X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bamtk.c;h=0941f6f16f9194db93b152a48e2007b63f498d54;hp=5886570a88f9fbdc43e6442f1f76df7f9e100243;hb=8a8212c76299ff302cdd41be704d8e0308bd2b1b;hpb=e42445c748ed193f8d0a4277a844fa848f30c132

diff --git a/bamtk.c b/bamtk.c
index 5886570..0941f6f 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -31,46 +31,6 @@ int main_depth(int argc, char *argv[]);
 int faidx_main(int argc, char *argv[]);
 int glf3_view_main(int argc, char *argv[]);
 
-int bam_tagview(int argc, char *argv[])
-{
-	bamFile fp;
-	bam_header_t *header;
-	bam1_t *b;
-	char tag[2];
-	int ret;
-	if (argc < 3) {
-		fprintf(stderr, "Usage: samtools tagview <in.bam> <tag>\n");
-		return 1;
-	}
-	fp = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
-	assert(fp);
-	header = bam_header_read(fp);
-	if (header == 0) {
-		fprintf(stderr, "[bam_view] fail to read the BAM header. Abort!\n");
-		return 1;
-	}
-	tag[0] = argv[2][0]; tag[1] = argv[2][1];
-	b = (bam1_t*)calloc(1, sizeof(bam1_t));
-	while ((ret = bam_read1(fp, b)) >= 0) {
-		uint8_t *d = bam_aux_get(b, tag);
-		if (d) {
-			printf("%s\t%d\t", bam1_qname(b), b->core.flag);
-			if (d[0] == 'Z' || d[0] == 'H') printf("%s\n", bam_aux2Z(d));
-			else if (d[0] == 'f') printf("%f\n", bam_aux2f(d));
-			else if (d[0] == 'd') printf("%lf\n", bam_aux2d(d));
-			else if (d[0] == 'A') printf("%c\n", bam_aux2A(d));
-			else if (d[0] == 'c' || d[0] == 's' || d[0] == 'i') printf("%d\n", bam_aux2i(d));
-			else if (d[0] == 'C' || d[0] == 'S' || d[0] == 'I') printf("%u\n", bam_aux2i(d));
-			else printf("\n");
-		}
-	}
-	if (ret < -1) fprintf(stderr, "[bam_view] truncated file? Continue anyway. (%d)\n", ret);
-	free(b->data); free(b);
-	bam_header_destroy(header);
-	bam_close(fp);
-	return 0;
-}
-
 static int usage()
 {
 	fprintf(stderr, "\n");
@@ -131,7 +91,6 @@ int main(int argc, char *argv[])
 	else if (strcmp(argv[1], "rmdup") == 0) return bam_rmdup(argc-1, argv+1);
 	else if (strcmp(argv[1], "glfview") == 0) return glf3_view_main(argc-1, argv+1);
 	else if (strcmp(argv[1], "flagstat") == 0) return bam_flagstat(argc-1, argv+1);
-	else if (strcmp(argv[1], "tagview") == 0) return bam_tagview(argc-1, argv+1);
 	else if (strcmp(argv[1], "calmd") == 0) return bam_fillmd(argc-1, argv+1);
 	else if (strcmp(argv[1], "fillmd") == 0) return bam_fillmd(argc-1, argv+1);
 	else if (strcmp(argv[1], "reheader") == 0) return main_reheader(argc-1, argv+1);