add get_blocks to Alignment

Victorian-Bioinformatics-Consortium · May 7, 2020 · 2a9b6fa · 2a9b6fa
1 parent fc6cc73
commit 2a9b6fa
Showing 1 changed file with 16 additions and 0 deletions.
diff --git a/nesoni/sam.py b/nesoni/sam.py
@@ -174,6 +174,22 @@ def next_reference_name(self): return self.mrnm
     @property
     def next_reference_start(self): return self.mpos
 
+    def get_blocks(self):
+        pos = self.reference_start
+
+        blocks = [ ]
+        n = 0
+        for char in self.cigar:
+            if '0' <= char <= '9':
+                n = n*10+(ord(char)-48)
+            else:
+                if char == 'M':
+                    blocks.append((pos,pos+n))
+                if char in ('M','D','N','P','=','X'): #'MDNP=X':
+                    pos += n
+                n = 0
+
+        return blocks