vcfsort.c

/*  vcfsort.c -- sort subcommand

   Copyright (C) 2017 Genome Research Ltd.

   Author: Petr Danecek <pd3@sanger.ac.uk>
   
   Permission is hereby granted, free of charge, to any person obtaining a copy
   of this software and associated documentation files (the "Software"), to deal
   in the Software without restriction, including without limitation the rights
   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
   copies of the Software, and to permit persons to whom the Software is
   furnished to do so, subject to the following conditions:
   
   The above copyright notice and this permission notice shall be included in
   all copies or substantial portions of the Software.
   
   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
   THE SOFTWARE.

 */

#include <stdio.h>
#include <unistd.h>
#include <getopt.h>
#include <ctype.h>
#include <string.h>
#include <errno.h>
#include <sys/stat.h>
#include <sys/types.h>
#include <fcntl.h>
#include <math.h>
#include <htslib/vcf.h>
#include <htslib/kstring.h>
#include "kheap.h"
#include "bcftools.h"

typedef struct
{
    char *fname;
    htsFile *fh;
    bcf1_t *rec;
}
blk_t;

typedef struct _args_t
{
    bcf_hdr_t *hdr;
    char **argv, *fname, *output_fname, *tmp_dir;
    int argc, output_type;
    size_t max_mem, mem;
    bcf1_t **buf;
    size_t nbuf, mbuf, nblk;
    blk_t *blk;
}
args_t;

int cmp_bcf_pos(const void *aptr, const void *bptr)
{
    bcf1_t *a = *((bcf1_t**)aptr);
    bcf1_t *b = *((bcf1_t**)bptr);
    if ( a->rid < b->rid ) return -1;
    if ( a->rid > b->rid ) return 1;
    if ( a->pos < b->pos ) return -1;
    if ( a->pos > b->pos ) return 1;

    // Sort the same chr:pos records lexicographically by ref,alt.
    // This will be called rarely so should not slow the sorting down
    // noticeably.

    if ( !a->unpacked ) bcf_unpack(a, BCF_UN_STR);
    if ( !b->unpacked ) bcf_unpack(b, BCF_UN_STR);
    int i, ret;
    for (i=0; i<a->n_allele; i++)
    { 
        if ( i >= b->n_allele ) return 1;
        int ret = strcasecmp(a->d.allele[i],b->d.allele[i]);
        if ( ret ) return ret;
    }
    if ( a->n_allele < b->n_allele ) return -1;
    return 0;
}

void buf_flush(args_t *args)
{
    if ( !args->nbuf ) return;

    qsort(args->buf, args->nbuf, sizeof(*args->buf), cmp_bcf_pos);

    args->nblk++;
    args->blk = (blk_t*) realloc(args->blk, sizeof(blk_t)*args->nblk);
    blk_t *blk = args->blk + args->nblk - 1;

    kstring_t str = {0,0,0};
    ksprintf(&str, "%s/%05d.bcf", args->tmp_dir, (int)args->nblk);
    blk->fname = str.s;

    htsFile *fh = hts_open(blk->fname, "wbu");
    if ( fh == NULL ) error("Cannot write %s: %s\n", blk->fname, strerror(errno));
    bcf_hdr_write(fh, args->hdr);
    
    int i;
    for (i=0; i<args->nbuf; i++)
    {
        bcf_write(fh, args->hdr, args->buf[i]);
        bcf_destroy(args->buf[i]);
    }
    hts_close(fh);

    args->nbuf = 0;
    args->mem  = 0;
}

void buf_push(args_t *args, bcf1_t *rec)
{
    int delta = sizeof(bcf1_t) + rec->shared.l + rec->indiv.l + sizeof(bcf1_t*);
    if ( args->mem + delta > args->max_mem ) buf_flush(args);
    args->nbuf++;
    args->mem += delta;
    hts_expand(bcf1_t*, args->nbuf, args->mbuf, args->buf);
    args->buf[args->nbuf-1] = rec;
}

void sort_blocks(args_t *args) 
{
    htsFile *in = hts_open(args->fname, "r");
    if ( !in ) error("Could not read %s\n", args->fname);
    args->hdr = bcf_hdr_read(in);

    while ( 1 )
    {
        bcf1_t *rec = bcf_init();
        int ret = bcf_read1(in, args->hdr, rec);
        if ( ret < -1 ) error("Error encountered while parsing the input\n");
        if ( ret == -1 )
        {
            bcf_destroy(rec);
            break;
        }
        buf_push(args, rec);
    }
    buf_flush(args);
    free(args->buf);

    if ( hts_close(in)!=0 ) error("Close failed: %s\n", args->fname);
}

static inline int blk_is_smaller(blk_t **aptr, blk_t **bptr)
{
    blk_t *a = *aptr;
    blk_t *b = *bptr;
    int ret = cmp_bcf_pos(&a->rec, &b->rec);
    if ( ret < 0 ) return 1;
    return 0;
}
KHEAP_INIT(blk, blk_t*, blk_is_smaller)

void blk_read(khp_blk_t *bhp, bcf_hdr_t *hdr, blk_t *blk)
{
    if ( !blk->fh ) return;
    int ret = bcf_read(blk->fh, hdr, blk->rec);
    if ( ret < -1 ) error("Error reading %s\n", blk->fname);
    if ( ret == -1 )
    {
        if ( hts_close(blk->fh)!=0 ) error("Close failed: %s\n", blk->fname);
        blk->fh = 0;
        return;
    }
    khp_insert(blk, bhp, &blk);
}

void merge_blocks(args_t *args) 
{
    fprintf(stderr,"Merging %d temporary files\n", (int)args->nblk);

    khp_blk_t *bhp = khp_init(blk);

    int i;
    for (i=0; i<args->nblk; i++)
    {
        blk_t *blk = args->blk + i;
        blk->fh = hts_open(blk->fname, "r");
        if ( !blk->fh ) error("Could not read %s: %s\n", blk->fname, strerror(errno));
        bcf_hdr_t *hdr = bcf_hdr_read(blk->fh);
        bcf_hdr_destroy(hdr);
        blk->rec = bcf_init();
        blk_read(bhp, args->hdr, blk);
    }

    htsFile *out = hts_open(args->output_fname, hts_bcf_wmode(args->output_type));
    bcf_hdr_write(out, args->hdr);
    while ( bhp->ndat )
    {
        blk_t *blk = bhp->dat[0];
        bcf_write(out, args->hdr, blk->rec);
        khp_delete(blk, bhp);
        blk_read(bhp, args->hdr, blk);
    }
    if ( hts_close(out)!=0 ) error("Close failed: %s\n", args->output_fname);

    fprintf(stderr,"Cleaning\n");
    for (i=0; i<args->nblk; i++)
    {
        blk_t *blk = args->blk + i;
        unlink(blk->fname);
        free(blk->fname);
        bcf_destroy(blk->rec);
    }
    rmdir(args->tmp_dir);
    free(args->blk);
    khp_destroy(blk, bhp);
    fprintf(stderr,"Done\n");
}

static void usage(args_t *args)
{
    fprintf(stderr, "\n");
    fprintf(stderr, "About:   Sort VCF/BCF file.\n");
    fprintf(stderr, "Usage:   bcftools sort [OPTIONS] <FILE.vcf>\n");
    fprintf(stderr, "\n");
    fprintf(stderr, "Options:\n");
    fprintf(stderr, "    -m, --max-mem <float>[kMG]    maximum memory to use [768M]\n");    // using metric units, 1M=1e6
    fprintf(stderr, "    -o, --output-file <file>      output file name [stdout]\n");
    fprintf(stderr, "    -O, --output-type <b|u|z|v>   b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]\n");
    fprintf(stderr, "    -T, --temp-dir <dir>          temporary files [/tmp/bcftools-sort.XXXXXX/]\n");
    fprintf(stderr, "\n");
    exit(1);
}

size_t parse_mem_string(char *str) 
{
    char *tmp;
    double mem = strtod(str, &tmp);
    if ( tmp==str ) error("Could not parse: --max-mem %s\n", str);
    if ( !strcasecmp("k",tmp) ) mem *= 1000;
    else if ( !strcasecmp("m",tmp) ) mem *= 1000*1000;
    else if ( !strcasecmp("g",tmp) ) mem *= 1000*1000*1000;
    return mem;
}

void mkdir_p(const char *fmt, ...);
void init(args_t *args)
{
    if ( !args->tmp_dir )
    {
        args->tmp_dir = strdup("/tmp/bcftools-sort.XXXXXX");
        char *tmp_dir = mkdtemp(args->tmp_dir);
        if ( !tmp_dir ) error("mkdtemp(%s) failed: %s\n", args->tmp_dir,strerror(errno));
    }
    else
    {
        args->tmp_dir = strdup(args->tmp_dir);
        mkdir_p(args->tmp_dir);
    }
    fprintf(stderr,"Writing to %s\n", args->tmp_dir);
}
void destroy(args_t *args)
{
    bcf_hdr_destroy(args->hdr);
    free(args->tmp_dir);
    free(args);
}

int main_sort(int argc, char *argv[])
{
    int c;
    args_t *args  = (args_t*) calloc(1,sizeof(args_t));
    args->argc    = argc; args->argv = argv;
    args->max_mem = 768*1000*1000;
    args->output_fname = "-";

    static struct option loptions[] =
    {
        {"max-mem",required_argument,NULL,'m'},
        {"temp-dir",required_argument,NULL,'T'},
        {"output-type",required_argument,NULL,'O'},
        {"output-file",required_argument,NULL,'o'},
        {"help",no_argument,NULL,'h'},
        {0,0,0,0}
    };
    while ((c = getopt_long(argc, argv, "m:T:O:o:h?",loptions,NULL)) >= 0)
    {
        switch (c)
        {
            case 'm': args->max_mem = parse_mem_string(optarg); break;
            case 'T': args->tmp_dir = optarg; break;
            case 'o': args->output_fname = optarg; break;
            case 'O':
                      switch (optarg[0]) {
                          case 'b': args->output_type = FT_BCF_GZ; break;
                          case 'u': args->output_type = FT_BCF; break;
                          case 'z': args->output_type = FT_VCF_GZ; break;
                          case 'v': args->output_type = FT_VCF; break;
                          default: error("The output type \"%s\" not recognised\n", optarg);
                      };
                      break;
            case 'h': usage(args);
            case '?': usage(args);
            default: error("Unknown argument: %s\n", optarg);
        }
    }

    if ( optind>=argc )
    {
        if ( !isatty(fileno((FILE *)stdin)) ) args->fname = "-";  // reading from stdin
        else usage(args);
    }
    else args->fname = argv[optind];

    init(args);
    sort_blocks(args);
    merge_blocks(args);
    destroy(args);

    return 0;
}