Added an example of using mpileup

[samtools.git] / bamtk.c

diff --git a/bamtk.c b/bamtk.c
index 096cd95c18359904ca3867af2f414959fd2bfbf0..5886570a88f9fbdc43e6442f1f76df7f9e100243 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -8,10 +8,6 @@
 #include "knetfile.h"
 #endif
 
-#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.12-11 (r896:110)"
-#endif
-
 int bam_taf2baf(int argc, char *argv[]);
 int bam_pileup(int argc, char *argv[]);
 int bam_mpileup(int argc, char *argv[]);
@@ -29,6 +25,8 @@ 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[]);
@@ -77,12 +75,13 @@ 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");
@@ -96,6 +95,7 @@ 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");
@@ -135,8 +135,10 @@ int main(int argc, char *argv[])
        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