X-Git-Url: http://woldlab.caltech.edu/gitweb/?a=blobdiff_plain;f=main.c;h=8ae6b2e69d78c0b7251635041344e90e02782c85;hb=a3f2132b77c1d5d5b084aeb60bd6e56dded44f6c;hp=a05939dd96f306843d877859148246c30a44f90b;hpb=d1fcb739b58e050328dcfc47c3af235bc0e41455;p=tabix.git

diff --git a/main.c b/main.c
index a05939d..8ae6b2e 100644
--- a/main.c
+++ b/main.c
@@ -6,13 +6,13 @@
 #include "bgzf.h"
 #include "tabix.h"
 
-#define PACKAGE_VERSION "0.1.6 (r565)"
+#define PACKAGE_VERSION "0.2.3 (r876)"
 
 int main(int argc, char *argv[])
 {
-	int c, skip = -1, meta = -1, list_chrms = 0, force = 0;
+	int c, skip = -1, meta = -1, list_chrms = 0, force = 0, print_header = 0;
 	ti_conf_t conf = ti_conf_gff;
-	while ((c = getopt(argc, argv, "p:s:b:e:0S:c:lf")) >= 0) {
+	while ((c = getopt(argc, argv, "p:s:b:e:0S:c:lhf")) >= 0) {
 		switch (c) {
 		case '0': conf.preset |= TI_FLAG_UCSC; break;
 		case 'S': skip = atoi(optarg); break;
@@ -21,7 +21,7 @@ int main(int argc, char *argv[])
 			if (strcmp(optarg, "gff") == 0) conf = ti_conf_gff;
 			else if (strcmp(optarg, "bed") == 0) conf = ti_conf_bed;
 			else if (strcmp(optarg, "sam") == 0) conf = ti_conf_sam;
-			else if (strcmp(optarg, "vcf") == 0) conf = ti_conf_vcf;
+			else if (strcmp(optarg, "vcf") == 0 || strcmp(optarg, "vcf4") == 0) conf = ti_conf_vcf;
 			else if (strcmp(optarg, "psltbl") == 0) conf = ti_conf_psltbl;
 			else {
 				fprintf(stderr, "[main] unrecognized preset '%s'\n", optarg);
@@ -32,6 +32,7 @@ int main(int argc, char *argv[])
 		case 'b': conf.bc = atoi(optarg); break;
 		case 'e': conf.ec = atoi(optarg); break;
         case 'l': list_chrms = 1; break;
+        case 'h': print_header = 1; break;
 		case 'f': force = 1; break;
 		}
 	}
@@ -49,6 +50,7 @@ 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, "         -h         print the VCF header\n");
 		fprintf(stderr, "         -l         list chromosome names\n");
 		fprintf(stderr, "         -f         force to overwrite the index\n");
 		fprintf(stderr, "\n");
@@ -81,12 +83,16 @@ int main(int argc, char *argv[])
 			}
 			free(fnidx);
 		}
+        if ( is_bgzipped(argv[optind])!=1 )
+        {
+            fprintf(stderr,"[tabix] was bgzip used to compress this file? %s\n", argv[optind]);
+            return 1;
+        }
 		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;
 		}
@@ -94,36 +100,45 @@ int main(int argc, char *argv[])
 			ti_iter_t iter;
 			const char *s;
 			int len;
-			iter = ti_first(fp);
-			while ((s = ti_iter_read(iter, &len)) != 0) {
+			iter = ti_query(t, 0, 0, 0);
+			while ((s = ti_read(t, iter, &len)) != 0) {
 				fputs(s, stdout); fputc('\n', stdout);
 			}
 			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;
-			}
+			if ( ti_lazy_index_load(t) ) 
+            {
+                fprintf(stderr,"[tabix] failed to load the index file.\n");
+                return 1;
+            }
+
+            ti_iter_t iter;
+            const char *s;
+            int len;
+            if ( print_header )
+            {
+                // If requested, print the header lines here
+                iter = ti_query(t, 0, 0, 0);
+                while ((s = ti_read(t, iter, &len)) != 0) {
+                    if ( *s != '#' ) break;
+                    fputs(s, stdout); fputc('\n', stdout);
+                }
+                ti_iter_destroy(iter);
+            }
 			for (i = optind + 1; i < argc; ++i) {
 				int tid, beg, end;
-				if (ti_parse_region(idx, argv[i], &tid, &beg, &end) == 0) {
-					ti_iter_t iter;
-					const char *s;
-					int len;
-					iter = ti_query(fp, idx, tid, beg, end);
-					while ((s = ti_iter_read(iter, &len)) != 0) {
+				if (ti_parse_region(t->idx, argv[i], &tid, &beg, &end) == 0) {
+					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");
+				} 
+                // 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;
 }