Imported Upstream version 1.4.6-p4+dfsg

parent 00a94add
SUBREAD_VERSION="1.4.6-p3"
SUBREAD_VERSION="1.4.6-p4"
STATIC_MAKE=
#STATIC_MAKE= -static
......@@ -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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