#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 main_phase(int argc, char *argv[]);
int main_cat(int argc, char *argv[]);
int main_depth(int argc, char *argv[]);
+int main_bam2fq(int argc, char *argv[]);
+int main_pad2unpad(int argc, char *argv[]);
+int main_bedcov(int argc, char *argv[]);
+int main_bamshuf(int argc, char *argv[]);
int faidx_main(int argc, char *argv[]);
-int glf3_view_main(int argc, char *argv[]);
static int usage()
{
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");
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");
fprintf(stderr, " calmd recalculate MD/NM tags and '=' bases\n");
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, " bedcov read depth per BED region\n");
fprintf(stderr, " targetcut cut fosmid regions (for fosmid pool only)\n");
fprintf(stderr, " phase phase heterozygotes\n");
+ fprintf(stderr, " bamshuf shuffle and group alignments by name\n");
+// fprintf(stderr, " depad convert padded BAM to unpadded BAM\n"); // not stable
fprintf(stderr, "\n");
#ifdef _WIN32
fprintf(stderr, "\
if (argc < 2) return usage();
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], "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);
- else if (strcmp(argv[1], "glfview") == 0) return glf3_view_main(argc-1, argv+1);
else if (strcmp(argv[1], "flagstat") == 0) return bam_flagstat(argc-1, argv+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], "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);
+ else if (strcmp(argv[1], "bam2fq") == 0) return main_bam2fq(argc-1, argv+1);
+ else if (strcmp(argv[1], "pad2unpad") == 0) return main_pad2unpad(argc-1, argv+1);
+ else if (strcmp(argv[1], "depad") == 0) return main_pad2unpad(argc-1, argv+1);
+ else if (strcmp(argv[1], "bedcov") == 0) return main_bedcov(argc-1, argv+1);
+ else if (strcmp(argv[1], "bamshuf") == 0) return main_bamshuf(argc-1, argv+1);
+ else if (strcmp(argv[1], "pileup") == 0) {
+ fprintf(stderr, "[main] The `pileup' command has been removed. Please use `mpileup' instead.\n");
+ return 1;
+ }
#if _CURSES_LIB != 0
else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
#endif