X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=kprobaln.c;h=04e526a1c3b639f29c8265f2c3f638c2c40abcb0;hb=0ccd9d36ebf35ce620a8248ecf4336c84065e6c0;hp=5201c1af75b9c24636ee67481b0461ab7713e7a1;hpb=fe9d679264cafa551db00fe309eea2858a536ee8;p=samtools.git

diff --git a/kprobaln.c b/kprobaln.c
index 5201c1a..04e526a 100644
--- a/kprobaln.c
+++ b/kprobaln.c
@@ -77,6 +77,8 @@ int kpa_glocal(const uint8_t *_ref, int l_ref, const uint8_t *_query, int l_quer
 	const uint8_t *ref, *query;
 	int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
 
+    if ( l_ref<=0 || l_query<=0 ) return 0; // FIXME: this may not be an ideal fix, just prevents sefgault
+
 	/*** initialization ***/
 	is_backward = state && q? 1 : 0;
 	ref = _ref - 1; query = _query - 1; // change to 1-based coordinate
@@ -87,7 +89,7 @@ int kpa_glocal(const uint8_t *_ref, int l_ref, const uint8_t *_query, int l_quer
 	// allocate the forward and backward matrices f[][] and b[][] and the scaling array s[]
 	f = calloc(l_query+1, sizeof(void*));
 	if (is_backward) b = calloc(l_query+1, sizeof(void*));
-	for (i = 0; i <= l_query; ++i) {
+	for (i = 0; i <= l_query; ++i) {    // FIXME: this will lead in segfault for l_query==0
 		f[i] = calloc(bw2 * 3 + 6, sizeof(double)); // FIXME: this is over-allocated for very short seqs
 		if (is_backward) b[i] = calloc(bw2 * 3 + 6, sizeof(double));
 	}
@@ -161,7 +163,7 @@ int kpa_glocal(const uint8_t *_ref, int l_ref, const uint8_t *_query, int l_quer
 		double p = 1., Pr1 = 0.;
 		for (i = 0; i <= l_query + 1; ++i) {
 			p *= s[i];
-			if (p < 1e-100) Pr += -4.343 * log(p), p = 1.;
+			if (p < 1e-100) Pr1 += -4.343 * log(p), p = 1.;
 		}
 		Pr1 += -4.343 * log(p * l_ref * l_query);
 		Pr = (int)(Pr1 + .499);