X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=tabix.git;a=blobdiff_plain;f=index.c;h=cfb2938ee4ee9d490cd70f5635608b8f21abe291;hp=704b037d2add76bf0c9d02624c3f449ac2bd314b;hb=c70c92b7a385548d8e670638a93a083401f49e4d;hpb=7f5c10e58cb433a02137112209d408ecb9e65751

diff --git a/index.c b/index.c
index 704b037..cfb2938 100644
--- a/index.c
+++ b/index.c
@@ -1,5 +1,6 @@
 #include <ctype.h>
 #include <assert.h>
+#include <sys/stat.h>
 #include "khash.h"
 #include "ksort.h"
 #include "kstring.h"
@@ -161,6 +162,9 @@ static int get_intv(ti_index_t *idx, kstring_t *str, ti_intv_t *intv)
 				// here ->beg is 0-based.
 				intv->beg = intv->end = strtol(str->s + b, &s, 0);
 				if (!(idx->conf.preset&TI_FLAG_UCSC)) --intv->beg;
+				else ++intv->end;
+				if (intv->beg < 0) intv->beg = 0;
+				if (intv->end < 1) intv->end = 1;
 			} else {
 				if ((idx->conf.preset&0xffff) == TI_PRESET_GENERIC) {
 					if (id == idx->conf.ec) intv->end = strtol(str->s + b, &s, 0);
@@ -174,6 +178,7 @@ static int get_intv(ti_index_t *idx, kstring_t *str, ti_intv_t *intv)
 							if (op == 'M' || op == 'D' || op == 'N') l += x;
 							s = t + 1;
 						}
+						if (l == 0) l = 1;
 						intv->end = intv->beg + l;
 					}
 				} else if ((idx->conf.preset&0xffff) == TI_PRESET_VCF) {
@@ -262,6 +267,17 @@ static void merge_chunks(ti_index_t *idx)
 	} // ~for(i)
 }
 
+static void fill_missing(ti_index_t *idx)
+{
+	int i, j;
+	for (i = 0; i < idx->n; ++i) {
+		ti_lidx_t *idx2 = &idx->index2[i];
+		for (j = 1; j < idx2->n; ++j)
+			if (idx2->offset[j] == 0)
+				idx2->offset[j] = idx2->offset[j-1];
+	}
+}
+
 ti_index_t *ti_index_core(BGZF *fp, const ti_conf_t *conf)
 {
 	int ret;
@@ -316,6 +332,7 @@ ti_index_t *ti_index_core(BGZF *fp, const ti_conf_t *conf)
 	}
 	if (save_tid >= 0) insert_offset(idx->index[save_tid], save_bin, save_off, bgzf_tell(fp));
 	merge_chunks(idx);
+	fill_missing(idx);
 
 	free(str->s); free(str);
 	return idx;
@@ -523,22 +540,10 @@ static ti_index_t *ti_index_load_core(BGZF *fp)
 	return idx;
 }
 
-ti_index_t *ti_index_load_local(const char *_fn)
+ti_index_t *ti_index_load_local(const char *fnidx)
 {
 	BGZF *fp;
-	char *fnidx, *fn;
-
-	if (strstr(_fn, "ftp://") == _fn || strstr(_fn, "http://") == _fn) {
-		const char *p;
-		int l = strlen(_fn);
-		for (p = _fn + l - 1; p >= _fn; --p)
-			if (*p == '/') break;
-		fn = strdup(p + 1);
-	} else fn = strdup(_fn);
-	fnidx = (char*)calloc(strlen(fn) + 5, 1);
-	strcpy(fnidx, fn); strcat(fnidx, ".tbi");
 	fp = bgzf_open(fnidx, "r");
-	free(fnidx); free(fn);
 	if (fp) {
 		ti_index_t *idx = ti_index_load_core(fp);
 		bgzf_close(fp);
@@ -584,17 +589,53 @@ static void download_from_remote(const char *url)
 }
 #endif
 
+static char *get_local_version(const char *fn)
+{
+    struct stat sbuf;
+	char *fnidx = (char*)calloc(strlen(fn) + 5, 1);
+	strcat(strcpy(fnidx, fn), ".tbi");
+	if ((strstr(fnidx, "ftp://") == fnidx || strstr(fnidx, "http://") == fnidx)) {
+		char *p, *url;
+		int l = strlen(fnidx);
+		for (p = fnidx + l - 1; p >= fnidx; --p)
+			if (*p == '/') break;
+		url = fnidx; fnidx = strdup(p + 1);
+		if (stat(fnidx, &sbuf) == 0) {
+			free(url);
+			return fnidx;
+		}
+		fprintf(stderr, "[%s] downloading the index file...\n", __func__);
+		download_from_remote(url);
+		free(url);
+	}
+    if (stat(fnidx, &sbuf) == 0) return fnidx;
+	free(fnidx); return 0;
+}
+
+int ti_list_chromosomes(const char *fn)
+{
+	ti_index_t *idx;
+	char **names;
+	int i;
+	khint_t k;
+	idx = ti_index_load(fn);
+	names = calloc(idx->n, sizeof(void*));
+	for (k = kh_begin(idx->tname); k < kh_end(idx->tname); ++k)
+		if (kh_exist(idx->tname, k))
+			names[kh_val(idx->tname, k)] = (char*)kh_key(idx->tname, k);
+	for (i = 0; i < idx->n; ++i) printf("%s\n", names[i]);
+	free(names);
+	ti_index_destroy(idx);
+	return 0;
+}
+
 ti_index_t *ti_index_load(const char *fn)
 {
 	ti_index_t *idx;
-	idx = ti_index_load_local(fn);
-	if (idx == 0 && (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn)) {
-		char *fnidx = calloc(strlen(fn) + 5, 1);
-		strcat(strcpy(fnidx, fn), ".tbi");
-		fprintf(stderr, "[ti_index_load] attempting to download the remote index file.\n");
-		download_from_remote(fnidx);
-		idx = ti_index_load_local(fn);
-	}
+    char *fname = get_local_version(fn);
+	if (fname == 0) return 0;
+	idx = ti_index_load_local(fname);
+    free(fname);
 	if (idx == 0) fprintf(stderr, "[ti_index_load] fail to load BAM index.\n");
 	return idx;
 }
@@ -709,7 +750,8 @@ pair64_t *get_chunk_coordinates(const ti_index_t *idx, int tid, int beg, int end
 	bins = (uint16_t*)calloc(MAX_BIN, 2);
 	n_bins = reg2bins(beg, end, bins);
 	index = idx->index[tid];
-	min_off = (beg>>TAD_LIDX_SHIFT >= idx->index2[tid].n)? 0 : idx->index2[tid].offset[beg>>TAD_LIDX_SHIFT];
+	min_off = (beg>>TAD_LIDX_SHIFT >= idx->index2[tid].n)? idx->index2[tid].offset[idx->index2[tid].n-1]
+		: idx->index2[tid].offset[beg>>TAD_LIDX_SHIFT];
 	for (i = n_off = 0; i < n_bins; ++i) {
 		if ((k = kh_get(i, index, bins[i])) != kh_end(index))
 			n_off += kh_value(index, k).n;