Logo Search packages:      
Sourcecode: samtools version File versions  Download package

bam_sort.c

#include <stdlib.h>
#include <ctype.h>
#include <assert.h>
#include <errno.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;
}

#define MERGE_RG     1
#define MERGE_UNCOMP 2

/*!
  @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.
 */
int bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn,
                              int flag, const char *reg)
{
      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;
      bam_iter_t *iter = 0;

      if (headers) {
            tamFile fpheaders = sam_open(headers);
            if (fpheaders == 0) {
                  const char *message = strerror(errno);
                  fprintf(stderr, "[bam_merge_core] cannot open '%s': %s\n", headers, message);
                  return -1;
            }
            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));
      iter = (bam_iter_t*)calloc(n, sizeof(bam_iter_t));
      // prepare RG tag
      if (flag & MERGE_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) {
            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 -1;
            }
            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);
                                    if (!reg) return -1;
                              }
                              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);
                                          if (!reg) return -1;
                                    }
                        }
                        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. Continue anyway!\n", fn[i]);
                  } else {
                        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'. Continue anyway!\n",
                                                hout->target_name[j], hin->target_name[j], fn[i]);
                              }
                        }
                  }
                  bam_header_destroy(hin);
            }
      }

      if (reg) {
            int tid, beg, end;
            if (bam_parse_region(hout, reg, &tid, &beg, &end) < 0) {
                  fprintf(stderr, "[%s] Malformated region string or undefined reference name\n", __func__);
                  return -1;
            }
            for (i = 0; i < n; ++i) {
                  bam_index_t *idx;
                  idx = bam_index_load(fn[i]);
                  iter[i] = bam_iter_query(idx, tid, beg, end);
                  bam_index_destroy(idx);
            }
      }

      for (i = 0; i < n; ++i) {
            heap1_t *h = heap + i;
            h->i = i;
            h->b = (bam1_t*)calloc(1, sizeof(bam1_t));
            if (bam_iter_read(fp[i], iter[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;
      }
      if (flag & MERGE_UNCOMP) {
            fpout = strcmp(out, "-")? bam_open(out, "wu") : bam_dopen(fileno(stdout), "wu");
      } else {
            fpout = strcmp(out, "-")? bam_open(out, "w") : bam_dopen(fileno(stdout), "w");
      }
      if (fpout == 0) {
            fprintf(stderr, "[%s] fail to create the output file.\n", __func__);
            return -1;
      }
      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 ((flag & MERGE_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_iter_read(fp[heap->i], iter[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 (flag & MERGE_RG) {
            for (i = 0; i != n; ++i) free(RG[i]);
            free(RG); free(RG_len);
      }
      for (i = 0; i != n; ++i) {
            bam_iter_destroy(iter[i]);
            bam_close(fp[i]);
      }
      bam_close(fpout);
      free(fp); free(heap); free(iter);
      return 0;
}

int bam_merge(int argc, char *argv[])
{
      int c, is_by_qname = 0, flag = 0, ret = 0;
      char *fn_headers = NULL, *reg = 0;

      while ((c = getopt(argc, argv, "h:nruR:")) >= 0) {
            switch (c) {
            case 'r': flag |= MERGE_RG; break;
            case 'h': fn_headers = strdup(optarg); break;
            case 'n': is_by_qname = 1; break;
            case 'u': flag |= MERGE_UNCOMP; break;
            case 'R': reg = strdup(optarg); 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, "         -u       uncompressed BAM output\n");
            fprintf(stderr, "         -R STR   merge file in the specified region STR [all]\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;
      }
      if (bam_merge_core(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, flag, reg) < 0) ret = 1;
      free(reg);
      free(fn_headers);
      return ret;
}

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, 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;
}

Generated by  Doxygen 1.6.0   Back to index