#endif
#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.7-13 (r590)"
+#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[]);
int bam_merge(int argc, char *argv[]);
int bam_index(int argc, char *argv[]);
int bam_sort(int argc, char *argv[]);
int bam_rmdup(int argc, char *argv[]);
int bam_flagstat(int argc, char *argv[]);
int bam_fillmd(int argc, char *argv[]);
-
+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[]);
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, " faidx index/extract FASTA\n");
#if _CURSES_LIB != 0
fprintf(stderr, " tview text alignment viewer\n");
#endif
fprintf(stderr, " index index alignment\n");
+ fprintf(stderr, " idxstats BAM index stats (r595 or later)\n");
fprintf(stderr, " fixmate fix mate information\n");
fprintf(stderr, " glfview print GLFv3 file\n");
fprintf(stderr, " flagstat simple stats\n");
if (strcmp(argv[1], "view") == 0) return main_samview(argc-1, argv+1);
else if (strcmp(argv[1], "import") == 0) return main_import(argc-1, argv+1);
else if (strcmp(argv[1], "pileup") == 0) return bam_pileup(argc-1, argv+1);
+ else if (strcmp(argv[1], "mpileup") == 0) return bam_mpileup(argc-1, argv+1);
else if (strcmp(argv[1], "merge") == 0) return bam_merge(argc-1, argv+1);
else if (strcmp(argv[1], "sort") == 0) return bam_sort(argc-1, argv+1);
else if (strcmp(argv[1], "index") == 0) return bam_index(argc-1, argv+1);
+ else if (strcmp(argv[1], "idxstats") == 0) return bam_idxstats(argc-1, argv+1);
else if (strcmp(argv[1], "faidx") == 0) return faidx_main(argc-1, argv+1);
else if (strcmp(argv[1], "fixmate") == 0) return bam_mating(argc-1, argv+1);
else if (strcmp(argv[1], "rmdup") == 0) return bam_rmdup(argc-1, argv+1);