From 557daabf38aa226470400e6dbbf7633fc024639e Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Tue, 12 Feb 2013 17:48:46 -0500
Subject: [PATCH] bugfix: bug in the new ksw.c

On my test data, one alignment is different, caused by polyA
---
 bwtsw2_pair.c | 12 +++++++++---
 ksw.c         |  6 +++---
 2 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/bwtsw2_pair.c b/bwtsw2_pair.c
index 85ba1eb..cf29087 100644
--- a/bwtsw2_pair.c
+++ b/bwtsw2_pair.c
@@ -128,17 +128,23 @@ void bsw2_pair1(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, const b
 	}
 #ifndef _NO_SSE2
 	{ // FIXME!!! The following block has not been tested since the update of the ksw library
-		int flag = KSW_XSUBO | KSW_XSTOP | KSW_XSTART | (l_mseq * g_mat[0] < 250? KSW_XBYTE : 0);
+		int flag = KSW_XSUBO | KSW_XSTART | (l_mseq * g_mat[0] < 250? KSW_XBYTE : 0) | opt->t;
 		kswr_t aln;
 		aln = ksw_align(l_mseq, seq, end - beg, ref, 5, g_mat, opt->q, opt->r, flag, 0);
 		a->G = aln.score;
 		a->G2 = aln.score2;
+		if (a->G < opt->t) a->G = 0;
 		if (a->G2 < opt->t) a->G2 = 0;
 		if (a->G2) a->flag |= BSW2_FLAG_TANDEM;
 		a->k = beg + aln.tb;
-		a->len = aln.te - aln.tb;
+		a->len = aln.te - aln.tb + 1;
 		a->beg = aln.qb;
-		a->end = aln.qe;
+		a->end = aln.qe + 1;
+		/*
+		printf("[Q] "); for (i = 0; i < l_mseq; ++i) putchar("ACGTN"[(int)seq[i]]); putchar('\n');
+		printf("[R] "); for (i = 0; i < end - beg; ++i) putchar("ACGTN"[(int)ref[i]]); putchar('\n');
+		printf("G=%d,G2=%d,beg=%d,end=%d,k=%lld,len=%d\n", a->G, a->G2, a->beg, a->end, a->k, a->len);
+		*/
 	}
 #else
 	{
diff --git a/ksw.c b/ksw.c
index 4599c6b..8d741a6 100644
--- a/ksw.c
+++ b/ksw.c
@@ -211,7 +211,7 @@ end_loop16:
 			low = te - i; high = te + i;
 			for (i = 0; i < n_b; ++i) {
 				int e = (int32_t)b[i];
-				if ((e < low || e > high) && b[i]>>32 > (uint32_t)r.score2)
+				if ((e < low || e > high) && (int)(b[i]>>32) > r.score2)
 					r.score2 = b[i]>>32, r.te2 = e;
 			}
 		}
@@ -311,7 +311,7 @@ end_loop8:
 			low = te - i; high = te + i;
 			for (i = 0; i < n_b; ++i) {
 				int e = (int32_t)b[i];
-				if ((e < low || e > high) && b[i]>>32 > (uint32_t)r.score2)
+				if ((e < low || e > high) && (int)(b[i]>>32) > r.score2)
 					r.score2 = b[i]>>32, r.te2 = e;
 			}
 		}
@@ -587,7 +587,7 @@ int main(int argc, char *argv[])
 		return 1;
 	}
 	if (minsc > 0xffff) minsc = 0xffff;
-	if (minsc > 0) xtra |= KSW_XSUBO | minsc;
+	xtra |= KSW_XSUBO | minsc;
 	// initialize scoring matrix
 	for (i = k = 0; i < 4; ++i) {
 		for (j = 0; j < 4; ++j)