# HG changeset patch
# User peterjc
# Date 1496758671 14400
# Node ID 2429bebcab1399534a8a86765ed66b27bae35dd8
# Parent  cc86a2b3dc8e88649c9a14cc3bef62dfb320b718
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants commit 79bbb921cb5aa953f0323accd6c8c293c6e486cf-dirty

diff -r cc86a2b3dc8e -r 2429bebcab13 tools/count_roi_variants/README.rst
--- a/tools/count_roi_variants/README.rst	Fri May 19 06:19:10 2017 -0400
+++ b/tools/count_roi_variants/README.rst	Tue Jun 06 10:17:51 2017 -0400
@@ -83,6 +83,7 @@
 v0.0.5  - Fix samtools dependency version inconsistency, using v1.2 now.
         - 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 cc86a2b3dc8e -r 2429bebcab13 tools/count_roi_variants/count_roi_variants.py
--- a/tools/count_roi_variants/count_roi_variants.py	Fri May 19 06:19:10 2017 -0400
+++ b/tools/count_roi_variants/count_roi_variants.py	Tue Jun 06 10:17:51 2017 -0400
@@ -20,7 +20,7 @@
 
 if "-v" in sys.argv or "--version" in sys.argv:
     # Galaxy seems to invert the order of the two lines
-    print("BAM coverage statistics v0.0.4 (using samtools)")
+    print("BAM coverage statistics v0.0.6 (using samtools)")
     cmd = "samtools 2>&1 | grep -i ^Version"
     sys.exit(os.system(cmd))
 
@@ -219,6 +219,7 @@
     # Call samtools view, don't need header so no -h added.
     # Only want mapped reads, thus flag filter -F 4.
     child = subprocess.Popen(["samtools", "view", "-F", "4", bam_file, region],
+                             universal_newlines=True,
                              stdout=subprocess.PIPE, stderr=subprocess.PIPE)
     for line in child.stdout:
         assert line[0] != "@", "Got unexpected SAM header line: %s" % line
diff -r cc86a2b3dc8e -r 2429bebcab13 tools/count_roi_variants/count_roi_variants.xml
--- a/tools/count_roi_variants/count_roi_variants.xml	Fri May 19 06:19:10 2017 -0400
+++ b/tools/count_roi_variants/count_roi_variants.xml	Tue Jun 06 10:17:51 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="count_roi_variants" name="Count sequence variants in region of interest" version="0.0.5">
+<tool id="count_roi_variants" name="Count sequence variants in region of interest" version="0.0.6">
     <description>using samtools view</description>
     <requirements>
         <requirement type="package" version="1.2">samtools</requirement>