[med-svn] [subread] 01/03: Imported Upstream version 1.4.6-p4+dfsg

[Alex Mestiashvili]

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malex-guest pushed a commit to branch master
in repository subread.

commit 91f65e51ae9b406db5a055ebaffe4f9ef63fe411
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Mon Jul 6 15:39:32 2015 +0200

    Imported Upstream version 1.4.6-p4+dfsg
---
 src/makefile.version |  2 +-
 src/readSummary.c    | 10 +++++++---
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/src/makefile.version b/src/makefile.version
index 296e933..5bcf28f 100644
--- a/src/makefile.version
+++ b/src/makefile.version
@@ -1,3 +1,3 @@
-SUBREAD_VERSION="1.4.6-p3"
+SUBREAD_VERSION="1.4.6-p4"
 STATIC_MAKE=
 #STATIC_MAKE= -static
diff --git a/src/readSummary.c b/src/readSummary.c
index 72812ed..25625f9 100644
--- a/src/readSummary.c
+++ b/src/readSummary.c
@@ -1382,8 +1382,12 @@ void process_line_buffer(fc_thread_global_context_t * global_context, fc_thread_
 		}
 
 		int is_this_negative_strand = (alignment_masks & SAM_FLAG_REVERSE_STRAND_MATCHED)?1:0; 
-		int is_second_read_in_pair = alignment_masks & SAM_FLAG_SECOND_READ_IN_PAIR;
-		int is_fragment_negative_strand = is_second_read_in_pair?(!is_this_negative_strand):is_this_negative_strand;
+		int is_fragment_negative_strand = is_this_negative_strand;
+
+		if( global_context -> is_paired_end_mode_assign ){
+			int is_second_read_in_pair = alignment_masks & SAM_FLAG_SECOND_READ_IN_PAIR;
+			is_fragment_negative_strand = is_second_read_in_pair?(!is_this_negative_strand):is_this_negative_strand;
+		}
 
 		fc_chromosome_index_info * this_chro_info = HashTableGet(global_context -> exontable_chro_table, read_chr);
 		if(this_chro_info == NULL)
@@ -3066,7 +3070,7 @@ int readSummary(int argc,char *argv[]){
 
 	sort_feature_info(&global_context, nexons, loaded_features, &chr, &geneid, &start, &stop, &sorted_strand, &anno_chr_2ch, &anno_chrs, &anno_chr_head, & block_end_index, & block_min_start, & block_max_end);
 	print_in_box(80,0,0,"   Meta-features : %d", global_context . gene_name_table -> numOfElements);
-	print_in_box(80,0,0,"   Chromosomes : %d", global_context . exontable_nchrs);
+	print_in_box(80,0,0,"   Chromosomes/contigs : %d", global_context . exontable_nchrs);
 
 	print_in_box(80,0,0,"");
 

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