sw_mat

ydLiu-HIT · Aug 20, 2020 · 733831b · 733831b
1 parent 3d281ee
commit 733831b
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Showing 3 changed files with 23 additions and 6 deletions.
diff --git a/src/aln_2pass.c b/src/aln_2pass.c
@@ -1965,10 +1965,27 @@ void align_non_splice(void *km, uint8_t *qseq, uint8_t *tseq, uint32_t qlen, uin
 	if ((int64_t)tlen * qlen > opt->max_sw_mat)
 	{
 		ksw_reset_extz(ez);
-        ez->n_cigar = 2;
-        ez->cigar[0] = qlen<<4 | 1;
-        ez->cigar[1] = tlen<<4 | 3;
-        ez->score = 0;
+
+        if(ez->m_cigar < 2)
+        {
+            ez->n_cigar = 2;
+            ez->m_cigar = (ez->n_cigar)<<2;
+            ez->cigar = (uint32_t *)krealloc(km, ez->cigar, (ez->m_cigar)<<4);
+        }
+
+        if(qlen > tlen/2)
+        {
+            ez->n_cigar = 1;
+            ez->cigar[0] = qlen<<4 | 0;
+            ez->score = qlen * opt->match_R;
+        }
+        else
+        {
+            ez->n_cigar = 2;
+            ez->cigar[0] = qlen<<4 | 1;
+            ez->cigar[1] = tlen<<4 | 3;
+            ez->score = 0;    
+        }
 	}
 	else if (type == 0) //left extend
 	{

diff --git a/src/deSALT b/src/deSALT
diff --git a/src/read_seeding.c b/src/read_seeding.c
@@ -89,8 +89,8 @@ static void init_map_param(param_map *opt)
 	opt->max_read_join_gap = 2000;
 	opt->max_intron_length = SPLICDISTANCE;
 	// opt->max_sw_mat = opt->max_read_join_gap * opt->max_intron_length;
-	// opt->max_sw_mat = 4000000000;
-	opt->max_sw_mat = 1000000000;
+	opt->max_sw_mat = 3000000000;
+	//opt->max_sw_mat = 1000000000;
 	opt->Eindel = 20;
 	opt->thread_n = 4;
 	opt->top_n = TOP_NUM_ALN; //2, 3