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comparison ezBAMQC/src/htslib/htsfile.c @ 0:dfa3745e5fd8

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author youngkim
date Thu, 24 Mar 2016 17:12:52 -0400
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1 /* htsfile.c -- file identifier and minimal viewer.
2
3 Copyright (C) 2014-2015 Genome Research Ltd.
4
5 Author: John Marshall <jm18@sanger.ac.uk>
6
7 Permission is hereby granted, free of charge, to any person obtaining a copy
8 of this software and associated documentation files (the "Software"), to deal
9 in the Software without restriction, including without limitation the rights
10 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
11 copies of the Software, and to permit persons to whom the Software is
12 furnished to do so, subject to the following conditions:
13
14 The above copyright notice and this permission notice shall be included in
15 all copies or substantial portions of the Software.
16
17 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
18 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
19 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
20 THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
21 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
22 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
23 DEALINGS IN THE SOFTWARE. */
24
25 #include <errno.h>
26 #include <stdio.h>
27 #include <stdlib.h>
28 #include <getopt.h>
29 #include <unistd.h>
30
31 #include "htslib/hfile.h"
32 #include "htslib/hts.h"
33 #include "htslib/sam.h"
34 #include "htslib/vcf.h"
35
36 enum { identify, view_headers, view_all } mode = identify;
37 int show_headers = 1;
38
39 static htsFile *dup_stdout(const char *mode)
40 {
41 int fd = dup(STDOUT_FILENO);
42 hFILE *hfp = (fd >= 0)? hdopen(fd, mode) : NULL;
43 return hfp? hts_hopen(hfp, "-", mode) : NULL;
44 }
45
46 static int view_sam(hFILE *hfp, const char *filename)
47 {
48 samFile *in = hts_hopen(hfp, filename, "r");
49 if (in == NULL) return 0;
50 samFile *out = dup_stdout("w");
51 bam_hdr_t *hdr = sam_hdr_read(in);
52
53 if (show_headers) sam_hdr_write(out, hdr);
54 if (mode == view_all) {
55 bam1_t *b = bam_init1();
56 while (sam_read1(in, hdr, b) >= 0)
57 sam_write1(out, hdr, b);
58 bam_destroy1(b);
59 }
60
61 bam_hdr_destroy(hdr);
62 hts_close(out);
63 hts_close(in);
64 return 1;
65 }
66
67 static int view_vcf(hFILE *hfp, const char *filename)
68 {
69 vcfFile *in = hts_hopen(hfp, filename, "r");
70 if (in == NULL) return 0;
71 vcfFile *out = dup_stdout("w");
72 bcf_hdr_t *hdr = bcf_hdr_read(in);
73
74 if (show_headers) bcf_hdr_write(out, hdr);
75 if (mode == view_all) {
76 bcf1_t *rec = bcf_init();
77 while (bcf_read(in, hdr, rec) >= 0)
78 bcf_write(out, hdr, rec);
79 bcf_destroy(rec);
80 }
81
82 bcf_hdr_destroy(hdr);
83 hts_close(out);
84 hts_close(in);
85 return 1;
86 }
87
88 static void usage(FILE *fp, int status)
89 {
90 fprintf(fp,
91 "Usage: htsfile [-chH] FILE...\n"
92 "Options:\n"
93 " -c, --view Write textual form of FILEs to standard output\n"
94 " -h, --header-only Display only headers in view mode, not records\n"
95 " -H, --no-header Suppress header display in view mode\n");
96 exit(status);
97 }
98
99 int main(int argc, char **argv)
100 {
101 static const struct option options[] = {
102 { "header-only", no_argument, NULL, 'h' },
103 { "no-header", no_argument, NULL, 'H' },
104 { "view", no_argument, NULL, 'c' },
105 { "help", no_argument, NULL, '?' },
106 { "version", no_argument, NULL, 1 },
107 { NULL, 0, NULL, 0 }
108 };
109
110 int status = EXIT_SUCCESS;
111 int c, i;
112 while ((c = getopt_long(argc, argv, "chH?", options, NULL)) >= 0)
113 switch (c) {
114 case 'c': mode = view_all; break;
115 case 'h': mode = view_headers; show_headers = 1; break;
116 case 'H': show_headers = 0; break;
117 case 1:
118 printf(
119 "htsfile (htslib) %s\n"
120 "Copyright (C) 2015 Genome Research Ltd.\n",
121 hts_version());
122 exit(EXIT_SUCCESS);
123 break;
124 case '?': usage(stdout, EXIT_SUCCESS); break;
125 default: usage(stderr, EXIT_FAILURE); break;
126 }
127
128 if (optind == argc) usage(stderr, EXIT_FAILURE);
129
130 for (i = optind; i < argc; i++) {
131 htsFormat fmt;
132 hFILE *fp = hopen(argv[i], "r");
133 if (fp == NULL) {
134 fprintf(stderr, "htsfile: can't open \"%s\": %s\n", argv[i], strerror(errno));
135 status = EXIT_FAILURE;
136 continue;
137 }
138
139 if (hts_detect_format(fp, &fmt) < 0) {
140 fprintf(stderr, "htsfile: detecting \"%s\" format failed: %s\n", argv[i], strerror(errno));
141 hclose_abruptly(fp);
142 status = EXIT_FAILURE;
143 continue;
144 }
145
146 if (mode == identify) {
147 char *description = hts_format_description(&fmt);
148 printf("%s:\t%s\n", argv[i], description);
149 free(description);
150 }
151 else
152 switch (fmt.category) {
153 case sequence_data: if (view_sam(fp, argv[i])) fp = NULL; break;
154 case variant_data: if (view_vcf(fp, argv[i])) fp = NULL; break;
155 default:
156 fprintf(stderr, "htsfile: can't view %s: unknown format\n", argv[i]);
157 status = EXIT_FAILURE;
158 break;
159 }
160
161 if (fp && hclose(fp) < 0) {
162 fprintf(stderr, "htsfile: closing %s failed\n", argv[i]);
163 status = EXIT_FAILURE;
164 }
165 }
166
167 return status;
168 }