Merge pull request #689 from CGATOxford/{IS}_dos_line_ends

Strip fastq lines, rather than explicitly removing last char.

Author: IanSudbery

umi_tools/umi_methods.py

@@ -103,19 +103,19 @@ def removeReadIDSuffix(line):
             break
         if not line1.startswith('@'):
             U.error("parsing error: expected '@' in line %s" % line1)
-        line2 = convert2string(infile.readline())
-        line3 = convert2string(infile.readline())
+        line2 = convert2string(infile.readline()).rstrip()
+        line3 = convert2string(infile.readline()).rstrip()
         if not line3.startswith('+'):
             U.error("parsing error: expected '+' in line %s" % line3)
-        line4 = convert2string(infile.readline())
+        line4 = convert2string(infile.readline()).rstrip()
         # incomplete entry
         if not line4:
             U.error("incomplete entry for %s" % line1)
 
         if remove_suffix:
             line1 = removeReadIDSuffix(line1)
 
-        yield Record(line1[1:], line2[:-1], line4[:-1])
+        yield Record(line1[1:], line2, line4)
 
 # End of FastqIterate()
 ###############################################################################