#endif
#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.8-13 (r698)"
+#define PACKAGE_VERSION "0.1.12-11 (r896:110)"
#endif
int bam_taf2baf(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[]);
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;
}
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