6 #include "sam_header.h"
11 KHASH_SET_INIT_STR(rg)
13 // When counting records instead of printing them,
14 // data passed to the bam_fetch callback is encapsulated in this struct.
20 typedef khash_t(rg) *rghash_t;
22 // FIXME: we'd better use no global variables...
23 static rghash_t g_rghash = 0;
24 static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0, g_qual_scale = 0, g_min_qlen = 0;
25 static uint32_t g_subsam_seed = 0;
26 static double g_subsam_frac = -1.;
27 static char *g_library, *g_rg;
30 void *bed_read(const char *fn);
31 void bed_destroy(void *_h);
32 int bed_overlap(const void *_h, const char *chr, int beg, int end);
34 static int process_aln(const bam_header_t *h, bam1_t *b)
36 if (g_qual_scale > 1) {
38 uint8_t *qual = bam1_qual(b);
39 for (i = 0; i < b->core.l_qseq; ++i) {
40 int c = qual[i] * g_qual_scale;
41 qual[i] = c < 93? c : 93;
46 uint32_t *cigar = bam1_cigar(b);
47 for (k = 0; k < b->core.n_cigar; ++k)
48 if ((bam_cigar_type(bam_cigar_op(cigar[k]))&1) || bam_cigar_op(cigar[k]) == BAM_CHARD_CLIP)
49 qlen += bam_cigar_oplen(cigar[k]);
50 if (qlen < g_min_qlen) return 1;
52 if (b->core.qual < g_min_mapQ || ((b->core.flag & g_flag_on) != g_flag_on) || (b->core.flag & g_flag_off))
54 if (g_bed && b->core.tid >= 0 && !bed_overlap(g_bed, h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b))))
56 if (g_subsam_frac > 0.) {
57 uint32_t k = __ac_X31_hash_string(bam1_qname(b)) + g_subsam_seed;
58 if ((double)(k&0xffffff) / 0x1000000 >= g_subsam_frac) return 1;
60 if (g_rg || g_rghash) {
61 uint8_t *s = bam_aux_get(b, "RG");
63 if (g_rg) return (strcmp(g_rg, (char*)(s + 1)) == 0)? 0 : 1;
65 khint_t k = kh_get(rg, g_rghash, (char*)(s + 1));
66 return (k != kh_end(g_rghash))? 0 : 1;
71 const char *p = bam_get_library((bam_header_t*)h, b);
72 return (p && strcmp(p, g_library) == 0)? 0 : 1;
77 static char *drop_rg(char *hdtxt, rghash_t h, int *len)
79 char *p = hdtxt, *q, *r, *s;
81 memset(&str, 0, sizeof(kstring_t));
85 if (q == 0) q = p + strlen(p);
86 if (q - p < 3) break; // the line is too short; then stop
87 if (strncmp(p, "@RG\t", 4) == 0) {
90 if ((r = strstr(p, "\tID:")) != 0) {
92 for (s = r; *s != '\0' && *s != '\n' && *s != '\t'; ++s);
96 if (k != kh_end(h)) toprint = 1;
100 kputsn(p, q - p, &str); kputc('\n', &str);
108 // callback function for bam_fetch() that prints nonskipped records
109 static int view_func(const bam1_t *b, void *data)
111 if (!process_aln(((samfile_t*)data)->header, (bam1_t*)b))
112 samwrite((samfile_t*)data, b);
116 // callback function for bam_fetch() that counts nonskipped records
117 static int count_func(const bam1_t *b, void *data)
119 if (!process_aln(((count_func_data_t*)data)->header, (bam1_t*)b)) {
120 (*((count_func_data_t*)data)->count)++;
125 static int usage(int is_long_help);
127 int main_samview(int argc, char *argv[])
129 int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, compress_level = -1, is_bamout = 0, is_count = 0;
130 int of_type = BAM_OFDEC, is_long_help = 0, n_threads = 0;
132 samfile_t *in = 0, *out = 0;
133 char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0, *fn_rg = 0, *q;
135 /* parse command-line options */
136 strcpy(in_mode, "r"); strcpy(out_mode, "w");
137 while ((c = getopt(argc, argv, "SbBct:h1Ho:q:f:F:ul:r:xX?T:R:L:s:Q:@:m:")) >= 0) {
140 if ((g_subsam_seed = strtol(optarg, &q, 10)) != 0) {
141 srand(g_subsam_seed);
142 g_subsam_seed = rand();
144 g_subsam_frac = strtod(q, &q);
146 case 'm': g_min_qlen = atoi(optarg); break;
147 case 'c': is_count = 1; break;
148 case 'S': is_bamin = 0; break;
149 case 'b': is_bamout = 1; break;
150 case 't': fn_list = strdup(optarg); is_bamin = 0; break;
151 case 'h': is_header = 1; break;
152 case 'H': is_header_only = 1; break;
153 case 'o': fn_out = strdup(optarg); break;
154 case 'f': g_flag_on = strtol(optarg, 0, 0); break;
155 case 'F': g_flag_off = strtol(optarg, 0, 0); break;
156 case 'q': g_min_mapQ = atoi(optarg); break;
157 case 'u': compress_level = 0; break;
158 case '1': compress_level = 1; break;
159 case 'l': g_library = strdup(optarg); break;
160 case 'L': g_bed = bed_read(optarg); break;
161 case 'r': g_rg = strdup(optarg); break;
162 case 'R': fn_rg = strdup(optarg); break;
163 case 'x': of_type = BAM_OFHEX; break;
164 case 'X': of_type = BAM_OFSTR; break;
165 case '?': is_long_help = 1; break;
166 case 'T': fn_ref = strdup(optarg); is_bamin = 0; break;
167 case 'B': bam_no_B = 1; break;
168 case 'Q': g_qual_scale = atoi(optarg); break;
169 case '@': n_threads = strtol(optarg, 0, 0); break;
170 default: return usage(is_long_help);
173 if (compress_level >= 0) is_bamout = 1;
174 if (is_header_only) is_header = 1;
175 if (is_bamout) strcat(out_mode, "b");
177 if (of_type == BAM_OFHEX) strcat(out_mode, "x");
178 else if (of_type == BAM_OFSTR) strcat(out_mode, "X");
180 if (is_bamin) strcat(in_mode, "b");
181 if (is_header) strcat(out_mode, "h");
182 if (compress_level >= 0) {
184 tmp[0] = compress_level + '0'; tmp[1] = '\0';
185 strcat(out_mode, tmp);
187 if (argc == optind) return usage(is_long_help); // potential memory leak...
189 // read the list of read groups
194 g_rghash = kh_init(rg);
195 fp_rg = fopen(fn_rg, "r");
196 while (!feof(fp_rg) && fscanf(fp_rg, "%s", buf) > 0) // this is not a good style, but bear me...
197 kh_put(rg, g_rghash, strdup(buf), &ret); // we'd better check duplicates...
201 // generate the fn_list if necessary
202 if (fn_list == 0 && fn_ref) fn_list = samfaipath(fn_ref);
203 // open file handlers
204 if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
205 fprintf(stderr, "[main_samview] fail to open \"%s\" for reading.\n", argv[optind]);
209 if (in->header == 0) {
210 fprintf(stderr, "[main_samview] fail to read the header from \"%s\".\n", argv[optind]);
214 if (g_rghash) { // FIXME: I do not know what "bam_header_t::n_text" is for...
217 tmp = drop_rg(in->header->text, g_rghash, &l);
218 free(in->header->text);
219 in->header->text = tmp;
220 in->header->l_text = l;
222 if (!is_count && (out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
223 fprintf(stderr, "[main_samview] fail to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
227 if (n_threads > 1) samthreads(out, n_threads, 256);
228 if (is_header_only) goto view_end; // no need to print alignments
230 if (argc == optind + 1) { // convert/print the entire file
231 bam1_t *b = bam_init1();
233 while ((r = samread(in, b)) >= 0) { // read one alignment from `in'
234 if (!process_aln(in->header, b)) {
235 if (!is_count) samwrite(out, b); // write the alignment to `out'
240 fprintf(stderr, "[main_samview] truncated file.\n");
244 } else { // retrieve alignments in specified regions
246 bam_index_t *idx = 0;
247 if (is_bamin) idx = bam_index_load(argv[optind]); // load BAM index
248 if (idx == 0) { // index is unavailable
249 fprintf(stderr, "[main_samview] random alignment retrieval only works for indexed BAM files.\n");
253 for (i = optind + 1; i < argc; ++i) {
254 int tid, beg, end, result;
255 bam_parse_region(in->header, argv[i], &tid, &beg, &end); // parse a region in the format like `chr2:100-200'
256 if (tid < 0) { // reference name is not found
257 fprintf(stderr, "[main_samview] region \"%s\" specifies an unknown reference name. Continue anyway.\n", argv[i]);
262 count_func_data_t count_data = { in->header, &count };
263 result = bam_fetch(in->x.bam, idx, tid, beg, end, &count_data, count_func);
265 result = bam_fetch(in->x.bam, idx, tid, beg, end, out, view_func);
267 fprintf(stderr, "[main_samview] retrieval of region \"%s\" failed due to truncated file or corrupt BAM index file\n", argv[i]);
272 bam_index_destroy(idx); // destroy the BAM index
276 if (is_count && ret == 0) {
277 printf("%d\n", count);
279 // close files, free and return
280 free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg); free(fn_rg);
281 if (g_bed) bed_destroy(g_bed);
284 for (k = 0; k < kh_end(g_rghash); ++k)
285 if (kh_exist(g_rghash, k)) free((char*)kh_key(g_rghash, k));
286 kh_destroy(rg, g_rghash);
294 static int usage(int is_long_help)
296 fprintf(stderr, "\n");
297 fprintf(stderr, "Usage: samtools view [options] <in.bam>|<in.sam> [region1 [...]]\n\n");
298 fprintf(stderr, "Options: -b output BAM\n");
299 fprintf(stderr, " -h print header for the SAM output\n");
300 fprintf(stderr, " -H print header only (no alignments)\n");
301 fprintf(stderr, " -S input is SAM\n");
302 fprintf(stderr, " -u uncompressed BAM output (force -b)\n");
303 fprintf(stderr, " -1 fast compression (force -b)\n");
304 fprintf(stderr, " -x output FLAG in HEX (samtools-C specific)\n");
305 fprintf(stderr, " -X output FLAG in string (samtools-C specific)\n");
306 fprintf(stderr, " -c print only the count of matching records\n");
307 fprintf(stderr, " -B collapse the backward CIGAR operation\n");
308 fprintf(stderr, " -@ INT number of BAM compression threads [0]\n");
309 fprintf(stderr, " -L FILE output alignments overlapping the input BED FILE [null]\n");
310 fprintf(stderr, " -t FILE list of reference names and lengths (force -S) [null]\n");
311 fprintf(stderr, " -T FILE reference sequence file (force -S) [null]\n");
312 fprintf(stderr, " -o FILE output file name [stdout]\n");
313 fprintf(stderr, " -R FILE list of read groups to be outputted [null]\n");
314 fprintf(stderr, " -f INT required flag, 0 for unset [0]\n");
315 fprintf(stderr, " -F INT filtering flag, 0 for unset [0]\n");
316 fprintf(stderr, " -q INT minimum mapping quality [0]\n");
317 fprintf(stderr, " -l STR only output reads in library STR [null]\n");
318 fprintf(stderr, " -r STR only output reads in read group STR [null]\n");
319 fprintf(stderr, " -s FLOAT fraction of templates to subsample; integer part as seed [-1]\n");
320 fprintf(stderr, " -? longer help\n");
321 fprintf(stderr, "\n");
323 fprintf(stderr, "Notes:\n\
325 1. By default, this command assumes the file on the command line is in\n\
326 the BAM format and it prints the alignments in SAM. If `-t' is\n\
327 applied, the input file is assumed to be in the SAM format. The\n\
328 file supplied with `-t' is SPACE/TAB delimited with the first two\n\
329 fields of each line consisting of the reference name and the\n\
330 corresponding sequence length. The `.fai' file generated by `faidx'\n\
331 can be used here. This file may be empty if reads are unaligned.\n\
333 2. SAM->BAM conversion: `samtools view -bT ref.fa in.sam.gz'.\n\
335 3. BAM->SAM conversion: `samtools view in.bam'.\n\
337 4. A region should be presented in one of the following formats:\n\
338 `chr1', `chr2:1,000' and `chr3:1000-2,000'. When a region is\n\
339 specified, the input alignment file must be an indexed BAM file.\n\
341 5. Option `-u' is preferred over `-b' when the output is piped to\n\
342 another samtools command.\n\
344 6. In a string FLAG, each character represents one bit with\n\
345 p=0x1 (paired), P=0x2 (properly paired), u=0x4 (unmapped),\n\
346 U=0x8 (mate unmapped), r=0x10 (reverse), R=0x20 (mate reverse)\n\
347 1=0x40 (first), 2=0x80 (second), s=0x100 (not primary), \n\
348 f=0x200 (failure) and d=0x400 (duplicate). Note that `-x' and\n\
349 `-X' are samtools-C specific. Picard and older samtools do not\n\
350 support HEX or string flags.\n\
355 int main_import(int argc, char *argv[])
360 fprintf(stderr, "Usage: bamtk import <in.ref_list> <in.sam> <out.bam>\n");
364 argv2 = calloc(6, sizeof(char*));
365 argv2[0] = "import", argv2[1] = "-o", argv2[2] = argv[3], argv2[3] = "-bt", argv2[4] = argv[1], argv2[5] = argv[2];
366 ret = main_samview(argc2, argv2);
371 int8_t seq_comp_table[16] = { 0, 8, 4, 12, 2, 10, 9, 14, 1, 6, 5, 13, 3, 11, 7, 15 };
373 int main_bam2fq(int argc, char *argv[])
379 int max_buf, c, no12 = 0;
380 while ((c = getopt(argc, argv, "n")) > 0)
381 if (c == 'n') no12 = 1;
383 fprintf(stderr, "Usage: samtools bam2fq <in.bam>\n");
386 fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
387 if (fp == 0) return 1;
388 h = bam_header_read(fp);
392 while (bam_read1(fp, b) >= 0) {
393 int i, qlen = b->core.l_qseq;
395 putchar('@'); fputs(bam1_qname(b), stdout);
396 if (no12) putchar('\n');
398 if ((b->core.flag & 0x40) && !(b->core.flag & 0x80)) puts("/1");
399 else if ((b->core.flag & 0x80) && !(b->core.flag & 0x40)) puts("/2");
402 if (max_buf < qlen + 1) {
405 buf = realloc(buf, max_buf);
409 for (i = 0; i < qlen; ++i)
410 buf[i] = bam1_seqi(seq, i);
411 if (b->core.flag & 16) { // reverse complement
412 for (i = 0; i < qlen>>1; ++i) {
413 int8_t t = seq_comp_table[buf[qlen - 1 - i]];
414 buf[qlen - 1 - i] = seq_comp_table[buf[i]];
417 if (qlen&1) buf[i] = seq_comp_table[buf[i]];
419 for (i = 0; i < qlen; ++i)
420 buf[i] = bam_nt16_rev_table[buf[i]];
424 for (i = 0; i < qlen; ++i)
425 buf[i] = 33 + seq[i];
426 if (b->core.flag & 16) { // reverse
427 for (i = 0; i < qlen>>1; ++i) {
428 int8_t t = buf[qlen - 1 - i];
429 buf[qlen - 1 - i] = buf[i];
437 bam_header_destroy(h);