|
0
|
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 }
|
