+++ /dev/null
-#include <stdlib.h>
-#include <ctype.h>
-#include <assert.h>
-#include <stdio.h>
-#include <string.h>
-#include <unistd.h>
-#include "bam.h"
-#include "ksort.h"
-
-static int g_is_by_qname = 0;
-
-static inline int strnum_cmp(const char *a, const char *b)
-{
- char *pa, *pb;
- pa = (char*)a; pb = (char*)b;
- while (*pa && *pb) {
- if (isdigit(*pa) && isdigit(*pb)) {
- long ai, bi;
- ai = strtol(pa, &pa, 10);
- bi = strtol(pb, &pb, 10);
- if (ai != bi) return ai<bi? -1 : ai>bi? 1 : 0;
- } else {
- if (*pa != *pb) break;
- ++pa; ++pb;
- }
- }
- if (*pa == *pb)
- return (pa-a) < (pb-b)? -1 : (pa-a) > (pb-b)? 1 : 0;
- return *pa<*pb? -1 : *pa>*pb? 1 : 0;
-}
-
-#define HEAP_EMPTY 0xffffffffffffffffull
-
-typedef struct {
- int i;
- uint64_t pos, idx;
- bam1_t *b;
-} heap1_t;
-
-#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))))
-
-static inline int heap_lt(const heap1_t a, const heap1_t b)
-{
- if (g_is_by_qname) {
- int t;
- if (a.b == 0 || b.b == 0) return a.b == 0? 1 : 0;
- t = strnum_cmp(bam1_qname(a.b), bam1_qname(b.b));
- return (t > 0 || (t == 0 && __pos_cmp(a, b)));
- } else return __pos_cmp(a, b);
-}
-
-KSORT_INIT(heap, heap1_t, heap_lt)
-
-static void swap_header_text(bam_header_t *h1, bam_header_t *h2)
-{
- int tempi;
- char *temps;
- tempi = h1->l_text, h1->l_text = h2->l_text, h2->l_text = tempi;
- temps = h1->text, h1->text = h2->text, h2->text = temps;
-}
-
-/*!
- @abstract Merge multiple sorted BAM.
- @param is_by_qname whether to sort by query name
- @param out output BAM file name
- @param headers name of SAM file from which to copy '@' header lines,
- or NULL to copy them from the first file to be merged
- @param n number of files to be merged
- @param fn names of files to be merged
-
- @discussion Padding information may NOT correctly maintained. This
- function is NOT thread safe.
- */
-void bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn, int add_RG)
-{
- bamFile fpout, *fp;
- heap1_t *heap;
- bam_header_t *hout = 0;
- bam_header_t *hheaders = NULL;
- int i, j, *RG_len = 0;
- uint64_t idx = 0;
- char **RG = 0;
-
- if (headers) {
- tamFile fpheaders = sam_open(headers);
- if (fpheaders == 0) {
- fprintf(stderr, "[bam_merge_core] Cannot open file `%s'. Continue anyway.\n", headers);
- } else {
- hheaders = sam_header_read(fpheaders);
- sam_close(fpheaders);
- }
- }
-
- g_is_by_qname = by_qname;
- fp = (bamFile*)calloc(n, sizeof(bamFile));
- heap = (heap1_t*)calloc(n, sizeof(heap1_t));
- // prepare RG tag
- if (add_RG) {
- RG = (char**)calloc(n, sizeof(void*));
- RG_len = (int*)calloc(n, sizeof(int));
- for (i = 0; i != n; ++i) {
- int l = strlen(fn[i]);
- const char *s = fn[i];
- if (l > 4 && strcmp(s + l - 4, ".bam") == 0) l -= 4;
- for (j = l - 1; j >= 0; --j) if (s[j] == '/') break;
- ++j; l -= j;
- RG[i] = calloc(l + 1, 1);
- RG_len[i] = l;
- strncpy(RG[i], s + j, l);
- }
- }
- // read the first
- for (i = 0; i != n; ++i) {
- heap1_t *h;
- bam_header_t *hin;
- fp[i] = bam_open(fn[i], "r");
- if (fp[i] == 0) {
- int j;
- fprintf(stderr, "[bam_merge_core] fail to open file %s\n", fn[i]);
- for (j = 0; j < i; ++j) bam_close(fp[j]);
- free(fp); free(heap);
- // FIXME: possible memory leak
- return;
- }
- hin = bam_header_read(fp[i]);
- if (i == 0) { // the first SAM
- hout = hin;
- if (hheaders) {
- // If the text headers to be swapped in include any @SQ headers,
- // check that they are consistent with the existing binary list
- // of reference information.
- if (hheaders->n_targets > 0) {
- if (hout->n_targets != hheaders->n_targets)
- fprintf(stderr, "[bam_merge_core] number of @SQ headers in `%s' differs from number of target sequences", headers);
- for (j = 0; j < hout->n_targets; ++j)
- if (strcmp(hout->target_name[j], hheaders->target_name[j]) != 0)
- fprintf(stderr, "[bam_merge_core] @SQ header '%s' in '%s' differs from target sequence", hheaders->target_name[j], headers);
- }
- swap_header_text(hout, hheaders);
- bam_header_destroy(hheaders);
- hheaders = NULL;
- }
- } else { // validate multiple baf
- if (hout->n_targets != hin->n_targets) {
- fprintf(stderr, "[bam_merge_core] file '%s' has different number of target sequences. Abort!\n", fn[i]);
- exit(1);
- }
- for (j = 0; j < hout->n_targets; ++j) {
- if (strcmp(hout->target_name[j], hin->target_name[j])) {
- fprintf(stderr, "[bam_merge_core] different target sequence name: '%s' != '%s' in file '%s'. Abort!\n",
- hout->target_name[j], hin->target_name[j], fn[i]);
- exit(1);
- }
- }
- bam_header_destroy(hin);
- }
- h = heap + i;
- h->i = i;
- h->b = (bam1_t*)calloc(1, sizeof(bam1_t));
- if (bam_read1(fp[i], h->b) >= 0) {
- h->pos = ((uint64_t)h->b->core.tid<<32) | (uint32_t)h->b->core.pos<<1 | bam1_strand(h->b);
- h->idx = idx++;
- }
- else h->pos = HEAP_EMPTY;
- }
- fpout = strcmp(out, "-")? bam_open(out, "w") : bam_dopen(fileno(stdout), "w");
- assert(fpout);
- bam_header_write(fpout, hout);
- bam_header_destroy(hout);
-
- ks_heapmake(heap, n, heap);
- while (heap->pos != HEAP_EMPTY) {
- bam1_t *b = heap->b;
- if (add_RG && bam_aux_get(b, "RG") == 0)
- bam_aux_append(b, "RG", 'Z', RG_len[heap->i] + 1, (uint8_t*)RG[heap->i]);
- bam_write1_core(fpout, &b->core, b->data_len, b->data);
- if ((j = bam_read1(fp[heap->i], b)) >= 0) {
- heap->pos = ((uint64_t)b->core.tid<<32) | (uint32_t)b->core.pos<<1 | bam1_strand(b);
- heap->idx = idx++;
- } else if (j == -1) {
- heap->pos = HEAP_EMPTY;
- free(heap->b->data); free(heap->b);
- heap->b = 0;
- } else fprintf(stderr, "[bam_merge_core] '%s' is truncated. Continue anyway.\n", fn[heap->i]);
- ks_heapadjust(heap, 0, n, heap);
- }
-
- if (add_RG) {
- for (i = 0; i != n; ++i) free(RG[i]);
- free(RG); free(RG_len);
- }
- for (i = 0; i != n; ++i) bam_close(fp[i]);
- bam_close(fpout);
- free(fp); free(heap);
-}
-int bam_merge(int argc, char *argv[])
-{
- int c, is_by_qname = 0, add_RG = 0;
- char *fn_headers = NULL;
-
- while ((c = getopt(argc, argv, "h:nr")) >= 0) {
- switch (c) {
- case 'r': add_RG = 1; break;
- case 'h': fn_headers = strdup(optarg); break;
- case 'n': is_by_qname = 1; break;
- }
- }
- if (optind + 2 >= argc) {
- fprintf(stderr, "\n");
- fprintf(stderr, "Usage: samtools merge [-nr] [-h inh.sam] <out.bam> <in1.bam> <in2.bam> [...]\n\n");
- fprintf(stderr, "Options: -n sort by read names\n");
- fprintf(stderr, " -r attach RG tag (inferred from file names)\n");
- fprintf(stderr, " -h FILE copy the header in FILE to <out.bam> [in1.bam]\n\n");
- fprintf(stderr, "Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users\n");
- fprintf(stderr, " must provide the correct header with -h, or uses Picard which properly maintains\n");
- fprintf(stderr, " the header dictionary in merging.\n\n");
- return 1;
- }
- bam_merge_core(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, add_RG);
- free(fn_headers);
- return 0;
-}
-
-typedef bam1_t *bam1_p;
-
-static inline int bam1_lt(const bam1_p a, const bam1_p b)
-{
- if (g_is_by_qname) {
- int t = strnum_cmp(bam1_qname(a), bam1_qname(b));
- return (t < 0 || (t == 0 && (((uint64_t)a->core.tid<<32|a->core.pos) < ((uint64_t)b->core.tid<<32|b->core.pos))));
- } else return (((uint64_t)a->core.tid<<32|a->core.pos) < ((uint64_t)b->core.tid<<32|b->core.pos));
-}
-KSORT_INIT(sort, bam1_p, bam1_lt)
-
-static void sort_blocks(int n, int k, bam1_p *buf, const char *prefix, const bam_header_t *h, int is_stdout)
-{
- char *name;
- int i;
- bamFile fp;
- ks_mergesort(sort, k, buf, 0);
- name = (char*)calloc(strlen(prefix) + 20, 1);
- if (n >= 0) sprintf(name, "%s.%.4d.bam", prefix, n);
- else sprintf(name, "%s.bam", prefix);
- fp = is_stdout? bam_dopen(fileno(stdout), "w") : bam_open(name, "w");
- if (fp == 0) {
- fprintf(stderr, "[sort_blocks] fail to create file %s.\n", name);
- free(name);
- // FIXME: possible memory leak
- return;
- }
- free(name);
- bam_header_write(fp, h);
- for (i = 0; i < k; ++i)
- bam_write1_core(fp, &buf[i]->core, buf[i]->data_len, buf[i]->data);
- bam_close(fp);
-}
-
-/*!
- @abstract Sort an unsorted BAM file based on the chromosome order
- and the leftmost position of an alignment
-
- @param is_by_qname whether to sort by query name
- @param fn name of the file to be sorted
- @param prefix prefix of the output and the temporary files; upon
- sucessess, prefix.bam will be written.
- @param max_mem approxiate maximum memory (very inaccurate)
-
- @discussion It may create multiple temporary subalignment files
- and then merge them by calling bam_merge_core(). This function is
- NOT thread safe.
- */
-void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size_t max_mem, int is_stdout)
-{
- int n, ret, k, i;
- size_t mem;
- bam_header_t *header;
- bamFile fp;
- bam1_t *b, **buf;
-
- g_is_by_qname = is_by_qname;
- n = k = 0; mem = 0;
- fp = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
- if (fp == 0) {
- fprintf(stderr, "[bam_sort_core] fail to open file %s\n", fn);
- return;
- }
- header = bam_header_read(fp);
- buf = (bam1_t**)calloc(max_mem / BAM_CORE_SIZE, sizeof(bam1_t*));
- // write sub files
- for (;;) {
- if (buf[k] == 0) buf[k] = (bam1_t*)calloc(1, sizeof(bam1_t));
- b = buf[k];
- if ((ret = bam_read1(fp, b)) < 0) break;
- mem += ret;
- ++k;
- if (mem >= max_mem) {
- sort_blocks(n++, k, buf, prefix, header, 0);
- mem = 0; k = 0;
- }
- }
- if (ret != -1)
- fprintf(stderr, "[bam_sort_core] truncated file. Continue anyway.\n");
- if (n == 0) sort_blocks(-1, k, buf, prefix, header, is_stdout);
- else { // then merge
- char **fns, *fnout;
- fprintf(stderr, "[bam_sort_core] merging from %d files...\n", n+1);
- sort_blocks(n++, k, buf, prefix, header, 0);
- fnout = (char*)calloc(strlen(prefix) + 20, 1);
- if (is_stdout) sprintf(fnout, "-");
- else sprintf(fnout, "%s.bam", prefix);
- fns = (char**)calloc(n, sizeof(char*));
- for (i = 0; i < n; ++i) {
- fns[i] = (char*)calloc(strlen(prefix) + 20, 1);
- sprintf(fns[i], "%s.%.4d.bam", prefix, i);
- }
- bam_merge_core(is_by_qname, fnout, 0, n, fns, 0);
- free(fnout);
- for (i = 0; i < n; ++i) {
- unlink(fns[i]);
- free(fns[i]);
- }
- free(fns);
- }
- for (k = 0; k < max_mem / BAM_CORE_SIZE; ++k) {
- if (buf[k]) {
- free(buf[k]->data);
- free(buf[k]);
- }
- }
- free(buf);
- bam_header_destroy(header);
- bam_close(fp);
-}
-
-void bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem)
-{
- bam_sort_core_ext(is_by_qname, fn, prefix, max_mem, 0);
-}
-
-int bam_sort(int argc, char *argv[])
-{
- size_t max_mem = 500000000;
- int c, is_by_qname = 0, is_stdout = 0;
- while ((c = getopt(argc, argv, "nom:")) >= 0) {
- switch (c) {
- case 'o': is_stdout = 1; break;
- case 'n': is_by_qname = 1; break;
- case 'm': max_mem = atol(optarg); break;
- }
- }
- if (optind + 2 > argc) {
- fprintf(stderr, "Usage: samtools sort [-on] [-m <maxMem>] <in.bam> <out.prefix>\n");
- return 1;
- }
- bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout);
- return 0;
-}
projects / pysam.git / blobdiff