From 07921659cf28db08961545351ba188287c40c2b4 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Tue, 5 Mar 2013 09:38:12 -0500
Subject: [PATCH] move mem_fill_scmat() to bwa.{h,c}

---
 bwa.c     | 11 +++++++++++
 bwa.h     |  1 +
 bwamem.c  | 13 +------------
 fastmap.c |  2 +-
 4 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/bwa.c b/bwa.c
index beea6d1..76b54ae 100644
--- a/bwa.c
+++ b/bwa.c
@@ -69,6 +69,17 @@ bseq1_t *bseq_read(int chunk_size, int *n_, void *ks1_, void *ks2_)
  * CIGAR related *
  *****************/
 
+void bwa_fill_scmat(int a, int b, int8_t mat[25])
+{
+	int i, j, k;
+	for (i = k = 0; i < 4; ++i) {
+		for (j = 0; j < 4; ++j)
+			mat[k++] = i == j? a : -b;
+		mat[k++] = 0; // ambiguous base
+	}
+	for (j = 0; j < 5; ++j) mat[k++] = 0;
+}
+
 // Generate CIGAR when the alignment end points are known
 uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM)
 {
diff --git a/bwa.h b/bwa.h
index 81d40e0..9d5b2aa 100644
--- a/bwa.h
+++ b/bwa.h
@@ -30,6 +30,7 @@ extern "C" {
 
 	bseq1_t *bseq_read(int chunk_size, int *n_, void *ks1_, void *ks2_);
 
+	void bwa_fill_scmat(int a, int b, int8_t mat[25]);
 	uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM);
 	int bwa_fix_xref(const int8_t mat[25], int q, int r, int w, const bntseq_t *bns, const uint8_t *pac, uint8_t *query, int *qb, int *qe, int64_t *rb, int64_t *re);
 
diff --git a/bwamem.c b/bwamem.c
index a6897ba..cd3a1f5 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -58,21 +58,10 @@ mem_opt_t *mem_opt_init()
 	o->chunk_size = 10000000;
 	o->n_threads = 1;
 	o->max_matesw = 100;
-	mem_fill_scmat(o->a, o->b, o->mat);
+	bwa_fill_scmat(o->a, o->b, o->mat);
 	return o;
 }
 
-void mem_fill_scmat(int a, int b, int8_t mat[25])
-{
-	int i, j, k;
-	for (i = k = 0; i < 4; ++i) {
-		for (j = 0; j < 4; ++j)
-			mat[k++] = i == j? a : -b;
-		mat[k++] = 0; // ambiguous base
-	}
-	for (j = 0; j < 5; ++j) mat[k++] = 0;
-}
-
 /***************************
  * SMEM iterator interface *
  ***************************/
diff --git a/fastmap.c b/fastmap.c
index 40c3a02..d4e5626 100644
--- a/fastmap.c
+++ b/fastmap.c
@@ -84,7 +84,7 @@ int main_mem(int argc, char *argv[])
 		return 1;
 	}
 
-	mem_fill_scmat(opt->a, opt->b, opt->mat);
+	bwa_fill_scmat(opt->a, opt->b, opt->mat);
 	if ((idx = bwa_idx_load(argv[optind], BWA_IDX_ALL)) == 0) return 1; // FIXME: memory leak
 	bwa_print_sam_hdr(idx->bns, rg_line);