X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bamtk.c;h=0941f6f16f9194db93b152a48e2007b63f498d54;hp=4c2a4a282b7d351999f05c5e12d7d891acf93ba2;hb=9f4bebab2e0917c676ae739b2d05cb22ad6c4ed5;hpb=6a0c6f060a60789b48e10a72b1381f6e54599302

diff --git a/bamtk.c b/bamtk.c
index 4c2a4a2..0941f6f 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -8,10 +8,6 @@
 #include "knetfile.h"
 #endif
 
-#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.11 (r851)"
-#endif
-
 int bam_taf2baf(int argc, char *argv[]);
 int bam_pileup(int argc, char *argv[]);
 int bam_mpileup(int argc, char *argv[]);
@@ -27,60 +23,25 @@ int bam_idxstats(int argc, char *argv[]);
 int main_samview(int argc, char *argv[]);
 int main_import(int argc, char *argv[]);
 int main_reheader(int argc, char *argv[]);
+int main_cut_target(int argc, char *argv[]);
+int main_phase(int argc, char *argv[]);
+int main_cat(int argc, char *argv[]);
+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");
 	fprintf(stderr, "Program: samtools (Tools for alignments in the SAM format)\n");
-	fprintf(stderr, "Version: %s\n\n", PACKAGE_VERSION);
+	fprintf(stderr, "Version: %s\n\n", BAM_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, "         mpileup     multi-way pileup\n");
+	fprintf(stderr, "         depth       compute the depth\n");
 	fprintf(stderr, "         faidx       index/extract FASTA\n");
 #if _CURSES_LIB != 0
 	fprintf(stderr, "         tview       text alignment viewer\n");
@@ -94,7 +55,16 @@ static int usage()
 	fprintf(stderr, "         merge       merge sorted alignments\n");
 	fprintf(stderr, "         rmdup       remove PCR duplicates\n");
 	fprintf(stderr, "         reheader    replace BAM header\n");
+	fprintf(stderr, "         cat         concatenate BAMs\n");
+	fprintf(stderr, "         targetcut   cut fosmid regions (for fosmid pool only)\n");
+	fprintf(stderr, "         phase       phase heterozygotes\n");
 	fprintf(stderr, "\n");
+#ifdef _WIN32
+	fprintf(stderr, "\
+Note: The Windows version of SAMtools is mainly designed for read-only\n\
+      operations, such as viewing the alignments and generating the pileup.\n\
+      Binary files generated by the Windows version may be buggy.\n\n");
+#endif
 	return 1;
 }
 
@@ -121,10 +91,13 @@ 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);
+	else if (strcmp(argv[1], "cat") == 0) return main_cat(argc-1, argv+1);
+	else if (strcmp(argv[1], "targetcut") == 0) return main_cut_target(argc-1, argv+1);
+	else if (strcmp(argv[1], "phase") == 0) return main_phase(argc-1, argv+1);
+	else if (strcmp(argv[1], "depth") == 0) return main_depth(argc-1, argv+1);
 #if _CURSES_LIB != 0
 	else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
 #endif