From 2a9b6faf0685cd0a2fa6488db291b4c0d30b3978 Mon Sep 17 00:00:00 2001
From: Paul Harrison <paul.harrison@monash.edu>
Date: Thu, 7 May 2020 20:43:36 +1000
Subject: [PATCH] add get_blocks to Alignment

---
 nesoni/sam.py | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/nesoni/sam.py b/nesoni/sam.py
index d3c30ee..012fdde 100644
--- 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