Now original SHRiMP format outputs the posterior score instead of the…

… raw SW score in colour space.
marta- · Oct 31, 2011 · 47e40bf · 47e40bf
1 parent 0dd10f4
commit 47e40bf
Showing 1 changed file with 3 additions and 0 deletions.
diff --git a/gmapper/output.c b/gmapper/output.c
@@ -230,6 +230,8 @@ hit_output(struct read_entry * re, struct read_hit * rh, struct read_hit * rh_mp
       char * tmp_output;
 
       if (rh != NULL) {
+	int score=rh->sfrp->score;
+	rh->sfrp->score=rh->score_full;
 	tmp_output = output_normal(re->name, contig_names[rh->cn], rh->sfrp,
 				   genome_len[rh->cn], shrimp_mode == MODE_COLOUR_SPACE, re->read[rh->st],
 				   re->read_len, re->initbp[rh->st], rh->gen_st, Rflag);
@@ -244,6 +246,7 @@ hit_output(struct read_entry * re, struct read_hit * rh, struct read_hit * rh_mp
 	  *output_buffer += snprintf(*output_buffer, output_buffer_end - *output_buffer, "%s\n", tmp_output);
 	  free(tmp_output);
 	}
+	rh->sfrp->score=score;
       } else { // this is an unmapped read (part of a pair)
 	*output_buffer += snprintf(*output_buffer, output_buffer_end - *output_buffer, ">%s\n", re->name);
       }