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* map3 target length bug

* scoring threshold increased
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commit aaf9cc7707395848be5818fb10af0716849c59c1 1 parent 2c7e54b
iontorrent-dev authored May 16, 2011
3  src/map/tmap_map3_aux.c
@@ -347,6 +347,9 @@ tmap_map3_aux_core(tmap_seq_t *seq[2],
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                   s->seqid = seqid;
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                   s->pos = pos;
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                   s->target_len = seq_len[i]; 
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+                  if(refseq->annos[seqid].len < s->target_len) {
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+                      s->target_len = refseq->annos[seqid].len;
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+                  }
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                   s->score_subo = INT32_MIN;
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                   // map3 aux data
2  src/map/tmap_map_util.c
@@ -71,7 +71,7 @@ tmap_map_opt_init(int32_t algo_id)
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   opt->softclip_type = TMAP_MAP_UTIL_SOFT_CLIP_RIGHT;
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   opt->dup_window = 128;
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   opt->max_seed_band = 15;
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-  opt->score_thr = 1;
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+  opt->score_thr = 8;
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   opt->reads_queue_size = 262144;
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   opt->num_threads = 1;
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   opt->aln_output_mode = TMAP_MAP_UTIL_ALN_MODE_RAND_BEST;

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