From 4dcb6eff3431d436ee5ef6495d10e80f3864db62 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Karel=20B=C5=99inda?= <karel.brinda@gmail.com>
Date: Mon, 26 Feb 2018 17:51:58 -0500
Subject: [PATCH] Don't modify SAM headers

fixes #18
---
 samsift/samsift.py | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/samsift/samsift.py b/samsift/samsift.py
index ab505af..4fd2ee1 100755
--- a/samsift/samsift.py
+++ b/samsift/samsift.py
@@ -265,17 +265,17 @@ def run(self):
             #print("@PG", "ID:{}".format(PROGRAM), "PN:{}".format(PROGRAM), "VN:{}".format(VERSION), "CL:{}".format(" ".join(sys.argv)), sep="\t")
             header=in_sam.header
 
-            pg={
-                    "ID":PROGRAM,
-                    "PN":PROGRAM,
-                    "VN":VERSION,
-                    "CL":" ".join(map(lambda x:"'{}'".format(x),sys.argv)),
-                }
-
-            try:
-                header['PG'].insert(0,pg)
-            except KeyError:
-                header['PG']=[pg]
+            #pg={
+            #        "ID":PROGRAM,
+            #        "PN":PROGRAM,
+            #        "VN":VERSION,
+            #        "CL":" ".join(map(lambda x:"'{}'".format(x),sys.argv)),
+            #    }
+
+            #try:
+            #    header['PG'].insert(0,pg)
+            #except KeyError:
+            #    header['PG']=[pg]
 
             with pysam.AlignmentFile(self.out_sam_fn, self.pysam_out_mode, header=header) as out_sam:
                 self.out_sam=out_sam