diff multicov.py @ 6:7c4feda2d9c7 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"

--- a/multicov.py	Sat Jun 02 07:10:17 2018 -0400
+++ b/multicov.py	Tue Jan 07 06:08:56 2020 -0500
@@ -26,9 +26,9 @@
         chr = fields[0]
         start = fields[1]
         end = fields[2]
-        coverage = bam_object.count_coverage(reference=chr,
+        coverage = bam_object.count_coverage(contig=chr,
                                              start=int(start)-1,
-                                             end=int(end),
+                                             stop=int(end),
                                              quality_threshold=quality)
         """ Add the 4 coverage values """
         coverage = [sum(x) for x in zip(*coverage)]