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comparison pyPRADA_1.2/tools/samtools-0.1.16/bam_sort.c @ 0:acc2ca1a3ba4

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author siyuan
date Thu, 20 Feb 2014 00:44:58 -0500
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1 #include <stdlib.h>
2 #include <ctype.h>
3 #include <assert.h>
4 #include <errno.h>
5 #include <stdio.h>
6 #include <string.h>
7 #include <unistd.h>
8 #include "bam.h"
9 #include "ksort.h"
10
11 static int g_is_by_qname = 0;
12
13 static inline int strnum_cmp(const char *a, const char *b)
14 {
15 char *pa, *pb;
16 pa = (char*)a; pb = (char*)b;
17 while (*pa && *pb) {
18 if (isdigit(*pa) && isdigit(*pb)) {
19 long ai, bi;
20 ai = strtol(pa, &pa, 10);
21 bi = strtol(pb, &pb, 10);
22 if (ai != bi) return ai<bi? -1 : ai>bi? 1 : 0;
23 } else {
24 if (*pa != *pb) break;
25 ++pa; ++pb;
26 }
27 }
28 if (*pa == *pb)
29 return (pa-a) < (pb-b)? -1 : (pa-a) > (pb-b)? 1 : 0;
30 return *pa<*pb? -1 : *pa>*pb? 1 : 0;
31 }
32
33 #define HEAP_EMPTY 0xffffffffffffffffull
34
35 typedef struct {
36 int i;
37 uint64_t pos, idx;
38 bam1_t *b;
39 } heap1_t;
40
41 #define __pos_cmp(a, b) ((a).pos > (b).pos || ((a).pos == (b).pos && ((a).i > (b).i || ((a).i == (b).i && (a).idx > (b).idx))))
42
43 static inline int heap_lt(const heap1_t a, const heap1_t b)
44 {
45 if (g_is_by_qname) {
46 int t;
47 if (a.b == 0 || b.b == 0) return a.b == 0? 1 : 0;
48 t = strnum_cmp(bam1_qname(a.b), bam1_qname(b.b));
49 return (t > 0 || (t == 0 && __pos_cmp(a, b)));
50 } else return __pos_cmp(a, b);
51 }
52
53 KSORT_INIT(heap, heap1_t, heap_lt)
54
55 static void swap_header_targets(bam_header_t *h1, bam_header_t *h2)
56 {
57 bam_header_t t;
58 t.n_targets = h1->n_targets, h1->n_targets = h2->n_targets, h2->n_targets = t.n_targets;
59 t.target_name = h1->target_name, h1->target_name = h2->target_name, h2->target_name = t.target_name;
60 t.target_len = h1->target_len, h1->target_len = h2->target_len, h2->target_len = t.target_len;
61 }
62
63 static void swap_header_text(bam_header_t *h1, bam_header_t *h2)
64 {
65 int tempi;
66 char *temps;
67 tempi = h1->l_text, h1->l_text = h2->l_text, h2->l_text = tempi;
68 temps = h1->text, h1->text = h2->text, h2->text = temps;
69 }
70
71 #define MERGE_RG 1
72 #define MERGE_UNCOMP 2
73 #define MERGE_LEVEL1 4
74 #define MERGE_FORCE 8
75
76 /*!
77 @abstract Merge multiple sorted BAM.
78 @param is_by_qname whether to sort by query name
79 @param out output BAM file name
80 @param headers name of SAM file from which to copy '@' header lines,
81 or NULL to copy them from the first file to be merged
82 @param n number of files to be merged
83 @param fn names of files to be merged
84
85 @discussion Padding information may NOT correctly maintained. This
86 function is NOT thread safe.
87 */
88 int bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn,
89 int flag, const char *reg)
90 {
91 bamFile fpout, *fp;
92 heap1_t *heap;
93 bam_header_t *hout = 0;
94 bam_header_t *hheaders = NULL;
95 int i, j, *RG_len = 0;
96 uint64_t idx = 0;
97 char **RG = 0;
98 bam_iter_t *iter = 0;
99
100 if (headers) {
101 tamFile fpheaders = sam_open(headers);
102 if (fpheaders == 0) {
103 const char *message = strerror(errno);
104 fprintf(stderr, "[bam_merge_core] cannot open '%s': %s\n", headers, message);
105 return -1;
106 }
107 hheaders = sam_header_read(fpheaders);
108 sam_close(fpheaders);
109 }
110
111 g_is_by_qname = by_qname;
112 fp = (bamFile*)calloc(n, sizeof(bamFile));
113 heap = (heap1_t*)calloc(n, sizeof(heap1_t));
114 iter = (bam_iter_t*)calloc(n, sizeof(bam_iter_t));
115 // prepare RG tag
116 if (flag & MERGE_RG) {
117 RG = (char**)calloc(n, sizeof(void*));
118 RG_len = (int*)calloc(n, sizeof(int));
119 for (i = 0; i != n; ++i) {
120 int l = strlen(fn[i]);
121 const char *s = fn[i];
122 if (l > 4 && strcmp(s + l - 4, ".bam") == 0) l -= 4;
123 for (j = l - 1; j >= 0; --j) if (s[j] == '/') break;
124 ++j; l -= j;
125 RG[i] = calloc(l + 1, 1);
126 RG_len[i] = l;
127 strncpy(RG[i], s + j, l);
128 }
129 }
130 // read the first
131 for (i = 0; i != n; ++i) {
132 bam_header_t *hin;
133 fp[i] = bam_open(fn[i], "r");
134 if (fp[i] == 0) {
135 int j;
136 fprintf(stderr, "[bam_merge_core] fail to open file %s\n", fn[i]);
137 for (j = 0; j < i; ++j) bam_close(fp[j]);
138 free(fp); free(heap);
139 // FIXME: possible memory leak
140 return -1;
141 }
142 hin = bam_header_read(fp[i]);
143 if (i == 0) { // the first BAM
144 hout = hin;
145 } else { // validate multiple baf
146 int min_n_targets = hout->n_targets;
147 if (hin->n_targets < min_n_targets) min_n_targets = hin->n_targets;
148
149 for (j = 0; j < min_n_targets; ++j)
150 if (strcmp(hout->target_name[j], hin->target_name[j]) != 0) {
151 fprintf(stderr, "[bam_merge_core] different target sequence name: '%s' != '%s' in file '%s'\n",
152 hout->target_name[j], hin->target_name[j], fn[i]);
153 return -1;
154 }
155
156 // If this input file has additional target reference sequences,
157 // add them to the headers to be output
158 if (hin->n_targets > hout->n_targets) {
159 swap_header_targets(hout, hin);
160 // FIXME Possibly we should also create @SQ text headers
161 // for the newly added reference sequences
162 }
163
164 bam_header_destroy(hin);
165 }
166 }
167
168 if (hheaders) {
169 // If the text headers to be swapped in include any @SQ headers,
170 // check that they are consistent with the existing binary list
171 // of reference information.
172 if (hheaders->n_targets > 0) {
173 if (hout->n_targets != hheaders->n_targets) {
174 fprintf(stderr, "[bam_merge_core] number of @SQ headers in '%s' differs from number of target sequences\n", headers);
175 if (!reg) return -1;
176 }
177 for (j = 0; j < hout->n_targets; ++j)
178 if (strcmp(hout->target_name[j], hheaders->target_name[j]) != 0) {
179 fprintf(stderr, "[bam_merge_core] @SQ header '%s' in '%s' differs from target sequence\n", hheaders->target_name[j], headers);
180 if (!reg) return -1;
181 }
182 }
183
184 swap_header_text(hout, hheaders);
185 bam_header_destroy(hheaders);
186 }
187
188 if (reg) {
189 int tid, beg, end;
190 if (bam_parse_region(hout, reg, &tid, &beg, &end) < 0) {
191 fprintf(stderr, "[%s] Malformated region string or undefined reference name\n", __func__);
192 return -1;
193 }
194 for (i = 0; i < n; ++i) {
195 bam_index_t *idx;
196 idx = bam_index_load(fn[i]);
197 iter[i] = bam_iter_query(idx, tid, beg, end);
198 bam_index_destroy(idx);
199 }
200 }
201
202 for (i = 0; i < n; ++i) {
203 heap1_t *h = heap + i;
204 h->i = i;
205 h->b = (bam1_t*)calloc(1, sizeof(bam1_t));
206 if (bam_iter_read(fp[i], iter[i], h->b) >= 0) {
207 h->pos = ((uint64_t)h->b->core.tid<<32) | (uint32_t)((int32_t)h->b->core.pos+1)<<1 | bam1_strand(h->b);
208 h->idx = idx++;
209 }
210 else h->pos = HEAP_EMPTY;
211 }
212 if (flag & MERGE_UNCOMP) fpout = strcmp(out, "-")? bam_open(out, "wu") : bam_dopen(fileno(stdout), "wu");
213 else if (flag & MERGE_LEVEL1) fpout = strcmp(out, "-")? bam_open(out, "w1") : bam_dopen(fileno(stdout), "w1");
214 else fpout = strcmp(out, "-")? bam_open(out, "w") : bam_dopen(fileno(stdout), "w");
215 if (fpout == 0) {
216 fprintf(stderr, "[%s] fail to create the output file.\n", __func__);
217 return -1;
218 }
219 bam_header_write(fpout, hout);
220 bam_header_destroy(hout);
221
222 ks_heapmake(heap, n, heap);
223 while (heap->pos != HEAP_EMPTY) {
224 bam1_t *b = heap->b;
225 if (flag & MERGE_RG) {
226 uint8_t *rg = bam_aux_get(b, "RG");
227 if (rg) bam_aux_del(b, rg);
228 bam_aux_append(b, "RG", 'Z', RG_len[heap->i] + 1, (uint8_t*)RG[heap->i]);
229 }
230 bam_write1_core(fpout, &b->core, b->data_len, b->data);
231 if ((j = bam_iter_read(fp[heap->i], iter[heap->i], b)) >= 0) {
232 heap->pos = ((uint64_t)b->core.tid<<32) | (uint32_t)((int)b->core.pos+1)<<1 | bam1_strand(b);
233 heap->idx = idx++;
234 } else if (j == -1) {
235 heap->pos = HEAP_EMPTY;
236 free(heap->b->data); free(heap->b);
237 heap->b = 0;
238 } else fprintf(stderr, "[bam_merge_core] '%s' is truncated. Continue anyway.\n", fn[heap->i]);
239 ks_heapadjust(heap, 0, n, heap);
240 }
241
242 if (flag & MERGE_RG) {
243 for (i = 0; i != n; ++i) free(RG[i]);
244 free(RG); free(RG_len);
245 }
246 for (i = 0; i != n; ++i) {
247 bam_iter_destroy(iter[i]);
248 bam_close(fp[i]);
249 }
250 bam_close(fpout);
251 free(fp); free(heap); free(iter);
252 return 0;
253 }
254
255 int bam_merge(int argc, char *argv[])
256 {
257 int c, is_by_qname = 0, flag = 0, ret = 0;
258 char *fn_headers = NULL, *reg = 0;
259
260 while ((c = getopt(argc, argv, "h:nru1R:f")) >= 0) {
261 switch (c) {
262 case 'r': flag |= MERGE_RG; break;
263 case 'f': flag |= MERGE_FORCE; break;
264 case 'h': fn_headers = strdup(optarg); break;
265 case 'n': is_by_qname = 1; break;
266 case '1': flag |= MERGE_LEVEL1; break;
267 case 'u': flag |= MERGE_UNCOMP; break;
268 case 'R': reg = strdup(optarg); break;
269 }
270 }
271 if (optind + 2 >= argc) {
272 fprintf(stderr, "\n");
273 fprintf(stderr, "Usage: samtools merge [-nr] [-h inh.sam] <out.bam> <in1.bam> <in2.bam> [...]\n\n");
274 fprintf(stderr, "Options: -n sort by read names\n");
275 fprintf(stderr, " -r attach RG tag (inferred from file names)\n");
276 fprintf(stderr, " -u uncompressed BAM output\n");
277 fprintf(stderr, " -f overwrite the output BAM if exist\n");
278 fprintf(stderr, " -1 compress level 1\n");
279 fprintf(stderr, " -R STR merge file in the specified region STR [all]\n");
280 fprintf(stderr, " -h FILE copy the header in FILE to <out.bam> [in1.bam]\n\n");
281 fprintf(stderr, "Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users\n");
282 fprintf(stderr, " must provide the correct header with -h, or uses Picard which properly maintains\n");
283 fprintf(stderr, " the header dictionary in merging.\n\n");
284 return 1;
285 }
286 if (!(flag & MERGE_FORCE) && strcmp(argv[optind], "-")) {
287 FILE *fp = fopen(argv[optind], "rb");
288 if (fp != NULL) {
289 fclose(fp);
290 fprintf(stderr, "[%s] File '%s' exists. Please apply '-f' to overwrite. Abort.\n", __func__, argv[optind]);
291 return 1;
292 }
293 }
294 if (bam_merge_core(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, flag, reg) < 0) ret = 1;
295 free(reg);
296 free(fn_headers);
297 return ret;
298 }
299
300 typedef bam1_t *bam1_p;
301
302 static inline int bam1_lt(const bam1_p a, const bam1_p b)
303 {
304 if (g_is_by_qname) {
305 int t = strnum_cmp(bam1_qname(a), bam1_qname(b));
306 return (t < 0 || (t == 0 && (((uint64_t)a->core.tid<<32|(a->core.pos+1)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)))));
307 } else return (((uint64_t)a->core.tid<<32|(a->core.pos+1)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)));
308 }
309 KSORT_INIT(sort, bam1_p, bam1_lt)
310
311 static void sort_blocks(int n, int k, bam1_p *buf, const char *prefix, const bam_header_t *h, int is_stdout)
312 {
313 char *name, mode[3];
314 int i;
315 bamFile fp;
316 ks_mergesort(sort, k, buf, 0);
317 name = (char*)calloc(strlen(prefix) + 20, 1);
318 if (n >= 0) {
319 sprintf(name, "%s.%.4d.bam", prefix, n);
320 strcpy(mode, "w1");
321 } else {
322 sprintf(name, "%s.bam", prefix);
323 strcpy(mode, "w");
324 }
325 fp = is_stdout? bam_dopen(fileno(stdout), mode) : bam_open(name, mode);
326 if (fp == 0) {
327 fprintf(stderr, "[sort_blocks] fail to create file %s.\n", name);
328 free(name);
329 // FIXME: possible memory leak
330 return;
331 }
332 free(name);
333 bam_header_write(fp, h);
334 for (i = 0; i < k; ++i)
335 bam_write1_core(fp, &buf[i]->core, buf[i]->data_len, buf[i]->data);
336 bam_close(fp);
337 }
338
339 /*!
340 @abstract Sort an unsorted BAM file based on the chromosome order
341 and the leftmost position of an alignment
342
343 @param is_by_qname whether to sort by query name
344 @param fn name of the file to be sorted
345 @param prefix prefix of the output and the temporary files; upon
346 sucessess, prefix.bam will be written.
347 @param max_mem approxiate maximum memory (very inaccurate)
348
349 @discussion It may create multiple temporary subalignment files
350 and then merge them by calling bam_merge_core(). This function is
351 NOT thread safe.
352 */
353 void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size_t max_mem, int is_stdout)
354 {
355 int n, ret, k, i;
356 size_t mem;
357 bam_header_t *header;
358 bamFile fp;
359 bam1_t *b, **buf;
360
361 g_is_by_qname = is_by_qname;
362 n = k = 0; mem = 0;
363 fp = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
364 if (fp == 0) {
365 fprintf(stderr, "[bam_sort_core] fail to open file %s\n", fn);
366 return;
367 }
368 header = bam_header_read(fp);
369 buf = (bam1_t**)calloc(max_mem / BAM_CORE_SIZE, sizeof(bam1_t*));
370 // write sub files
371 for (;;) {
372 if (buf[k] == 0) buf[k] = (bam1_t*)calloc(1, sizeof(bam1_t));
373 b = buf[k];
374 if ((ret = bam_read1(fp, b)) < 0) break;
375 mem += ret;
376 ++k;
377 if (mem >= max_mem) {
378 sort_blocks(n++, k, buf, prefix, header, 0);
379 mem = 0; k = 0;
380 }
381 }
382 if (ret != -1)
383 fprintf(stderr, "[bam_sort_core] truncated file. Continue anyway.\n");
384 if (n == 0) sort_blocks(-1, k, buf, prefix, header, is_stdout);
385 else { // then merge
386 char **fns, *fnout;
387 fprintf(stderr, "[bam_sort_core] merging from %d files...\n", n+1);
388 sort_blocks(n++, k, buf, prefix, header, 0);
389 fnout = (char*)calloc(strlen(prefix) + 20, 1);
390 if (is_stdout) sprintf(fnout, "-");
391 else sprintf(fnout, "%s.bam", prefix);
392 fns = (char**)calloc(n, sizeof(char*));
393 for (i = 0; i < n; ++i) {
394 fns[i] = (char*)calloc(strlen(prefix) + 20, 1);
395 sprintf(fns[i], "%s.%.4d.bam", prefix, i);
396 }
397 bam_merge_core(is_by_qname, fnout, 0, n, fns, 0, 0);
398 free(fnout);
399 for (i = 0; i < n; ++i) {
400 unlink(fns[i]);
401 free(fns[i]);
402 }
403 free(fns);
404 }
405 for (k = 0; k < max_mem / BAM_CORE_SIZE; ++k) {
406 if (buf[k]) {
407 free(buf[k]->data);
408 free(buf[k]);
409 }
410 }
411 free(buf);
412 bam_header_destroy(header);
413 bam_close(fp);
414 }
415
416 void bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem)
417 {
418 bam_sort_core_ext(is_by_qname, fn, prefix, max_mem, 0);
419 }
420
421 int bam_sort(int argc, char *argv[])
422 {
423 size_t max_mem = 500000000;
424 int c, is_by_qname = 0, is_stdout = 0;
425 while ((c = getopt(argc, argv, "nom:")) >= 0) {
426 switch (c) {
427 case 'o': is_stdout = 1; break;
428 case 'n': is_by_qname = 1; break;
429 case 'm': max_mem = atol(optarg); break;
430 }
431 }
432 if (optind + 2 > argc) {
433 fprintf(stderr, "Usage: samtools sort [-on] [-m <maxMem>] <in.bam> <out.prefix>\n");
434 return 1;
435 }
436 bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout);
437 return 0;
438 }