# HG changeset patch
# User peterjc
# Date 1541778410 18000
# Node ID 4554d79f238b263128a5a50c367db8ab4ad04ce4
# Parent  2429bebcab1399534a8a86765ed66b27bae35dd8
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants commit 3ab3d1a9650dec0533344d710ceb027e482d2b10-dirty

diff -r 2429bebcab13 -r 4554d79f238b tools/count_roi_variants/count_roi_variants.py
--- a/tools/count_roi_variants/count_roi_variants.py	Tue Jun 06 10:17:51 2017 -0400
+++ b/tools/count_roi_variants/count_roi_variants.py	Fri Nov 09 10:46:50 2018 -0500
@@ -85,7 +85,7 @@
 
 
 def decode_cigar(cigar):
-    """Returns a list of 2-tuples, integer count and operator char."""
+    """Return a list of 2-tuples, integer count and operator char."""
     count = ""
     answer = []
     for letter in cigar:
@@ -105,12 +105,12 @@
 
 
 def align_len(cigar_ops):
-    """Sums the CIGAR M/=/X/D/N operators."""
+    """Sum the CIGAR M/=/X/D/N operators."""
     return sum(count for count, op in cigar_ops if op in "M=XDN")
 
 
 def expand_cigar(seq, cigar_ops):
-    """Yields (ref_offset, seq_base) pairs."""
+    """Yield (ref_offset, seq_base) pairs."""
     ref_offset = 0
     seq_offset = 0
     for count, op in cigar_ops:
diff -r 2429bebcab13 -r 4554d79f238b tools/count_roi_variants/count_roi_variants.xml
--- a/tools/count_roi_variants/count_roi_variants.xml	Tue Jun 06 10:17:51 2017 -0400
+++ b/tools/count_roi_variants/count_roi_variants.xml	Fri Nov 09 10:46:50 2018 -0500
@@ -96,7 +96,7 @@
 
 Heng Li et al (2009). The Sequence Alignment/Map format and SAMtools.
 Bioinformatics 25(16), 2078-9.
-http://dx.doi.org/10.1093/bioinformatics/btp352
+https://doi.org/10.1093/bioinformatics/btp352
 
 Peter J.A. Cock (2016), Count sequence variants in region of interest in BAM file.
 http://toolshed.g2.bx.psu.edu/view/peterjc/count_roi_variants