X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=tabix.git;a=blobdiff_plain;f=index.c;h=8eddcecb34bab21f8d4f6de7a88639f8c67d0358;hp=e5b227c1466eea9d8be901020ffc2726dc33cc9e;hb=f14cecb6523bd4275c2858c2d54167c94db25ede;hpb=07678d3f22da823d211cb5687fe51335ed0498fd

diff --git a/index.c b/index.c
index e5b227c..8eddcec 100644
--- a/index.c
+++ b/index.c
@@ -19,7 +19,7 @@ typedef struct {
 } pair64_t;
 
 #define pair64_lt(a,b) ((a).u < (b).u)
-KSORT_INIT(off, pair64_t, pair64_lt)
+KSORT_INIT(offt, pair64_t, pair64_lt)
 
 typedef struct {
 	uint32_t m, n;
@@ -192,17 +192,19 @@ static int get_intv(ti_index_t *idx, kstring_t *str, ti_intv_t *intv)
 					}
 				} else if ((idx->conf.preset&0xffff) == TI_PRESET_VCF) {
 					// FIXME: the following is NOT tested and is likely to be buggy
-					if (id == 5) { // ALT
-						char *t;
-						int max = 1;
-						for (s = str->s + b; s < str->s + i;) {
-							if (s[i] == 'D') {
-								long x = strtol(s + 1, &t, 10);
-								if (x > max) max = x;
-								s = t + 1;
-							} else ++s;
+					if (id == 4) {
+						if (b < i) intv->end = intv->beg + (i - b);
+					} else if (id == 8) { // look for "END="
+						int c = str->s[i];
+						str->s[i] = 0;
+						s = strstr(str->s + b, "END=");
+						if (s == str->s + b) s += 4;
+						else if (s) {
+							s = strstr(str->s + b, ";END=");
+							if (s) s += 5;
 						}
-						intv->end = intv->beg + max;
+						if (s) intv->end = strtol(s, &s, 0);
+						str->s[i] = c;
 					}
 				}
 			}
@@ -804,7 +806,7 @@ ti_iter_t ti_iter_query(const ti_index_t *idx, int tid, int beg, int end)
 	free(bins);
 	{
 		int l;
-		ks_introsort(off, n_off, off);
+		ks_introsort(offt, n_off, off);
 		// resolve completely contained adjacent blocks
 		for (i = 1, l = 0; i < n_off; ++i)
 			if (off[l].v < off[i].v)