X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bamtk.c;h=27dde036773d9febec2ceacf95d9c97b1ac87582;hb=647cc6ebb358b3089baad06998772457ab9cf093;hp=9ebaac6b4ccff5582f4c77a746265b036b9026b6;hpb=ecbde30918d2dc8ed3fcbad5e4cff44d0977dc34;p=samtools.git

diff --git a/bamtk.c b/bamtk.c
index 9ebaac6..27dde03 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.2-10"
+#define PACKAGE_VERSION "0.1.4-11 (r346)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
@@ -14,66 +14,53 @@ int bam_sort(int argc, char *argv[]);
 int bam_tview_main(int argc, char *argv[]);
 int bam_mating(int argc, char *argv[]);
 int bam_rmdup(int argc, char *argv[]);
+int bam_rmdupse(int argc, char *argv[]);
 int bam_flagstat(int argc, char *argv[]);
+int bam_fillmd(int argc, char *argv[]);
 
-int faidx_main(int argc, char *argv[]);
-int glf_view_main(int argc, char *argv[]);
+int main_samview(int argc, char *argv[]);
+int main_import(int argc, char *argv[]);
 
-static int view_aux(const bam1_t *b, void *data)
-{
-	bam_view1((bam_header_t*)data, b);
-	return 0;
-}
-static int view_auxb(const bam1_t *b, void *data)
-{
-	bam_write1((bamFile)data, b);
-	return 0;
-}
+int faidx_main(int argc, char *argv[]);
+int glf3_view_main(int argc, char *argv[]);
 
-int bam_view(int argc, char *argv[])
+int bam_tagview(int argc, char *argv[])
 {
-	bamFile fp, fpout = 0;
+	bamFile fp;
 	bam_header_t *header;
 	bam1_t *b;
-	int ret, c, is_bam = 0;
-	while ((c = getopt(argc, argv, "b")) >= 0) {
-		switch (c) {
-		case 'b': is_bam = 1; break;
-		default: fprintf(stderr, "Unrecognized option: -%c\n", c); return 1;
-		}
-	}
-	if (argc == optind) {
-		fprintf(stderr, "Usage: samtools view [-b] <in.bam> [<region> [...]]\n");
+	char tag[2];
+	int ret;
+	if (argc < 3) {
+		fprintf(stderr, "Usage: samtools tagview <in.bam> <tag>\n");
 		return 1;
 	}
-	fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
+	fp = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
 	assert(fp);
 	header = bam_header_read(fp);
-	if (is_bam) {
-		assert(fpout = bam_dopen(fileno(stdout), "w"));
-		bam_header_write(fpout, header);
+	if (header == 0) {
+		fprintf(stderr, "[bam_view] fail to read the BAM header. Abort!\n");
+		return 1;
 	}
-	if (optind + 1 == argc) {
-		b = (bam1_t*)calloc(1, sizeof(bam1_t));
-		while ((ret = bam_read1(fp, b)) >= 0) bam_view1(header, b);
-		if (ret < -1) fprintf(stderr, "[bam_view] truncated file? Continue anyway. (%d)\n", ret);
-		free(b->data); free(b);
-	} else {
-		int i;
-		bam_index_t *idx;
-		idx = bam_index_load(argv[optind]);
-		for (i = optind + 1; i < argc; ++i) {
-			int tid, beg, end;
-			bam_parse_region(header, argv[i], &tid, &beg, &end);
-			if (tid < 0) return 0;
-			if (is_bam) bam_fetch(fp, idx, tid, beg, end, fpout, view_auxb);
-			else bam_fetch(fp, idx, tid, beg, end, header, view_aux);
+	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");
 		}
-		bam_index_destroy(idx);
 	}
+	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);
-	if (is_bam) bam_close(fpout);
 	return 0;
 }
 
@@ -83,7 +70,7 @@ static int usage()
 	fprintf(stderr, "Program: samtools (Tools for alignments in the SAM format)\n");
 	fprintf(stderr, "Version: %s\n\n", PACKAGE_VERSION);
 	fprintf(stderr, "Usage:   samtools <command> [options]\n\n");
-	fprintf(stderr, "Command: import      import from the text format\n");
+	fprintf(stderr, "Command: import      import from SAM (obsolete; use `view')\n");
 	fprintf(stderr, "         view        export to the text format\n");
 	fprintf(stderr, "         sort        sort alignment file\n");
 	fprintf(stderr, "         merge       merge multiple sorted alignment files\n");
@@ -95,8 +82,9 @@ static int usage()
 	fprintf(stderr, "         index       index alignment\n");
 	fprintf(stderr, "         fixmate     fix mate information\n");
 	fprintf(stderr, "         rmdup       remove PCR duplicates\n");
-	fprintf(stderr, "         glfview     print GLFv2 file\n");
+	fprintf(stderr, "         glfview     print GLFv3 file\n");
 	fprintf(stderr, "         flagstat    simple stats\n");
+	fprintf(stderr, "         fillmd      fill the MD tag and change identical base to =\n");
 	fprintf(stderr, "\n");
 	return 1;
 }
@@ -104,8 +92,8 @@ static int usage()
 int main(int argc, char *argv[])
 {
 	if (argc < 2) return usage();
-	if (strcmp(argv[1], "view") == 0) return bam_view(argc-1, argv+1);
-	else if (strcmp(argv[1], "import") == 0) return bam_taf2baf(argc-1, argv+1);
+	if (strcmp(argv[1], "view") == 0) return main_samview(argc-1, argv+1);
+	else if (strcmp(argv[1], "import") == 0) return main_import(argc-1, argv+1);
 	else if (strcmp(argv[1], "pileup") == 0) return bam_pileup(argc-1, argv+1);
 	else if (strcmp(argv[1], "merge") == 0) return bam_merge(argc-1, argv+1);
 	else if (strcmp(argv[1], "sort") == 0) return bam_sort(argc-1, argv+1);
@@ -113,8 +101,11 @@ int main(int argc, char *argv[])
 	else if (strcmp(argv[1], "faidx") == 0) return faidx_main(argc-1, argv+1);
 	else if (strcmp(argv[1], "fixmate") == 0) return bam_mating(argc-1, argv+1);
 	else if (strcmp(argv[1], "rmdup") == 0) return bam_rmdup(argc-1, argv+1);
-	else if (strcmp(argv[1], "glfview") == 0) return glf_view_main(argc-1, argv+1);
+	else if (strcmp(argv[1], "rmdupse") == 0) return bam_rmdupse(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], "fillmd") == 0) return bam_fillmd(argc-1, argv+1);
 #ifndef _NO_CURSES
 	else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
 #endif