bwam in cluster.yaml set to 23h, detect_region_to_exclude modified

cluster.yaml

@@ -50,6 +50,9 @@ bed2fasta:
   mem: 16
   h_vmem: 16
 
+bwamap:
+  time: "36:00:00"	
+
 markduplicates:
   mem: 32
   h_vmem: 32

snakecnv/bin/detect_regions_to_exclude.py

@@ -95,8 +95,8 @@ def dump_overcovered_to_bed(overcovered_regions, fout, window_size):
     for chrom, pos in zip(overcovered_regions.chrom,
                           overcovered_regions.pos):
         fout.write("%s\t%d\t%d\n" % (chrom.decode("utf-8"),
-                                     pos - int(window_size/2),
-                                     pos + int(window_size/2)))
+                                     max(0, pos - int(window_size/2) - 200),
+                                     pos + int(window_size/2) + 200))
 
 
 def dump_illcovered_to_bed(overcovered_regions, fout, window_size):