X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bamtk.c;h=a9d852d49060732f9f543e936c267ab3f9f3fe5d;hb=17d530d96c290e6e3956c034117dce8f39480edd;hp=e162f076addfaaee2b653c7e2ca88ef387ce1e96;hpb=6c4f7da62ca46d02f16284bf3e586fc9842413c5;p=samtools.git

diff --git a/bamtk.c b/bamtk.c
index e162f07..a9d852d 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.2"
+#define PACKAGE_VERSION "0.1.2-22"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
@@ -14,9 +14,10 @@ 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_flagstat(int argc, char *argv[]);
 
 int faidx_main(int argc, char *argv[]);
-int glf_view_main(int argc, char *argv[]);
+int glf3_view_main(int argc, char *argv[]);
 
 static int view_aux(const bam1_t *b, void *data)
 {
@@ -34,15 +35,17 @@ int bam_view(int argc, char *argv[])
 	bamFile fp, fpout = 0;
 	bam_header_t *header;
 	bam1_t *b;
-	int ret, c, is_bam = 0;
-	while ((c = getopt(argc, argv, "b")) >= 0) {
+	int ret, c, is_bam = 0, is_header = 0, is_headeronly = 0;
+	while ((c = getopt(argc, argv, "bhH")) >= 0) {
 		switch (c) {
 		case 'b': is_bam = 1; break;
+		case 'h': is_header = 1; break;
+		case 'H': is_headeronly = 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");
+		fprintf(stderr, "Usage: samtools view [-bhH] <in.bam> [<region> [...]]\n");
 		return 1;
 	}
 	fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
@@ -52,6 +55,21 @@ int bam_view(int argc, char *argv[])
 		assert(fpout = bam_dopen(fileno(stdout), "w"));
 		bam_header_write(fpout, header);
 	}
+	if (is_header || is_headeronly) {
+		int i, c;
+		c = header->text[header->l_text-1];
+		header->text[header->l_text-1] = 0;
+		printf("%s", header->text);
+		if (c) putchar(c);
+		header->text[header->l_text-1] = c;
+		for (i = 0; i < header->n_targets; ++i)
+			printf("@SQ\tSN:%s\tLN:%d\n", header->target_name[i], header->target_len[i]);
+		if (is_headeronly) {
+			bam_header_destroy(header);
+			bam_close(fp);
+			return 0;
+		}
+	}
 	if (optind + 1 == argc) {
 		b = (bam1_t*)calloc(1, sizeof(bam1_t));
 		while ((ret = bam_read1(fp, b)) >= 0) bam_view1(header, b);
@@ -64,6 +82,7 @@ int bam_view(int argc, char *argv[])
 		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);
 		}
@@ -94,6 +113,7 @@ static int usage()
 	fprintf(stderr, "         fixmate     fix mate information\n");
 	fprintf(stderr, "         rmdup       remove PCR duplicates\n");
 	fprintf(stderr, "         glfview     print GLFv2 file\n");
+	fprintf(stderr, "         flagstat    simple stats\n");
 	fprintf(stderr, "\n");
 	return 1;
 }
@@ -110,7 +130,8 @@ 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], "glfview") == 0) return glf3_view_main(argc-1, argv+1);
+	else if (strcmp(argv[1], "flagstat") == 0) return bam_flagstat(argc-1, argv+1);
 #ifndef _NO_CURSES
 	else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
 #endif