X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Fbam_aux.c.pysam.c;h=a1c1890e26eb85ebb2f3b53bb554aa64119a4652;hp=14209cd831d0268150e5e6a62052ae264e9a3939;hb=e1756c41e7a1d7cc01fb95e42df9dd04da2d2991;hpb=ca46ef4ba4a883c57cea62d5bf1bc021f1185109

diff --git a/samtools/bam_aux.c.pysam.c b/samtools/bam_aux.c.pysam.c
index 14209cd..a1c1890 100644
--- a/samtools/bam_aux.c.pysam.c
+++ b/samtools/bam_aux.c.pysam.c
@@ -61,23 +61,6 @@ int bam_aux_del(bam1_t *b, uint8_t *s)
 	return 0;
 }
 
-int bam_aux_drop_other(bam1_t *b, uint8_t *s)
-{
-	if (s) {
-		uint8_t *p, *aux;
-		aux = bam1_aux(b);
-		p = s - 2;
-		__skip_tag(s);
-		memmove(aux, p, s - p);
-		b->data_len -= b->l_aux - (s - p);
-		b->l_aux = s - p;
-	} else {
-		b->data_len -= b->l_aux;
-		b->l_aux = 0;
-	}
-	return 0;
-}
-
 void bam_init_header_hash(bam_header_t *header)
 {
 	if (header->hash == 0) {
@@ -106,56 +89,47 @@ int32_t bam_get_tid(const bam_header_t *header, const char *seq_name)
 	return k == kh_end(h)? -1 : kh_value(h, k);
 }
 
-int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *beg, int *end)
+int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end)
 {
-	char *s;
-	int i, l, k, name_end;
+	char *s, *p;
+	int i, l, k;
 	khiter_t iter;
 	khash_t(s) *h;
 
 	bam_init_header_hash(header);
 	h = (khash_t(s)*)header->hash;
 
-	*ref_id = *beg = *end = -1;
-	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)) {
-				if (bam_verbose >= 2) fprintf(pysamerr, "[%s] fail to determine the sequence name.\n", __func__);
-				free(s); return -1;
-			} else s[name_end] = ':', name_end = l;
-		}
-	} else iter = kh_get(s, h, str);
-	*ref_id = kh_val(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) : 1<<29;
-		if (*beg > 0) --*beg;
-	} else *beg = 0, *end = 1<<29;
+	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)) { // name not found
+		*ref_id = -1; free(s);
+		return -1;
+	}
+	*ref_id = kh_value(h, iter);
+	if (i == k) { /* dump the whole sequence */
+		*begin = 0; *end = 1<<29; free(s);
+		return 0;
+	}
+	for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
+	*begin = atoi(p);
+	if (i < k) {
+		p = s + i + 1;
+		*end = atoi(p);
+	} else *end = 1<<29;
+	if (*begin > 0) --*begin;
 	free(s);
-	return *beg <= *end? 0 : -1;
+	if (*begin > *end) {
+		fprintf(pysamerr, "[bam_parse_region] invalid region.\n");
+		return -1;
+	}
+	return 0;
 }
 
 int32_t bam_aux2i(const uint8_t *s)