diff SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/bamtk.c @ 0:74f5ea818cea

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/bamtk.c	Wed Oct 12 19:50:38 2011 -0400
@@ -0,0 +1,130 @@
+#include <stdio.h>
+#include <unistd.h>
+#include <assert.h>
+#include <fcntl.h>
+#include "bam.h"
+
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+#endif
+
+#ifndef PACKAGE_VERSION
+#define PACKAGE_VERSION "0.1.6 (r453)"
+#endif
+
+int bam_taf2baf(int argc, char *argv[]);
+int bam_pileup(int argc, char *argv[]);
+int bam_merge(int argc, char *argv[]);
+int bam_index(int argc, char *argv[]);
+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 main_samview(int argc, char *argv[]);
+int main_import(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");
+	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: view        SAM<->BAM conversion\n");
+	fprintf(stderr, "         sort        sort alignment file\n");
+	fprintf(stderr, "         pileup      generate pileup output\n");
+	fprintf(stderr, "         faidx       index/extract FASTA\n");
+#if _CURSES_LIB != 0
+	fprintf(stderr, "         tview       text alignment viewer\n");
+#endif
+	fprintf(stderr, "         index       index alignment\n");
+	fprintf(stderr, "         fixmate     fix mate information\n");
+	fprintf(stderr, "         glfview     print GLFv3 file\n");
+	fprintf(stderr, "         flagstat    simple stats\n");
+	fprintf(stderr, "         calmd       recalculate MD/NM tags and '=' bases\n");
+	fprintf(stderr, "         merge       merge sorted alignments (Picard recommended)\n");
+	fprintf(stderr, "         rmdup       remove PCR duplicates (Picard recommended)\n");
+	fprintf(stderr, "\n");
+	return 1;
+}
+
+int main(int argc, char *argv[])
+{
+#ifdef _WIN32
+	setmode(fileno(stdout), O_BINARY);
+	setmode(fileno(stdin),  O_BINARY);
+#ifdef _USE_KNETFILE
+	knet_win32_init();
+#endif
+#endif
+	if (argc < 2) return usage();
+	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);
+	else if (strcmp(argv[1], "index") == 0) return bam_index(argc-1, argv+1);
+	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], "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], "calmd") == 0) return bam_fillmd(argc-1, argv+1);
+	else if (strcmp(argv[1], "fillmd") == 0) return bam_fillmd(argc-1, argv+1);
+#if _CURSES_LIB != 0
+	else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
+#endif
+	else {
+		fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
+		return 1;
+	}
+	return 0;	
+}