X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=faidx.c;h=fd0389393d8208098a5a6ace60047b1202f37509;hb=80658e4d152b53bd55927c432ceece7702ab49d7;hp=38292a13d73f33e75b12ad02baa3af2f66242bab;hpb=c350a570e955d5b4c2c13f607b7442df6d332c67;p=samtools.git

diff --git a/faidx.c b/faidx.c
index 38292a1..fd03893 100644
--- a/faidx.c
+++ b/faidx.c
@@ -305,8 +305,8 @@ faidx_t *fai_load(const char *fn)
 
 char *fai_fetch(const faidx_t *fai, const char *str, int *len)
 {
-	char *s, *p, c;
-	int i, l, k;
+	char *s, c;
+	int i, l, k, name_end;
 	khiter_t iter;
 	faidx1_t val;
 	khash_t(s) *h;
@@ -314,31 +314,43 @@ char *fai_fetch(const faidx_t *fai, const char *str, int *len)
 
 	beg = end = -1;
 	h = fai->hash;
-	l = strlen(str);
-	p = s = (char*)malloc(l+1);
-	/* squeeze out "," */
-	for (i = k = 0; i != l; ++i)
-		if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i];
-	s[k] = 0;
-	for (i = 0; i != k; ++i) if (s[i] == ':') break;
-	s[i] = 0;
-	iter = kh_get(s, h, s); /* get the ref_id */
-	if (iter == kh_end(h)) {
-		*len = 0;
-		free(s); return 0;
-	}
+	name_end = l = strlen(str);
+	s = (char*)malloc(l+1);
+	// remove space
+	for (i = k = 0; i < l; ++i)
+		if (!isspace(str[i])) s[k++] = str[i];
+	s[k] = 0; l = k;
+	// determine the sequence name
+	for (i = l - 1; i >= 0; --i) if (s[i] == ':') break; // look for colon from the end
+	if (i >= 0) name_end = i;
+	if (name_end < l) { // check if this is really the end
+		int n_hyphen = 0;
+		for (i = name_end + 1; i < l; ++i) {
+			if (s[i] == '-') ++n_hyphen;
+			else if (!isdigit(s[i]) && s[i] != ',') break;
+		}
+		if (i < l || n_hyphen > 1) name_end = l; // malformated region string; then take str as the name
+		s[name_end] = 0;
+		iter = kh_get(s, h, s);
+		if (iter == kh_end(h)) { // cannot find the sequence name
+			iter = kh_get(s, h, str); // try str as the name
+			if (iter == kh_end(h)) {
+				*len = 0;
+			free(s); return 0;
+			} else s[name_end] = ':', name_end = l;
+		}
+	} else iter = kh_get(s, h, str);
 	val = kh_value(h, iter);
-	if (i == k) { /* dump the whole sequence */
-		beg = 0; end = val.len;
-	} else {
-		for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
-		beg = atoi(p);
-		if (i < k) {
-			p = s + i + 1;
-			end = atoi(p);
-		} else end = val.len;
-	}
-	if (beg > 0) --beg;
+	// parse the interval
+	if (name_end < l) {
+		for (i = k = name_end + 1; i < l; ++i)
+			if (s[i] != ',') s[k++] = s[i];
+		s[k] = 0;
+		beg = atoi(s + name_end + 1);
+		for (i = name_end + 1; i != k; ++i) if (s[i] == '-') break;
+		end = i < k? atoi(s + i + 1) : val.len;
+		if (beg > 0) --beg;
+	} else beg = 0, end = val.len;
 	if (beg >= val.len) beg = val.len;
 	if (end >= val.len) end = val.len;
 	if (beg > end) beg = end;