Imported Upstream version 0.5

[pysam.git] / samtools / bam_aux.c.pysam.c

diff --git a/samtools/bam_aux.c.pysam.c b/samtools/bam_aux.c.pysam.c
index 14209cd831d0268150e5e6a62052ae264e9a3939..a1c1890e26eb85ebb2f3b53bb554aa64119a4652 100644 (file)
--- 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)