macs-1.4-fix-parser.patch

Downloaded from http://ashishagarwal.org/2011/03/26/macs14-patch/.
This patch corrects a problem with the parser when many of the initial
reads in an input SAM file are unaligned.

This patch has not been accepted upstream yet, but a bug report has
been opened: https://github.com/taoliu/MACS/issues/82

--- a/lib/IO/Parser.py	2011-02-14 15:50:12.000000000 -0500
+++ b/lib/IO/Parser.py	2011-03-26 14:50:29.000000000 -0400
@@ -641,11 +641,13 @@
         s = 0
         n = 0
         m = 0
-        while n<10 and m<1000:
+        c = 1000
+        while n<10 and m<c:
             m += 1
             thisline = self.fhd.readline()
             (chromosome,fpos,strand) = self.__fw_parse_line(thisline)
             if not fpos or not chromosome:
+                if c - m < 10: c += 1000
                 continue
             thisline = thisline.rstrip()
             thisfields = thisline.split("\t")