5 #include "sam_header.h"
10 bam_header_t *bam_header_dup(const bam_header_t *h0); /*in sam.c*/
12 static void replace_cigar(bam1_t *b, int n, uint32_t *cigar)
14 if (n != b->core.n_cigar) {
15 int o = b->core.l_qname + b->core.n_cigar * 4;
16 if (b->data_len + (n - b->core.n_cigar) * 4 > b->m_data) {
17 b->m_data = b->data_len + (n - b->core.n_cigar) * 4;
18 kroundup32(b->m_data);
19 b->data = (uint8_t*)realloc(b->data, b->m_data);
21 memmove(b->data + b->core.l_qname + n * 4, b->data + o, b->data_len - o);
22 memcpy(b->data + b->core.l_qname, cigar, n * 4);
23 b->data_len += (n - b->core.n_cigar) * 4;
25 } else memcpy(b->data + b->core.l_qname, cigar, n * 4);
28 #define write_cigar(_c, _n, _m, _v) do { \
31 _c = (uint32_t*)realloc(_c, _m * 4); \
36 static void unpad_seq(bam1_t *b, kstring_t *s)
40 uint32_t *cigar = bam1_cigar(b);
41 uint8_t *seq = bam1_seq(b);
42 // b->core.l_qseq gives length of the SEQ entry (including soft clips, S)
43 // We need the padded length after alignment from the CIGAR (excluding
44 // soft clips S, but including pads from CIGAR D operations)
46 for (k = 0; k < b->core.n_cigar; ++k) {
48 op= bam_cigar_op(cigar[k]);
49 ol = bam_cigar_oplen(cigar[k]);
50 if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF || op == BAM_CDEL)
54 for (k = 0, s->l = 0, j = 0; k < b->core.n_cigar; ++k) {
56 op = bam_cigar_op(cigar[k]);
57 ol = bam_cigar_oplen(cigar[k]);
58 if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
59 for (i = 0; i < ol; ++i, ++j) s->s[s->l++] = bam1_seqi(seq, j);
60 } else if (op == BAM_CSOFT_CLIP) {
62 } else if (op == BAM_CHARD_CLIP) {
64 } else if (op == BAM_CDEL) {
65 for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
67 fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in read %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
71 assert(length == s->l);
74 int load_unpadded_ref(faidx_t *fai, char *ref_name, int ref_len, kstring_t *seq)
78 int fai_ref_len = 0, k;
80 fai_ref = fai_fetch(fai, ref_name, &fai_ref_len);
81 if (fai_ref_len != ref_len) {
82 fprintf(stderr, "[depad] ERROR: FASTA sequence %s length %i, expected %i\n", ref_name, fai_ref_len, ref_len);
86 ks_resize(seq, ref_len);
88 for (k = 0; k < ref_len; ++k) {
90 if (base == '-' || base == '*') {
91 // Map gaps to null to match unpad_seq function
94 int i = bam_nt16_table[(int)base];
95 if (i == 0 || i==16) { // Equals maps to 0, anything unexpected to 16
96 fprintf(stderr, "[depad] ERROR: Invalid character %c (ASCII %i) in FASTA sequence %s\n", base, (int)base, ref_name);
100 seq->s[seq->l++] = i;
103 assert(ref_len == seq->l);
108 int get_unpadded_len(faidx_t *fai, char *ref_name, int padded_len)
112 int fai_ref_len = 0, k;
115 fai_ref = fai_fetch(fai, ref_name, &fai_ref_len);
116 if (fai_ref_len != padded_len) {
117 fprintf(stderr, "[depad] ERROR: FASTA sequence '%s' length %i, expected %i\n", ref_name, fai_ref_len, padded_len);
121 for (k = 0; k < padded_len; ++k) {
122 //fprintf(stderr, "[depad] checking base %i of %i or %i\n", k+1, ref_len, strlen(fai_ref));
124 if (base == '-' || base == '*') {
127 int i = bam_nt16_table[(int)base];
128 if (i == 0 || i==16) { // Equals maps to 0, anything unexpected to 16
129 fprintf(stderr, "[depad] ERROR: Invalid character %c (ASCII %i) in FASTA sequence '%s'\n", base, (int)base, ref_name);
137 assert (padded_len == bases + gaps);
141 inline int * update_posmap(int *posmap, kstring_t ref)
144 posmap = realloc(posmap, ref.m * sizeof(int));
145 for (i = k = 0; i < ref.l; ++i) {
152 int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
158 uint32_t *cigar2 = 0;
159 int ret = 0, n2 = 0, m2 = 0, *posmap = 0;
162 r.l = r.m = q.l = q.m = 0; r.s = q.s = 0;
165 while ((read_ret = samread(in, b)) >= 0) { // read one alignment from `in'
166 uint32_t *cigar = bam1_cigar(b);
168 if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) {
169 // fprintf(stderr, "[depad] Found embedded reference %s\n", bam1_qname(b));
172 if (h->target_len[r_tid] != r.l) {
173 fprintf(stderr, "[depad] ERROR: (Padded) length of '%s' is %d in BAM header, but %ld in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l);
177 // Check the embedded reference matches the FASTA file
178 if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &q)) {
179 fprintf(stderr, "[depad] ERROR: Failed to load embedded reference '%s' from FASTA\n", h->target_name[b->core.tid]);
184 for (i = 0; i < r.l; ++i) {
185 if (r.s[i] != q.s[i]) {
186 // Show gaps as ASCII 45
187 fprintf(stderr, "[depad] ERROR: Embedded sequence and reference FASTA don't match for %s base %i, '%c' vs '%c'\n",
188 h->target_name[b->core.tid], i+1,
189 r.s[i] ? bam_nt16_rev_table[(int)r.s[i]] : 45,
190 q.s[i] ? bam_nt16_rev_table[(int)q.s[i]] : 45);
195 write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
196 replace_cigar(b, n2, cigar2);
197 posmap = update_posmap(posmap, r);
198 } else if (b->core.n_cigar > 0) {
200 if (b->core.tid < 0) {
201 fprintf(stderr, "[depad] ERROR: Read '%s' has CIGAR but no RNAME\n", bam1_qname(b));
203 } else if (b->core.tid == r_tid) {
204 ; // good case, reference available
206 if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &r)) {
207 fprintf(stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", h->target_name[b->core.tid]);
210 posmap = update_posmap(posmap, r);
212 // fprintf(stderr, "[depad] Loaded %s from FASTA file\n", h->target_name[b->core.tid]);
214 fprintf(stderr, "[depad] ERROR: Missing %s embedded reference sequence (and no FASTA file)\n", h->target_name[b->core.tid]);
218 if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) {
219 write_cigar(cigar2, n2, m2, cigar[0]);
220 } else if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) {
221 write_cigar(cigar2, n2, m2, cigar[0]);
222 if (b->core.n_cigar > 2 && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) {
223 write_cigar(cigar2, n2, m2, cigar[1]);
226 /* Determine CIGAR operator for each base in the aligned read */
227 for (i = 0, k = b->core.pos; i < q.l; ++i, ++k)
228 q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD);
229 /* Include any pads if starts with an insert */
230 if (q.s[0] == BAM_CINS) {
231 for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k);
232 if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, BAM_CPAD));
234 /* Count consecutive CIGAR operators to turn into a CIGAR string */
235 for (i = k = 1, op = q.s[0]; i < q.l; ++i) {
237 write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
241 write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
242 if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) {
243 write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
244 } else if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) {
245 if (b->core.n_cigar > 2 && bam_cigar_op(cigar[b->core.n_cigar-2]) == BAM_CSOFT_CLIP) {
246 write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-2]);
248 write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
250 /* Remove redundant P operators between M/X/=/D operators, e.g. 5M2P10M -> 15M */
252 for (i = 2; i < n2; ++i)
253 if (bam_cigar_op(cigar2[i-1]) == BAM_CPAD) {
254 pre_op = bam_cigar_op(cigar2[i-2]);
255 post_op = bam_cigar_op(cigar2[i]);
256 /* Note don't need to check for X/= as code above will use M only */
257 if ((pre_op == BAM_CMATCH || pre_op == BAM_CDEL) && (post_op == BAM_CMATCH || post_op == BAM_CDEL)) {
258 /* This is a redundant P operator */
259 cigar2[i-1] = 0; // i.e. 0M
260 /* If had same operator either side, combine them in post_op */
261 if (pre_op == post_op) {
262 /* If CIGAR M, could treat as simple integers since BAM_CMATCH is zero*/
263 cigar2[i] = bam_cigar_gen(bam_cigar_oplen(cigar2[i-2]) + bam_cigar_oplen(cigar2[i]), post_op);
264 cigar2[i-2] = 0; // i.e. 0M
268 /* Remove the zero'd operators (0M) */
269 for (i = k = 0; i < n2; ++i)
270 if (cigar2[i]) cigar2[k++] = cigar2[i];
272 replace_cigar(b, n2, cigar2);
273 b->core.pos = posmap[b->core.pos];
278 fprintf(stderr, "[depad] truncated file.\n");
281 free(r.s); free(q.s); free(posmap);
286 bam_header_t * fix_header(bam_header_t *old, faidx_t *fai)
288 int i = 0, unpadded_len = 0;
289 bam_header_t *header = 0 ;
291 header = bam_header_dup(old);
292 for (i = 0; i < old->n_targets; ++i) {
293 unpadded_len = get_unpadded_len(fai, old->target_name[i], old->target_len[i]);
294 if (unpadded_len < 0) {
295 fprintf(stderr, "[depad] ERROR getting unpadded length of '%s', padded length %i\n", old->target_name[i], old->target_len[i]);
297 header->target_len[i] = unpadded_len;
298 //fprintf(stderr, "[depad] Recalculating '%s' length %i -> %i\n", old->target_name[i], old->target_len[i], header->target_len[i]);
301 /* Duplicating the header allocated new buffer for header string */
302 /* After modifying the @SQ lines it will only get smaller, since */
303 /* the LN entries will be the same or shorter, and we'll remove */
304 /* any MD entries (MD5 checksums). */
305 assert(strlen(old->text) == strlen(header->text));
306 assert (0==strcmp(old->text, header->text));
309 header->text[0] = '\0'; /* Resuse the allocated buffer */
310 char * newtext = header->text;
312 while (text[0]=='@') {
313 end = strchr(text, '\n');
315 if (text[1]=='S' && text[2]=='Q' && text[3]=='\t') {
316 /* TODO - edit the @SQ line here to remove MD and fix LN. */
317 /* For now just remove the @SQ line, and samtools will */
318 /* automatically generate a minimal replacement with LN. */
319 /* However, that discards any other tags like AS, SP, UR. */
320 //fprintf(stderr, "[depad] Removing @SQ line\n");
322 /* Copy this line to the new header */
323 strncat(newtext, text, end - text + 1);
327 assert (text[0]=='\0');
328 /* Check we didn't overflow the buffer */
329 assert (strlen(header->text) <= strlen(old->text));
330 if (strlen(header->text) < header->l_text) {
331 //fprintf(stderr, "[depad] Reallocating header buffer\n");
332 assert (newtext == header->text);
333 newtext = calloc(strlen(header->text) + 1, 1);
334 strcpy(newtext, header->text);
336 header->text = newtext;
337 header->l_text = strlen(newtext);
339 //fprintf(stderr, "[depad] Here is the new header (pending @SQ lines),\n\n%s\n(end)\n", header->text);
343 static int usage(int is_long_help);
345 int main_pad2unpad(int argc, char *argv[])
347 samfile_t *in = 0, *out = 0;
350 int c, is_bamin = 1, compress_level = -1, is_bamout = 1, is_long_help = 0;
351 char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0;
354 /* parse command-line options */
355 strcpy(in_mode, "r"); strcpy(out_mode, "w");
356 while ((c = getopt(argc, argv, "Sso:u1T:?")) >= 0) {
358 case 'S': is_bamin = 0; break;
359 case 's': assert(compress_level == -1); is_bamout = 0; break;
360 case 'o': fn_out = strdup(optarg); break;
361 case 'u': assert(is_bamout == 1); compress_level = 0; break;
362 case '1': assert(is_bamout == 1); compress_level = 1; break;
363 case 'T': fn_ref = strdup(optarg); break;
364 case '?': is_long_help = 1; break;
365 default: return usage(is_long_help);
368 if (argc == optind) return usage(is_long_help);
370 if (is_bamin) strcat(in_mode, "b");
371 if (is_bamout) strcat(out_mode, "b");
372 strcat(out_mode, "h");
373 if (compress_level >= 0) {
375 tmp[0] = compress_level + '0'; tmp[1] = '\0';
376 strcat(out_mode, tmp);
379 // Load FASTA reference (also needed for SAM -> BAM if missing header)
381 fn_list = samfaipath(fn_ref);
382 fai = fai_load(fn_ref);
384 // open file handlers
385 if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
386 fprintf(stderr, "[depad] failed to open \"%s\" for reading.\n", argv[optind]);
390 if (in->header == 0) {
391 fprintf(stderr, "[depad] failed to read the header from \"%s\".\n", argv[optind]);
395 if (in->header->text == 0 || in->header->l_text == 0) {
396 fprintf(stderr, "[depad] Warning - failed to read any header text from \"%s\".\n", argv[optind]);
397 assert (0 == in->header->l_text);
398 assert (0 == in->header->text);
401 h = fix_header(in->header, fai);
403 fprintf(stderr, "[depad] Warning - reference lengths will not be corrected without FASTA reference\n");
406 if ((out = samopen(fn_out? fn_out : "-", out_mode, h)) == 0) {
407 fprintf(stderr, "[depad] failed to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
413 ret = bam_pad2unpad(in, out, fai);
416 // close files, free and return
417 free(fn_list); free(fn_out);
418 if (h != in->header) bam_header_destroy(h);
425 static int usage(int is_long_help)
427 fprintf(stderr, "\n");
428 fprintf(stderr, "Usage: samtools depad <in.bam>\n\n");
429 fprintf(stderr, "Options: -s output is SAM (default is BAM)\n");
430 fprintf(stderr, " -S input is SAM (default is BAM)\n");
431 fprintf(stderr, " -u uncompressed BAM output (can't use with -s)\n");
432 fprintf(stderr, " -1 fast compression BAM output (can't use with -s)\n");
433 fprintf(stderr, " -T FILE reference sequence file [null]\n");
434 fprintf(stderr, " -o FILE output file name [stdout]\n");
435 fprintf(stderr, " -? longer help\n");
436 fprintf(stderr, "\n");
438 fprintf(stderr, "Notes:\n\
440 1. Requires embedded reference sequences (before the reads for that reference),\n\
441 with the future aim to also support a FASTA padded reference sequence file.\n\
443 2. The input padded alignment read's CIGAR strings must not use P or I operators.\n\