From d25a87cc500b4cb654a3299818ce6982f6667ed2 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Sat, 2 Feb 2013 15:14:24 -0500
Subject: [PATCH] code backup

---
 bwamem.c  | 6 ++++--
 bwamem.h  | 2 +-
 fastmap.c | 2 +-
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/bwamem.c b/bwamem.c
index ef09fd5..02f9591 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -176,10 +176,10 @@ mem_chain_t mem_chain(const mem_opt_t *opt, const bwt_t *bwt, int len, const uin
 	return chain;
 }
 
-mem_aln_t mem_chain2aln(int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain1_t *c)
+mem_aln_t mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain1_t *c)
 {
 	mem_aln_t a;
-	int i, j;
+	int i, j, max, max_i;
 	int64_t len;
 	for (i = 0; i < c->n; ++i) {
 		mem_seed_t *s = &c->seeds[i];
@@ -188,5 +188,7 @@ mem_aln_t mem_chain2aln(int64_t l_pac, const uint8_t *pac, int l_query, const ui
 		for (j = 0; j < s->len; ++j) putchar("ACGTN"[query[j+s->qbeg]]); putchar('\n');
 		free(seq);
 	}
+	for (i = max = 0, max_i = -1; i < c->n; ++i) // find the longest seed
+		if (max < c->seeds[i].len) max = c->seeds[i].len, max_i = i;
 	return a;
 }
diff --git a/bwamem.h b/bwamem.h
index 0ebd2eb..214d780 100644
--- a/bwamem.h
+++ b/bwamem.h
@@ -45,7 +45,7 @@ const bwtintv_v *smem_next(smem_i *itr, int split_len);
 mem_opt_t *mem_opt_init(void);
 
 mem_chain_t mem_chain(const mem_opt_t *opt, const bwt_t *bwt, int len, const uint8_t *seq);
-mem_aln_t mem_chain2aln(int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain1_t *c);
+mem_aln_t mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain1_t *c);
 
 #ifdef __cplusplus
 }
diff --git a/fastmap.c b/fastmap.c
index d8a0eca..c92311e 100644
--- a/fastmap.c
+++ b/fastmap.c
@@ -52,7 +52,7 @@ int main_mem(int argc, char *argv[])
 		chain = mem_chain(opt, bwt, seq->seq.l, (uint8_t*)seq->seq.s);
 		for (i = 0; i < chain.n; ++i) {
 			mem_chain1_t *p = &chain.chains[i];
-			mem_chain2aln(bns->l_pac, pac, seq->seq.l, (uint8_t*)seq->seq.s, p);
+			mem_chain2aln(opt, bns->l_pac, pac, seq->seq.l, (uint8_t*)seq->seq.s, p);
 			printf("%d\t%d", i, p->n);
 			for (j = 0; j < p->n; ++j) {
 				bwtint_t pos;