Imported Upstream version 0.2.3

[tabix.git] / main.c

diff --git a/main.c b/main.c
index 84e5cfc6c66a49e8b5406275e07cc6948e900694..8ae6b2e69d78c0b7251635041344e90e02782c85 100644 (file)
--- a/main.c
+++ b/main.c
@@ -6,13 +6,13 @@
 #include "bgzf.h"
 #include "tabix.h"
 
-#define PACKAGE_VERSION "0.2.2 (r603)"
+#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;
@@ -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");
@@ -81,6 +83,11 @@ 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
@@ -100,19 +107,35 @@ int main(int argc, char *argv[])
                        ti_iter_destroy(iter);
                } else { // retrieve from specified regions
                        int i;
-                       ti_lazy_index_load(t);
+                       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(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");
+                               } 
+                // else fprintf(stderr, "[main] invalid region: unknown target name or minus interval.\n");
                        }
                }
                ti_close(t);