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

… raw SW score in colour space.
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1 parent 0dd10f4 commit 47e40bf78d31db44c378aa7ef033d4cb85c22def @misko misko committed Oct 31, 2011
Showing with 3 additions and 0 deletions.
  1. +3 −0 gmapper/output.c
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@@ -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);
}

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