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1 /* htsfile.c -- file identifier and minimal viewer.
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2
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3 Copyright (C) 2014-2015 Genome Research Ltd.
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4
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5 Author: John Marshall <jm18@sanger.ac.uk>
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6
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7 Permission is hereby granted, free of charge, to any person obtaining a copy
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8 of this software and associated documentation files (the "Software"), to deal
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9 in the Software without restriction, including without limitation the rights
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10 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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11 copies of the Software, and to permit persons to whom the Software is
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12 furnished to do so, subject to the following conditions:
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13
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14 The above copyright notice and this permission notice shall be included in
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15 all copies or substantial portions of the Software.
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16
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17 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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18 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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19 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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20 THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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21 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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22 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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23 DEALINGS IN THE SOFTWARE. */
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24
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25 #include <errno.h>
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26 #include <stdio.h>
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27 #include <stdlib.h>
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28 #include <getopt.h>
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29 #include <unistd.h>
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30
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31 #include "htslib/hfile.h"
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32 #include "htslib/hts.h"
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33 #include "htslib/sam.h"
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34 #include "htslib/vcf.h"
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35
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36 enum { identify, view_headers, view_all } mode = identify;
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37 int show_headers = 1;
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38
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39 static htsFile *dup_stdout(const char *mode)
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40 {
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41 int fd = dup(STDOUT_FILENO);
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42 hFILE *hfp = (fd >= 0)? hdopen(fd, mode) : NULL;
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43 return hfp? hts_hopen(hfp, "-", mode) : NULL;
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44 }
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45
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46 static int view_sam(hFILE *hfp, const char *filename)
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47 {
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48 samFile *in = hts_hopen(hfp, filename, "r");
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49 if (in == NULL) return 0;
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50 samFile *out = dup_stdout("w");
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51 bam_hdr_t *hdr = sam_hdr_read(in);
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52
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53 if (show_headers) sam_hdr_write(out, hdr);
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54 if (mode == view_all) {
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55 bam1_t *b = bam_init1();
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56 while (sam_read1(in, hdr, b) >= 0)
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57 sam_write1(out, hdr, b);
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58 bam_destroy1(b);
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59 }
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60
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61 bam_hdr_destroy(hdr);
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62 hts_close(out);
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63 hts_close(in);
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64 return 1;
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65 }
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66
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67 static int view_vcf(hFILE *hfp, const char *filename)
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68 {
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69 vcfFile *in = hts_hopen(hfp, filename, "r");
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70 if (in == NULL) return 0;
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71 vcfFile *out = dup_stdout("w");
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72 bcf_hdr_t *hdr = bcf_hdr_read(in);
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73
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74 if (show_headers) bcf_hdr_write(out, hdr);
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75 if (mode == view_all) {
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76 bcf1_t *rec = bcf_init();
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77 while (bcf_read(in, hdr, rec) >= 0)
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78 bcf_write(out, hdr, rec);
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79 bcf_destroy(rec);
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80 }
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81
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82 bcf_hdr_destroy(hdr);
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83 hts_close(out);
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84 hts_close(in);
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85 return 1;
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86 }
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87
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88 static void usage(FILE *fp, int status)
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89 {
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90 fprintf(fp,
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91 "Usage: htsfile [-chH] FILE...\n"
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92 "Options:\n"
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93 " -c, --view Write textual form of FILEs to standard output\n"
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94 " -h, --header-only Display only headers in view mode, not records\n"
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95 " -H, --no-header Suppress header display in view mode\n");
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96 exit(status);
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97 }
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98
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99 int main(int argc, char **argv)
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100 {
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101 static const struct option options[] = {
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102 { "header-only", no_argument, NULL, 'h' },
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103 { "no-header", no_argument, NULL, 'H' },
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104 { "view", no_argument, NULL, 'c' },
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105 { "help", no_argument, NULL, '?' },
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106 { "version", no_argument, NULL, 1 },
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107 { NULL, 0, NULL, 0 }
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108 };
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109
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110 int status = EXIT_SUCCESS;
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111 int c, i;
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112 while ((c = getopt_long(argc, argv, "chH?", options, NULL)) >= 0)
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113 switch (c) {
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114 case 'c': mode = view_all; break;
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115 case 'h': mode = view_headers; show_headers = 1; break;
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116 case 'H': show_headers = 0; break;
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117 case 1:
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118 printf(
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119 "htsfile (htslib) %s\n"
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120 "Copyright (C) 2015 Genome Research Ltd.\n",
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121 hts_version());
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122 exit(EXIT_SUCCESS);
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123 break;
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124 case '?': usage(stdout, EXIT_SUCCESS); break;
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125 default: usage(stderr, EXIT_FAILURE); break;
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126 }
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127
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128 if (optind == argc) usage(stderr, EXIT_FAILURE);
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129
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130 for (i = optind; i < argc; i++) {
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131 htsFormat fmt;
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132 hFILE *fp = hopen(argv[i], "r");
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133 if (fp == NULL) {
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134 fprintf(stderr, "htsfile: can't open \"%s\": %s\n", argv[i], strerror(errno));
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135 status = EXIT_FAILURE;
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136 continue;
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137 }
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138
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139 if (hts_detect_format(fp, &fmt) < 0) {
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140 fprintf(stderr, "htsfile: detecting \"%s\" format failed: %s\n", argv[i], strerror(errno));
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141 hclose_abruptly(fp);
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142 status = EXIT_FAILURE;
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143 continue;
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144 }
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145
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146 if (mode == identify) {
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147 char *description = hts_format_description(&fmt);
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148 printf("%s:\t%s\n", argv[i], description);
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149 free(description);
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150 }
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151 else
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152 switch (fmt.category) {
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153 case sequence_data: if (view_sam(fp, argv[i])) fp = NULL; break;
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154 case variant_data: if (view_vcf(fp, argv[i])) fp = NULL; break;
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155 default:
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156 fprintf(stderr, "htsfile: can't view %s: unknown format\n", argv[i]);
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157 status = EXIT_FAILURE;
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158 break;
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159 }
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160
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161 if (fp && hclose(fp) < 0) {
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162 fprintf(stderr, "htsfile: closing %s failed\n", argv[i]);
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163 status = EXIT_FAILURE;
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164 }
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165 }
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166
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167 return status;
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168 }
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