--- a/test-data/samtools_flagstat_out1.txt	Thu Mar 27 15:23:45 2014 -0400
+++ b/test-data/samtools_flagstat_out1.txt	Tue Apr 21 15:56:53 2015 -0400
@@ -1,11 +1,13 @@
-10 + 0 in total (QC-passed reads + QC-failed reads)
+200 + 0 in total (QC-passed reads + QC-failed reads)
+0 + 0 secondary
+0 + 0 supplementary
 0 + 0 duplicates
-10 + 0 mapped (100.00%:nan%)
-0 + 0 paired in sequencing
-0 + 0 read1
-0 + 0 read2
-0 + 0 properly paired (nan%:nan%)
+25 + 0 mapped (12.50%:nan%)
+200 + 0 paired in sequencing
+100 + 0 read1
+100 + 0 read2
+0 + 0 properly paired (0.00%:nan%)
 0 + 0 with itself and mate mapped
-0 + 0 singletons (nan%:nan%)
+25 + 0 singletons (12.50%:nan%)
 0 + 0 with mate mapped to a different chr
 0 + 0 with mate mapped to a different chr (mapQ>=5)