X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=tabix.git;a=blobdiff_plain;f=main.c;h=a2a456566fb9f9a68e3692827cc8fd99943f3f2c;hp=a2271929838803f8b53be6ba54131df9f7ae7141;hb=36e5c2e93cc97d22f8b33768602d511697fa1adf;hpb=0a3bf89715283e4d322d28ba4147e987e3477ee3

diff --git a/main.c b/main.c
index a227192..a2a4565 100644
--- a/main.c
+++ b/main.c
@@ -2,22 +2,17 @@
 #include <unistd.h>
 #include <stdlib.h>
 #include <stdio.h>
+#include <sys/stat.h>
 #include "bgzf.h"
 #include "tabix.h"
 
-#define PACKAGE_VERSION "0.1.2 (r543)"
-
-static int fetch_func(int l, const char *s, void *data)
-{
-	printf("%s\n", s);
-	return 0;
-}
+#define PACKAGE_VERSION "0.1.6 (r565)"
 
 int main(int argc, char *argv[])
 {
-	int c, skip = -1, meta = -1;
+	int c, skip = -1, meta = -1, list_chrms = 0, force = 0;
 	ti_conf_t conf = ti_conf_gff;
-	while ((c = getopt(argc, argv, "p:s:b:e:0S:c:")) >= 0) {
+	while ((c = getopt(argc, argv, "p:s:b:e:0S:c:lf")) >= 0) {
 		switch (c) {
 		case '0': conf.preset |= TI_FLAG_UCSC; break;
 		case 'S': skip = atoi(optarg); break;
@@ -36,6 +31,8 @@ int main(int argc, char *argv[])
 		case 's': conf.sc = atoi(optarg); break;
 		case 'b': conf.bc = atoi(optarg); break;
 		case 'e': conf.ec = atoi(optarg); break;
+        case 'l': list_chrms = 1; break;
+		case 'f': force = 1; break;
 		}
 	}
 	if (skip >= 0) conf.line_skip = skip;
@@ -52,43 +49,73 @@ int main(int argc, char *argv[])
 		fprintf(stderr, "         -S INT     skip first INT lines [0]\n");
 		fprintf(stderr, "         -c CHAR    symbol for comment/meta lines [#]\n");
 		fprintf(stderr, "         -0         zero-based coordinate\n");
+		fprintf(stderr, "         -l         list chromosome names\n");
+		fprintf(stderr, "         -f         force to overwrite the index\n");
 		fprintf(stderr, "\n");
 		return 1;
 	}
-	if (optind + 1 == argc)
+    if (list_chrms) {
+		ti_index_t *idx;
+		int i, n;
+		const char **names;
+		idx = ti_index_load(argv[optind]);
+		if (idx == 0) {
+			fprintf(stderr, "[main] fail to load the index file.\n");
+			return 1;
+		}
+		names = ti_seqname(idx, &n);
+		for (i = 0; i < n; ++i) printf("%s\n", names[i]);
+		free(names);
+		ti_index_destroy(idx);
+		return 0;
+	}
+	if (optind + 1 == argc) {
+		if (force == 0) {
+			struct stat buf;
+			char *fnidx = calloc(strlen(argv[optind]) + 5, 1);
+			strcat(strcpy(fnidx, argv[optind]), ".tbi");
+			if (stat(fnidx, &buf) == 0) {
+				fprintf(stderr, "[tabix] the index file exists. Please use '-f' to overwrite.\n");
+				free(fnidx);
+				return 1;
+			}
+			free(fnidx);
+		}
 		return ti_index_build(argv[optind], &conf);
+	}
 	{ // retrieve
-		BGZF *fp;
-		fp = bgzf_open(argv[optind], "r");
-		if (fp == 0) {
+		tabix_t *t;
+		if ((t = ti_open(argv[optind], 0)) == 0) {
 			fprintf(stderr, "[main] fail to open the data file.\n");
 			return 1;
 		}
 		if (strcmp(argv[optind+1], ".") == 0) { // retrieve all
-			kstring_t *str = calloc(1, sizeof(kstring_t));
-			while (ti_readline(fp, str) >= 0) { // FIXME: check return code for error
-				fputs(str->s, stdout); fputc('\n', stdout);
+			ti_iter_t iter;
+			const char *s;
+			int len;
+			iter = ti_query(t, 0, 0, 0);
+			while ((s = ti_read(t, iter, &len)) != 0) {
+				fputs(s, stdout); fputc('\n', stdout);
 			}
-			free(str->s); free(str);
+			ti_iter_destroy(iter);
 		} else { // retrieve from specified regions
-			ti_index_t *idx;
 			int i;
-			idx = ti_index_load(argv[optind]);
-			if (idx == 0) {
-				bgzf_close(fp);
-				fprintf(stderr, "[main] fail to load the index.\n");
-				return 1;
-			}
+			ti_lazy_index_load(t);
 			for (i = optind + 1; i < argc; ++i) {
 				int tid, beg, end;
-				if (ti_parse_region(idx, argv[i], &tid, &beg, &end) == 0) {
-					fprintf(stderr, "%d,%d\n", beg, end);
-					ti_fetch(fp, idx, tid, beg, end, 0, fetch_func);
+				if (ti_parse_region(t->idx, argv[i], &tid, &beg, &end) == 0) {
+					ti_iter_t iter;
+					const char *s;
+					int len;
+					iter = ti_queryi(t, tid, beg, end);
+					while ((s = ti_read(t, iter, &len)) != 0) {
+						fputs(s, stdout); fputc('\n', stdout);
+					}
+					ti_iter_destroy(iter);
 				} else fprintf(stderr, "[main] invalid region: unknown target name or minus interval.\n");
 			}
-			ti_index_destroy(idx);
 		}
-		bgzf_close(fp);
+		ti_close(t);
 	}
 	return 0;
 }