Imported Upstream version 0.1.13

[samtools.git] / bamtk.c

diff --git a/bamtk.c b/bamtk.c
index 79635d6bf1bca8bad00abdaa5f926b35a3fc59a0..1d1151973fb08efbbb6d642480712fbc6b3b1563 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -8,10 +8,6 @@
 #include "knetfile.h"
 #endif
 
-#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.12a (r862)"
-#endif
-
 int bam_taf2baf(int argc, char *argv[]);
 int bam_pileup(int argc, char *argv[]);
 int bam_mpileup(int argc, char *argv[]);
@@ -27,6 +23,8 @@ 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 faidx_main(int argc, char *argv[]);
 int glf3_view_main(int argc, char *argv[]);
@@ -75,7 +73,7 @@ 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");
@@ -94,7 +92,15 @@ 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, "         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;
 }
 
@@ -125,6 +131,8 @@ 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], "targetcut") == 0) return main_cut_target(argc-1, argv+1);
+       else if (strcmp(argv[1], "phase") == 0) return main_phase(argc-1, argv+1);
 #if _CURSES_LIB != 0
        else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
 #endif