1 /* sam_utils.c -- various utilities internal to samtools.
2
3 Copyright (C) 2014-2016, 2018, 2019 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 <config.h>
26 #include <stdlib.h>
27
28 #include <stdio.h>
29 #include <stdarg.h>
30 #include <string.h>
31 #include <errno.h>
32
33 #include "samtools.h"
34
35 static htsFile *samtools_stdout = NULL;
36
autoflush_if_stdout(htsFile * fp,const char * fname)37 void autoflush_if_stdout(htsFile *fp, const char *fname) {
38 if (fname == NULL || strcmp(fname, "-") == 0) samtools_stdout = fp;
39 }
40
release_autoflush(htsFile * fp)41 void release_autoflush(htsFile *fp) {
42 if (samtools_stdout == fp) samtools_stdout = NULL;
43 }
44
vprint_error_core(const char * subcommand,const char * format,va_list args,const char * extra)45 static void vprint_error_core(const char *subcommand, const char *format, va_list args, const char *extra)
46 {
47 fflush(stdout);
48 if (samtools_stdout) hts_flush(samtools_stdout);
49
50 if (subcommand && *subcommand) fprintf(stderr, "samtools %s: ", subcommand);
51 else fprintf(stderr, "samtools: ");
52 vfprintf(stderr, format, args);
53 if (extra) fprintf(stderr, ": %s\n", extra);
54 else fprintf(stderr, "\n");
55 fflush(stderr);
56 }
57
print_error(const char * subcommand,const char * format,...)58 void print_error(const char *subcommand, const char *format, ...)
59 {
60 va_list args;
61 va_start(args, format);
62 vprint_error_core(subcommand, format, args, NULL);
63 va_end(args);
64 }
65
print_error_errno(const char * subcommand,const char * format,...)66 void print_error_errno(const char *subcommand, const char *format, ...)
67 {
68 int err = errno;
69 va_list args;
70 va_start(args, format);
71 vprint_error_core(subcommand, format, args, err? strerror(err) : NULL);
72 va_end(args);
73 }
74
check_sam_close(const char * subcmd,samFile * fp,const char * fname,const char * null_fname,int * retp)75 void check_sam_close(const char *subcmd, samFile *fp, const char *fname, const char *null_fname, int *retp)
76 {
77 release_autoflush(fp);
78 int r = sam_close(fp);
79 if (r >= 0) return;
80
81 // TODO Need error infrastructure so we can print a message instead of r
82 if (fname) print_error(subcmd, "error closing \"%s\": %d", fname, r);
83 else print_error(subcmd, "error closing %s: %d", null_fname, r);
84
85 *retp = EXIT_FAILURE;
86 }
87
88 /* Pick an index suffix based on the output file descriptor type. */
idx_suffix(htsFile * fp)89 static char *idx_suffix(htsFile *fp) {
90 switch (fp->format.format) {
91 case sam:
92 case bam:
93 // Tough cheese if you wanted bai!
94 // New feature => mandatory new index too, for simplicity of CLI.
95 return "csi";
96
97 case cram:
98 return "crai";
99
100 default:
101 return NULL;
102 }
103 }
104
105 /*
106 * Utility function to add an index to a file we've opened for write.
107 * NB: Call this after writing the header and before writing sequences.
108 *
109 * The returned index filename should be freed by the caller, but only
110 * after sam_idx_save has been called.
111 *
112 * Returns index filename on success,
113 * NULL on failure.
114 */
auto_index(htsFile * fp,const char * fn,bam_hdr_t * header)115 char *auto_index(htsFile *fp, const char *fn, bam_hdr_t *header) {
116 char *fn_idx;
117 int min_shift = 14; /* CSI */
118 if (!fn || !*fn || strcmp(fn, "-") == 0)
119 return NULL;
120
121 char *delim = strstr(fn, HTS_IDX_DELIM);
122 if (delim != NULL) {
123 delim += strlen(HTS_IDX_DELIM);
124
125 fn_idx = strdup(delim);
126 if (!fn_idx)
127 return NULL;
128
129 size_t l = strlen(fn_idx);
130 if (l >= 4 && strcmp(fn_idx + l - 4, ".bai") == 0)
131 min_shift = 0;
132 } else {
133 char *suffix = idx_suffix(fp);
134 if (!suffix)
135 return NULL;
136
137 fn_idx = malloc(strlen(fn)+6);
138 if (!fn_idx)
139 return NULL;
140
141 sprintf(fn_idx, "%s.%s", fn, suffix);
142 }
143
144 if (sam_idx_init(fp, header, min_shift, fn_idx) < 0) {
145 print_error_errno("auto_index", "failed to open index \"%s\" for writing", fn_idx);
146 free(fn_idx);
147 return NULL;
148 }
149
150 return fn_idx;
151 }
152