convert to 0-based coordinates for pysam compatability

Victorian-Bioinformatics-Consortium · Oct 14, 2016 · ee7ab3e · ee7ab3e
1 parent 25db38e
commit ee7ab3e
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/nesoni/peaks.py b/nesoni/peaks.py
@@ -476,6 +476,7 @@ def consider(start,end):
 
         return result
 
+
 @config.help(
     'Call peaks that are higher than everything within "radius", '
     'and higher than some minimum depth.\n'

diff --git a/nesoni/sam.py b/nesoni/sam.py
@@ -163,10 +163,10 @@ def query_name(self): return self.qname
     def reference_name(self): return self.rname
 
     @property
-    def reference_start(self): return self.pos
+    def reference_start(self): return self.pos-1
 
     @property
-    def reference_end(self): return self.pos+get_length(self.cigar)
+    def reference_end(self): return self.pos-1+get_length(self.cigar)
 
     @property
     def next_reference_name(self): return self.mrnm