* change the order of PL/GL according to the latest VCF spec

[samtools.git] / bamtk.c

diff --git a/bamtk.c b/bamtk.c
index 09d64adcfff113856a3fe8a23bde71aa66adc798..03e413dc966f6f582014832db8aca307e5725761 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.9-10 (r816)"
+#define PACKAGE_VERSION "0.1.12-11 (r921:118)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
@@ -27,6 +27,8 @@ 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[]);
@@ -94,7 +96,15 @@ 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 +135,8 @@ 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