From fa20c71920458e51ee0bdaf646f6b9f1e912224c Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Thu, 1 May 2014 14:27:38 -0400
Subject: [PATCH] r742: further control the max bandwidth

I am looking at 6kb bandwidth...
---
 bwamem.c | 4 +++-
 ksw.c    | 2 +-
 main.c   | 2 +-
 3 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/bwamem.c b/bwamem.c
index 8e97747..5709586 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -381,6 +381,7 @@ int mem_patch_reg(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac,
 	} else if (w > opt->w<<2 || r >= PATCH_MAX_R_BW*2) return 0; // more permissive if overlapping on both ref and query
 	// global alignment
 	w += a->w + b->w;
+	w = w < opt->w<<2? w : opt->w<<2;
 	if (bwa_verbose >= 4) printf("* test potential hit merge with global alignment; w=%d\n", w);
 	bwa_gen_cigar2(opt->mat, opt->o_del, opt->e_del, opt->o_ins, opt->e_ins, w, bns->l_pac, pac, b->qe - a->qb, query + a->qb, a->rb, b->re, &score, 0, 0);
 	q_s = (int)((double)(b->qe - a->qb) / ((b->qe - b->qb) + (a->qe - a->qb)) * (b->score + a->score) + .499); // predicted score from query
@@ -1044,9 +1045,10 @@ mem_aln_t mem_reg2aln2(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t
 	i = 0; a.cigar = 0;
 	do {
 		free(a.cigar);
+		w2 = w2 < opt->w<<2? w2 : opt->w<<2;
 		a.cigar = bwa_gen_cigar2(opt->mat, opt->o_del, opt->e_del, opt->o_ins, opt->e_ins, w2, bns->l_pac, pac, qe - qb, (uint8_t*)&query[qb], rb, re, &score, &a.n_cigar, &NM);
 		if (bwa_verbose >= 4) printf("* Final alignment: w2=%d, global_sc=%d, local_sc=%d\n", w2, score, ar->truesc);
-		if (score == last_sc) break; // it is possible that global alignment and local alignment give different scores
+		if (score == last_sc || w2 == opt->w<<2) break; // it is possible that global alignment and local alignment give different scores
 		last_sc = score;
 		w2 <<= 1;
 	} while (++i < 3 && score < ar->truesc - opt->a);
diff --git a/ksw.c b/ksw.c
index 40e226a..808bd3f 100644
--- a/ksw.c
+++ b/ksw.c
@@ -510,7 +510,7 @@ int ksw_global2(int qlen, const uint8_t *query, int tlen, const uint8_t *target,
 	if (n_cigar_) *n_cigar_ = 0;
 	// allocate memory
 	n_col = qlen < 2*w+1? qlen : 2*w+1; // maximum #columns of the backtrack matrix
-	z = n_cigar_ && cigar_? malloc(n_col * tlen) : 0;
+	z = n_cigar_ && cigar_? malloc((long)n_col * tlen) : 0;
 	qp = malloc(qlen * m);
 	eh = calloc(qlen + 1, 8);
 	// generate the query profile
diff --git a/main.c b/main.c
index 94904fa..e902a0a 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.8-r741-dirty"
+#define PACKAGE_VERSION "0.7.8-r742-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);