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"

#include "glibc_win64_flat/getopt.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_targets(bam_header_t *h1, bam_header_t *h2)
{
    bam_header_t t;
    t.n_targets = h1->n_targets, h1->n_targets = h2->n_targets, h2->n_targets = t.n_targets;
    t.target_name = h1->target_name, h1->target_name = h2->target_name, h2->target_name = t.target_name;
    t.target_len = h1->target_len, h1->target_len = h2->target_len, h2->target_len = t.target_len;
}

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
#define MERGE_LEVEL1 4
#define MERGE_FORCE  8

/*!
  @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 BAM
            hout = hin;
        } else { // validate multiple baf
            int min_n_targets = hout->n_targets;
            if (hin->n_targets < min_n_targets) min_n_targets = hin->n_targets;

            for (j = 0; j < min_n_targets; ++j)
                if (strcmp(hout->target_name[j], hin->target_name[j]) != 0) {
                    fprintf(stderr, "[bam_merge_core] different target sequence name: '%s' != '%s' in file '%s'\n",
                            hout->target_name[j], hin->target_name[j], fn[i]);
                    return -1;
                }

            // If this input file has additional target reference sequences,
            // add them to the headers to be output
            if (hin->n_targets > hout->n_targets) {
                swap_header_targets(hout, hin);
                // FIXME Possibly we should also create @SQ text headers
                // for the newly added reference sequences
            }

            bam_header_destroy(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\n", 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\n", hheaders->target_name[j], headers);
                    if (!reg) return -1;
                }
        }

        swap_header_text(hout, hheaders);
        bam_header_destroy(hheaders);
    }

    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", __FUNCTION__);
            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)((int32_t)h->b->core.pos+1)<<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 if (flag & MERGE_LEVEL1) fpout = strcmp(out, "-")? bam_open(out, "w1") : bam_dopen(_fileno(stdout), "w1");
    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", __FUNCTION__);
        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) {
            uint8_t *rg = bam_aux_get(b, "RG");
            if (rg) bam_aux_del(b, rg);
            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)((int)b->core.pos+1)<<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:nru1R:f")) >= 0) {
        switch (c) {
        case 'r': flag |= MERGE_RG; break;
        case 'f': flag |= MERGE_FORCE; break;
        case 'h': fn_headers = strdup(optarg); break;
        case 'n': is_by_qname = 1; break;
        case '1': flag |= MERGE_LEVEL1; 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, "         -f       overwrite the output BAM if exist\n");
        fprintf(stderr, "         -1       compress level 1\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 (!(flag & MERGE_FORCE) && strcmp(argv[optind], "-")) {
        FILE *fp = fopen(argv[optind], "rb");
        if (fp != NULL) {
            fclose(fp);
            fprintf(stderr, "[%s] File '%s' exists. Please apply '-f' to overwrite. Abort.\n", __FUNCTION__, argv[optind]);
            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+1)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)))));
    } else return (((uint64_t)a->core.tid<<32|(a->core.pos+1)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)));
}
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, mode[3];
    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);
        strcpy(mode, "w1");
    } else {
        sprintf(name, "%s.bam", prefix);
        strcpy(mode, "w");
    }
    fp = is_stdout? bam_dopen(_fileno(stdout), mode) : bam_open(name, mode);
    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 = _atoi64(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;
}