7 static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
8 static char *g_library, *g_rg;
10 static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
12 if (b->core.qual < g_min_mapQ || ((b->core.flag & g_flag_on) != g_flag_on) || (b->core.flag & g_flag_off))
14 if (g_library || g_rg) {
15 uint8_t *s = bam_aux_get(b, "RG");
17 if (g_rg && strcmp(g_rg, (char*)(s + 1)) == 0) return 0;
19 const char *p = bam_strmap_get(h->rg2lib, (char*)(s + 1));
20 return (p && strcmp(p, g_library) == 0)? 0 : 1;
26 // callback function for bam_fetch()
27 static int view_func(const bam1_t *b, void *data)
29 if (!__g_skip_aln(((samfile_t*)data)->header, b))
30 samwrite((samfile_t*)data, b);
34 static int usage(void);
36 int main_samview(int argc, char *argv[])
38 int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0;
39 samfile_t *in = 0, *out = 0;
40 char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0;
42 /* parse command-line options */
43 strcpy(in_mode, "r"); strcpy(out_mode, "w");
44 while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:ul:r:")) >= 0) {
46 case 'S': is_bamin = 0; break;
47 case 'b': is_bamout = 1; break;
48 case 't': fn_list = strdup(optarg); is_bamin = 0; break;
49 case 'h': is_header = 1; break;
50 case 'H': is_header_only = 1; break;
51 case 'o': fn_out = strdup(optarg); break;
52 case 'f': g_flag_on = strtol(optarg, 0, 0); break;
53 case 'F': g_flag_off = strtol(optarg, 0, 0); break;
54 case 'q': g_min_mapQ = atoi(optarg); break;
55 case 'u': is_uncompressed = 1; break;
56 case 'l': g_library = strdup(optarg); break;
57 case 'r': g_rg = strdup(optarg); break;
58 default: return usage();
61 if (is_uncompressed) is_bamout = 1;
62 if (is_header_only) is_header = 1;
63 if (is_bamout) strcat(out_mode, "b");
64 if (is_bamin) strcat(in_mode, "b");
65 if (is_header) strcat(out_mode, "h");
66 if (is_uncompressed) strcat(out_mode, "u");
67 if (argc == optind) return usage();
70 if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
71 fprintf(stderr, "[main_samview] fail to open file for reading.\n");
74 if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
75 fprintf(stderr, "[main_samview] fail to open file for writing.\n");
78 if (is_header_only) goto view_end; // no need to print alignments
80 if (argc == optind + 1) { // convert/print the entire file
81 bam1_t *b = bam_init1();
83 while ((r = samread(in, b)) >= 0) // read one alignment from `in'
84 if (!__g_skip_aln(in->header, b))
85 samwrite(out, b); // write the alignment to `out'
86 if (r < -1) fprintf(stderr, "[main_samview] truncated file.\n");
88 } else { // retrieve alignments in specified regions
91 if (is_bamin) idx = bam_index_load(argv[optind]); // load BAM index
92 if (idx == 0) { // index is unavailable
93 fprintf(stderr, "[main_samview] random alignment retrieval only works for indexed BAM files.\n");
97 for (i = optind + 1; i < argc; ++i) {
99 bam_parse_region(in->header, argv[i], &tid, &beg, &end); // parse a region in the format like `chr2:100-200'
100 if (tid < 0) { // reference name is not found
101 fprintf(stderr, "[main_samview] fail to get the reference name. Continue anyway.\n");
104 bam_fetch(in->x.bam, idx, tid, beg, end, out, view_func); // fetch alignments
106 bam_index_destroy(idx); // destroy the BAM index
110 // close files, free and return
111 free(fn_list); free(fn_out); free(g_library); free(g_rg);
119 fprintf(stderr, "\n");
120 fprintf(stderr, "Usage: samtools view [options] <in.bam>|<in.sam> [region1 [...]]\n\n");
121 fprintf(stderr, "Options: -b output BAM\n");
122 fprintf(stderr, " -h print header for the SAM output\n");
123 fprintf(stderr, " -H print header only (no alignments)\n");
124 fprintf(stderr, " -S input is SAM\n");
125 fprintf(stderr, " -u uncompressed BAM output (force -b)\n");
126 fprintf(stderr, " -t FILE list of reference names and lengths (force -S) [null]\n");
127 fprintf(stderr, " -o FILE output file name [stdout]\n");
128 fprintf(stderr, " -f INT required flag, 0 for unset [0]\n");
129 fprintf(stderr, " -F INT filtering flag, 0 for unset [0]\n");
130 fprintf(stderr, " -q INT minimum mapping quality [0]\n");
131 fprintf(stderr, " -l STR only output reads in library STR [null]\n");
132 fprintf(stderr, " -r STR only output reads in read group STR [null]\n");
136 1. By default, this command assumes the file on the command line is in\n\
137 the BAM format and it prints the alignments in SAM. If `-t' is\n\
138 applied, the input file is assumed to be in the SAM format. The\n\
139 file supplied with `-t' is SPACE/TAB delimited with the first two\n\
140 fields of each line consisting of the reference name and the\n\
141 corresponding sequence length. The `.fai' file generated by `faidx'\n\
142 can be used here. This file may be empty if reads are unaligned.\n\
144 2. SAM->BAM conversion: `samtools view -bt ref.fa.fai in.sam.gz'.\n\
146 3. BAM->SAM conversion: `samtools view in.bam'.\n\
148 4. A region should be presented in one of the following formats:\n\
149 `chr1', `chr2:1,000' and `chr3:1000-2,000'. When a region is\n\
150 specified, the input alignment file must be an indexed BAM file.\n\
152 5. Option `-u' is preferred over `-b' when the output is piped to\n\
153 another samtools command.\n\
158 int main_import(int argc, char *argv[])
163 fprintf(stderr, "Usage: bamtk import <in.ref_list> <in.sam> <out.bam>\n");
167 argv2 = calloc(6, sizeof(char*));
168 argv2[0] = "import", argv2[1] = "-o", argv2[2] = argv[3], argv2[3] = "-bt", argv2[4] = argv[1], argv2[5] = argv[2];
169 ret = main_samview(argc2, argv2);