage_stats/coverage_stats.xml	Fri May 19 06:19:37 2017 -0400
+++ b/tools/coverage_stats/coverage_stats.xml	Tue Jun 06 10:18:36 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="coverage_stats" name="BAM coverage statistics" version="0.0.5">
+<tool id="coverage_stats" name="BAM coverage statistics" version="0.0.6">
     <description>using samtools idxstats and depth</description>
     <requirements>
         <requirement type="package" version="1.4.1">samtools</requirement>