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1 #include <stdio.h>
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2 #include <unistd.h>
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3 #include <assert.h>
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4 #include <fcntl.h>
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5 #include "bam.h"
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6
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7 #ifdef _USE_KNETFILE
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8 #include "knetfile.h"
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9 #endif
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10
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11 int bam_taf2baf(int argc, char *argv[]);
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12 int bam_mpileup(int argc, char *argv[]);
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13 int bam_merge(int argc, char *argv[]);
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14 int bam_index(int argc, char *argv[]);
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15 int bam_sort(int argc, char *argv[]);
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16 int bam_tview_main(int argc, char *argv[]);
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17 int bam_mating(int argc, char *argv[]);
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18 int bam_rmdup(int argc, char *argv[]);
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19 int bam_flagstat(int argc, char *argv[]);
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20 int bam_fillmd(int argc, char *argv[]);
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21 int bam_idxstats(int argc, char *argv[]);
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22 int main_samview(int argc, char *argv[]);
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23 int main_import(int argc, char *argv[]);
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24 int main_reheader(int argc, char *argv[]);
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25 int main_cut_target(int argc, char *argv[]);
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26 int main_phase(int argc, char *argv[]);
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27 int main_cat(int argc, char *argv[]);
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28 int main_depth(int argc, char *argv[]);
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29 int main_bam2fq(int argc, char *argv[]);
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30 int main_pad2unpad(int argc, char *argv[]);
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31 int main_bedcov(int argc, char *argv[]);
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32 int main_bamshuf(int argc, char *argv[]);
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33
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34 int faidx_main(int argc, char *argv[]);
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35
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36 static int usage()
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37 {
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38 fprintf(stderr, "\n");
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39 fprintf(stderr, "Program: samtools (Tools for alignments in the SAM format)\n");
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40 fprintf(stderr, "Version: %s\n\n", BAM_VERSION);
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41 fprintf(stderr, "Usage: samtools <command> [options]\n\n");
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42 fprintf(stderr, "Command: view SAM<->BAM conversion\n");
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43 fprintf(stderr, " sort sort alignment file\n");
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44 fprintf(stderr, " mpileup multi-way pileup\n");
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45 fprintf(stderr, " depth compute the depth\n");
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46 fprintf(stderr, " faidx index/extract FASTA\n");
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47 #if _CURSES_LIB != 0
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48 fprintf(stderr, " tview text alignment viewer\n");
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49 #endif
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50 fprintf(stderr, " index index alignment\n");
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51 fprintf(stderr, " idxstats BAM index stats (r595 or later)\n");
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52 fprintf(stderr, " fixmate fix mate information\n");
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53 fprintf(stderr, " flagstat simple stats\n");
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54 fprintf(stderr, " calmd recalculate MD/NM tags and '=' bases\n");
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55 fprintf(stderr, " merge merge sorted alignments\n");
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56 fprintf(stderr, " rmdup remove PCR duplicates\n");
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57 fprintf(stderr, " reheader replace BAM header\n");
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58 fprintf(stderr, " cat concatenate BAMs\n");
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59 fprintf(stderr, " bedcov read depth per BED region\n");
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60 fprintf(stderr, " targetcut cut fosmid regions (for fosmid pool only)\n");
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61 fprintf(stderr, " phase phase heterozygotes\n");
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62 fprintf(stderr, " bamshuf shuffle and group alignments by name\n");
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63 // fprintf(stderr, " depad convert padded BAM to unpadded BAM\n"); // not stable
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64 fprintf(stderr, "\n");
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65 #ifdef _WIN32
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66 fprintf(stderr, "\
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67 Note: The Windows version of SAMtools is mainly designed for read-only\n\
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68 operations, such as viewing the alignments and generating the pileup.\n\
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69 Binary files generated by the Windows version may be buggy.\n\n");
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70 #endif
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71 return 1;
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72 }
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73
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74 int main(int argc, char *argv[])
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75 {
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76 #ifdef _WIN32
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77 setmode(fileno(stdout), O_BINARY);
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78 setmode(fileno(stdin), O_BINARY);
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79 #ifdef _USE_KNETFILE
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80 knet_win32_init();
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81 #endif
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82 #endif
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83 if (argc < 2) return usage();
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84 if (strcmp(argv[1], "view") == 0) return main_samview(argc-1, argv+1);
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85 else if (strcmp(argv[1], "import") == 0) return main_import(argc-1, argv+1);
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86 else if (strcmp(argv[1], "mpileup") == 0) return bam_mpileup(argc-1, argv+1);
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87 else if (strcmp(argv[1], "merge") == 0) return bam_merge(argc-1, argv+1);
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88 else if (strcmp(argv[1], "sort") == 0) return bam_sort(argc-1, argv+1);
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89 else if (strcmp(argv[1], "index") == 0) return bam_index(argc-1, argv+1);
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90 else if (strcmp(argv[1], "idxstats") == 0) return bam_idxstats(argc-1, argv+1);
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91 else if (strcmp(argv[1], "faidx") == 0) return faidx_main(argc-1, argv+1);
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92 else if (strcmp(argv[1], "fixmate") == 0) return bam_mating(argc-1, argv+1);
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93 else if (strcmp(argv[1], "rmdup") == 0) return bam_rmdup(argc-1, argv+1);
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94 else if (strcmp(argv[1], "flagstat") == 0) return bam_flagstat(argc-1, argv+1);
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95 else if (strcmp(argv[1], "calmd") == 0) return bam_fillmd(argc-1, argv+1);
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96 else if (strcmp(argv[1], "fillmd") == 0) return bam_fillmd(argc-1, argv+1);
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97 else if (strcmp(argv[1], "reheader") == 0) return main_reheader(argc-1, argv+1);
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98 else if (strcmp(argv[1], "cat") == 0) return main_cat(argc-1, argv+1);
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99 else if (strcmp(argv[1], "targetcut") == 0) return main_cut_target(argc-1, argv+1);
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100 else if (strcmp(argv[1], "phase") == 0) return main_phase(argc-1, argv+1);
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101 else if (strcmp(argv[1], "depth") == 0) return main_depth(argc-1, argv+1);
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102 else if (strcmp(argv[1], "bam2fq") == 0) return main_bam2fq(argc-1, argv+1);
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103 else if (strcmp(argv[1], "pad2unpad") == 0) return main_pad2unpad(argc-1, argv+1);
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104 else if (strcmp(argv[1], "depad") == 0) return main_pad2unpad(argc-1, argv+1);
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105 else if (strcmp(argv[1], "bedcov") == 0) return main_bedcov(argc-1, argv+1);
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106 else if (strcmp(argv[1], "bamshuf") == 0) return main_bamshuf(argc-1, argv+1);
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107 else if (strcmp(argv[1], "pileup") == 0) {
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108 fprintf(stderr, "[main] The `pileup' command has been removed. Please use `mpileup' instead.\n");
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109 return 1;
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110 }
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111 #if _CURSES_LIB != 0
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112 else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
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113 #endif
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114 else {
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115 fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
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116 return 1;
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117 }
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118 return 0;
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119 }
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