new pipeline

Author: WangHYLab

Sam_count.py

@@ -0,0 +1,11 @@
+#/usr/bin/python
+import sys
+def count_reads(samfile_path):
+    logfile = samfile_path.replace(".sam",".log")
+    with open(logfile, 'r') as f:
+        count = f.readline().split(' ')[0]
+    print(count)
+    return int(count)
+if __name__=='__main__':
+    count_reads(sys.argv[1])
+