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commit 91f65e51ae9b406db5a055ebaffe4f9ef63fe411 Author: Alexandre Mestiashvili <[email protected]> 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,""); -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/subread.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
