X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Ffaidx.c.pysam.c;h=526a9c0022ff477807e6475b2910c2497f4caf36;hp=376629ead6701fc4bebdec4337c10abbed1da06b;hb=e1756c41e7a1d7cc01fb95e42df9dd04da2d2991;hpb=ca46ef4ba4a883c57cea62d5bf1bc021f1185109

diff --git a/samtools/faidx.c.pysam.c b/samtools/faidx.c.pysam.c
index 376629e..526a9c0 100644
--- a/samtools/faidx.c.pysam.c
+++ b/samtools/faidx.c.pysam.c
@@ -9,8 +9,7 @@
 #include "khash.h"
 
 typedef struct {
-	int32_t line_len, line_blen;
-	int64_t len;
+	uint64_t len:32, line_len:16, line_blen:16;
 	uint64_t offset;
 } faidx1_t;
 KHASH_MAP_INIT_STR(s, faidx1_t)
@@ -67,11 +66,10 @@ faidx_t *fai_build_core(RAZF *rz)
 {
 	char c, *name;
 	int l_name, m_name, ret;
-	int line_len, line_blen, state;
+	int len, line_len, line_blen, state;
 	int l1, l2;
 	faidx_t *idx;
 	uint64_t offset;
-	int64_t len;
 
 	idx = (faidx_t*)calloc(1, sizeof(faidx_t));
 	idx->hash = kh_init(s);
@@ -123,6 +121,11 @@ faidx_t *fai_build_core(RAZF *rz)
 				return 0;
 			}
 			++l1; len += l2;
+			if (l2 >= 0x10000) {
+				fprintf(pysamerr, "[fai_build_core] line length exceeds 65535 in sequence '%s'.\n", name);
+				free(name); fai_destroy(idx);
+				return 0;
+			}
 			if (state == 1) line_len = l1, line_blen = l2, state = 0;
 			else if (state == 0) {
 				if (l1 != line_len || l2 != line_blen) state = 2;
@@ -304,8 +307,8 @@ faidx_t *fai_load(const char *fn)
 
 char *fai_fetch(const faidx_t *fai, const char *str, int *len)
 {
-	char *s, c;
-	int i, l, k, name_end;
+	char *s, *p, c;
+	int i, l, k;
 	khiter_t iter;
 	faidx1_t val;
 	khash_t(s) *h;
@@ -313,43 +316,31 @@ char *fai_fetch(const faidx_t *fai, const char *str, int *len)
 
 	beg = end = -1;
 	h = fai->hash;
-	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);
+	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;
+	}
 	val = kh_value(h, iter);
-	// 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 (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;
 	if (beg >= val.len) beg = val.len;
 	if (end >= val.len) end = val.len;
 	if (beg > end) beg = end;