diff --git a/setup.py b/setup.py
index 7653dbe..154301f 100644
--- a/setup.py
+++ b/setup.py
@@ -20,7 +20,7 @@
 
 setup(
     name = 'tiddit',
-    version = '3.4.0',
+    version = '3.5.0',
 
     url = "https://github.com/SciLifeLab/TIDDIT",
     author = "Jesper Eisfeldt",
diff --git a/tiddit/__main__.py b/tiddit/__main__.py
index e1d398e..f3276ac 100644
--- a/tiddit/__main__.py
+++ b/tiddit/__main__.py
@@ -17,7 +17,7 @@
 import tiddit.tiddit_contig_analysis as tiddit_contig_analysis
 
 def main():
-	version="3.4.0"
+	version="3.5.0"
 	parser = argparse.ArgumentParser("""tiddit-{}""".format(version),add_help=False)
 	parser.add_argument("--sv"	 , help="call structural variation", required=False, action="store_true")
 	parser.add_argument("--cov"        , help="generate a coverage bed file", required=False, action="store_true")
diff --git a/tiddit/tiddit_coverage_analysis.pyx b/tiddit/tiddit_coverage_analysis.pyx
index ddd3b07..afb51c8 100644
--- a/tiddit/tiddit_coverage_analysis.pyx
+++ b/tiddit/tiddit_coverage_analysis.pyx
@@ -1,4 +1,5 @@
 import numpy
+import re
 cimport numpy
 import pysam
 import gzip
@@ -19,7 +20,9 @@ def get_gc(str reference_fasta,bam_header,bin_size):
 		with gzip.open(reference_fasta, 'r') as f:
 			sequence=f.read()
 
-	split_reference=sequence.split(">")
+
+	#split_reference=sequence.split(">")
+	split_reference=re.split("\n>|^>", sequence)
 	del sequence
 	del split_reference[0]