7 static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
8 static char *g_library;
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))
15 uint8_t *s = bam_aux_get(b, "RG");
17 const char *p = bam_strmap_get(h->rg2lib, (char*)(s + 1));
18 return (p && strcmp(p, g_library) == 0)? 0 : 1;
23 // callback function for bam_fetch()
24 static int view_func(const bam1_t *b, void *data)
26 if (!__g_skip_aln(((samfile_t*)data)->header, b))
27 samwrite((samfile_t*)data, b);
31 static int usage(void);
33 int main_samview(int argc, char *argv[])
35 int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0;
36 samfile_t *in = 0, *out = 0;
37 char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0;
39 /* parse command-line options */
40 strcpy(in_mode, "r"); strcpy(out_mode, "w");
41 while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:ul:")) >= 0) {
43 case 'S': is_bamin = 0; break;
44 case 'b': is_bamout = 1; break;
45 case 't': fn_list = strdup(optarg); is_bamin = 0; break;
46 case 'h': is_header = 1; break;
47 case 'H': is_header_only = 1; break;
48 case 'o': fn_out = strdup(optarg); break;
49 case 'f': g_flag_on = strtol(optarg, 0, 0); break;
50 case 'F': g_flag_off = strtol(optarg, 0, 0); break;
51 case 'q': g_min_mapQ = atoi(optarg); break;
52 case 'u': is_uncompressed = 1; break;
53 case 'l': g_library = strdup(optarg); break;
54 default: return usage();
57 if (is_uncompressed) is_bamout = 1;
58 if (is_header_only) is_header = 1;
59 if (is_bamout) strcat(out_mode, "b");
60 if (is_bamin) strcat(in_mode, "b");
61 if (is_header) strcat(out_mode, "h");
62 if (is_uncompressed) strcat(out_mode, "u");
63 if (argc == optind) return usage();
66 if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
67 fprintf(stderr, "[main_samview] fail to open file for reading.\n");
70 if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
71 fprintf(stderr, "[main_samview] fail to open file for writing.\n");
74 if (is_header_only) goto view_end; // no need to print alignments
76 if (argc == optind + 1) { // convert/print the entire file
77 bam1_t *b = bam_init1();
79 while ((r = samread(in, b)) >= 0) // read one alignment from `in'
80 if (!__g_skip_aln(in->header, b))
81 samwrite(out, b); // write the alignment to `out'
82 if (r < -1) fprintf(stderr, "[main_samview] truncated file.\n");
84 } else { // retrieve alignments in specified regions
87 if (is_bamin) idx = bam_index_load(argv[optind]); // load BAM index
88 if (idx == 0) { // index is unavailable
89 fprintf(stderr, "[main_samview] random alignment retrieval only works for indexed BAM files.\n");
93 for (i = optind + 1; i < argc; ++i) {
95 bam_parse_region(in->header, argv[i], &tid, &beg, &end); // parse a region in the format like `chr2:100-200'
96 if (tid < 0) { // reference name is not found
97 fprintf(stderr, "[main_samview] fail to get the reference name. Continue anyway.\n");
100 bam_fetch(in->x.bam, idx, tid, beg, end, out, view_func); // fetch alignments
102 bam_index_destroy(idx); // destroy the BAM index
106 // close files, free and return
107 free(fn_list); free(fn_out); free(g_library);
115 fprintf(stderr, "\n");
116 fprintf(stderr, "Usage: samtools view [options] <in.bam>|<in.sam> [region1 [...]]\n\n");
117 fprintf(stderr, "Options: -b output BAM\n");
118 fprintf(stderr, " -h print header for the SAM output\n");
119 fprintf(stderr, " -H print header only (no alignments)\n");
120 fprintf(stderr, " -S input is SAM\n");
121 fprintf(stderr, " -u uncompressed BAM output (force -b)\n");
122 fprintf(stderr, " -t FILE list of reference names and lengths (force -S) [null]\n");
123 fprintf(stderr, " -o FILE output file name [stdout]\n");
124 fprintf(stderr, " -f INT required flag, 0 for unset [0]\n");
125 fprintf(stderr, " -F INT filtering flag, 0 for unset [0]\n");
126 fprintf(stderr, " -q INT minimum mapping quality [0]\n");
130 1. By default, this command assumes the file on the command line is in\n\
131 the BAM format and it prints the alignments in SAM. If `-t' is\n\
132 applied, the input file is assumed to be in the SAM format. The\n\
133 file supplied with `-t' is SPACE/TAB delimited with the first two\n\
134 fields of each line consisting of the reference name and the\n\
135 corresponding sequence length. The `.fai' file generated by `faidx'\n\
136 can be used here. This file may be empty if reads are unaligned.\n\
138 2. SAM->BAM conversion: `samtools view -bt ref.fa.fai in.sam.gz'.\n\
140 3. BAM->SAM conversion: `samtools view in.bam'.\n\
142 4. A region should be presented in one of the following formats:\n\
143 `chr1', `chr2:1,000' and `chr3:1000-2,000'. When a region is\n\
144 specified, the input alignment file must be an indexed BAM file.\n\
149 int main_import(int argc, char *argv[])
154 fprintf(stderr, "Usage: bamtk import <in.ref_list> <in.sam> <out.bam>\n");
158 argv2 = calloc(6, sizeof(char*));
159 argv2[0] = "import", argv2[1] = "-o", argv2[2] = argv[3], argv2[3] = "-bt", argv2[4] = argv[1], argv2[5] = argv[2];
160 ret = main_samview(argc2, argv2);