# HG changeset patch
# User brasset_jensen
# Date 1529267998 14400
# Node ID 82779d2aacdd0a691d1940fa510d62aa9df928e2
# Parent  360ec0ae04c9b395e0edfe6386d37300cf761b3c
Uploaded

diff -r 360ec0ae04c9 -r 82779d2aacdd bin/sRNAPipe.pl
--- a/bin/sRNAPipe.pl	Sun Jun 17 16:35:24 2018 -0400
+++ b/bin/sRNAPipe.pl	Sun Jun 17 16:39:58 2018 -0400
@@ -205,7 +205,7 @@
 		}
 
 		my $ex_count_file =  $type_dir.$type_prefix.'transcripts_reads_counts.txt';
-		my ( $ex_count, $ex_ref_size ) =  sam_count ( $type_sam_transcripts );
+		my ( $ex_count, $ex_ref_size ) =  sam_count_mis ( $type_sam_transcripts );
 		rpms_rpkm_te( $ex_count, $ex_ref_size, $ma, $ex_count_file, $pi, $mi, $bo );
 
 		my ( $TEs_count, $TEs_ref_size, $TEs_count_NoM, $TEs_count_M ) = sam_count_mis ( $type_sam_TEs );