FastBQSR/ext/htslib/vcf_sweep.c

/*  vcf_sweep.c -- forward/reverse sweep API.

    Copyright (C) 2013-2014, 2019 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.  */

#define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h
#include <config.h>

#include <assert.h>

#include "htslib/vcf_sweep.h"
#include "htslib/bgzf.h"

#define SW_FWD 0
#define SW_BWD 1

struct bcf_sweep_t
{
    htsFile *file;
    bcf_hdr_t *hdr;
    BGZF *fp;

    int direction;          // to tell if the direction has changed
    int block_size;         // the size of uncompressed data to hold in memory
    bcf1_t *rec;            // bcf buffer
    int nrec, mrec;         // number of used records; total size of the buffer
    int lrid, lpos, lnals, lals_len, mlals;   // to check uniqueness of a record
    char *lals;

    uint64_t *idx;          // uncompressed offsets of VCF/BCF records
    int iidx, nidx, midx;   // i: current offset; n: used; m: allocated
    int idx_done;           // the index is built during the first pass
};

BGZF *hts_get_bgzfp(htsFile *fp);
int hts_useek(htsFile *file, off_t uoffset, int where);
off_t hts_utell(htsFile *file);

static inline int sw_rec_equal(bcf_sweep_t *sw, bcf1_t *rec)
{
    if ( sw->lrid!=rec->rid ) return 0;
    if ( sw->lpos!=rec->pos ) return 0;
    if ( sw->lnals!=rec->n_allele ) return 0;

    char *t = rec->d.allele[sw->lnals-1];
    int len = t - rec->d.allele[0] + 1;
    while ( *t ) { t++; len++; }
    if ( sw->lals_len!=len ) return 0;
    if ( memcmp(sw->lals,rec->d.allele[0],len) ) return 0;
    return 1;
}

static int sw_rec_save(bcf_sweep_t *sw, bcf1_t *rec)
{
    sw->lrid  = rec->rid;
    sw->lpos  = rec->pos;
    sw->lnals = rec->n_allele;

    char *t = rec->d.allele[sw->lnals-1];
    int len = t - rec->d.allele[0] + 1;
    while ( *t ) { t++; len++; }
    sw->lals_len = len;
    hts_expand(char, len, sw->mlals, sw->lals);
    memcpy(sw->lals, rec->d.allele[0], len);

    return 0; // FIXME: check for errs in this function
}

static int sw_fill_buffer(bcf_sweep_t *sw)
{
    if ( !sw->iidx ) return 0;
    sw->iidx--;

    int ret = hts_useek(sw->file, sw->idx[sw->iidx], 0);
    assert( ret==0 );

    sw->nrec = 0;
    bcf1_t *rec = &sw->rec[sw->nrec];
    while ( (ret=bcf_read1(sw->file, sw->hdr, rec))==0 )
    {
        bcf_unpack(rec, BCF_UN_STR);

        // if not in the last block, stop at the saved record
        if ( sw->iidx+1 < sw->nidx && sw_rec_equal(sw,rec) ) break;

        sw->nrec++;
        hts_expand0(bcf1_t, sw->nrec+1, sw->mrec, sw->rec);
        rec = &sw->rec[sw->nrec];
    }
    sw_rec_save(sw, &sw->rec[0]);

    return 0; // FIXME: check for errs in this function
}

bcf_sweep_t *bcf_sweep_init(const char *fname)
{
    bcf_sweep_t *sw = (bcf_sweep_t*) calloc(1,sizeof(bcf_sweep_t));
    sw->file = hts_open(fname, "r");
    sw->fp   = hts_get_bgzfp(sw->file);
    if (sw->fp) bgzf_index_build_init(sw->fp);
    sw->hdr  = bcf_hdr_read(sw->file);
    sw->mrec = 1;
    sw->rec  = (bcf1_t*) calloc(sw->mrec,(sizeof(bcf1_t)));
    sw->block_size = 1024*1024*3;
    sw->direction = SW_FWD;
    return sw;
}

void bcf_sweep_destroy(bcf_sweep_t *sw)
{
    int i;
    for (i=0; i<sw->mrec; i++) bcf_empty1(&sw->rec[i]);
    free(sw->idx);
    free(sw->rec);
    free(sw->lals);
    bcf_hdr_destroy(sw->hdr);
    hts_close(sw->file);
    free(sw);
}

static void sw_seek(bcf_sweep_t *sw, int direction)
{
    sw->direction = direction;
    if ( direction==SW_FWD )
        hts_useek(sw->file, sw->idx[0], 0);
    else
    {
        sw->iidx = sw->nidx;
        sw->nrec = 0;
    }
}

bcf1_t *bcf_sweep_fwd(bcf_sweep_t *sw)
{
    if ( sw->direction==SW_BWD ) sw_seek(sw, SW_FWD);

    off_t pos = hts_utell(sw->file);

    bcf1_t *rec = &sw->rec[0];
    int ret = bcf_read1(sw->file, sw->hdr, rec);

    if ( ret!=0 )   // last record, get ready for sweeping backwards
    {
        sw->idx_done = 1;
        if (sw->fp) sw->fp->idx_build_otf = 0;
        sw_seek(sw, SW_BWD);
        return NULL;
    }

    if ( !sw->idx_done )
    {
        if ( !sw->nidx || pos - sw->idx[sw->nidx-1] > sw->block_size )
        {
            sw->nidx++;
            hts_expand(uint64_t, sw->nidx, sw->midx, sw->idx);
            sw->idx[sw->nidx-1] = pos;
        }
    }
    return rec;
}

bcf1_t *bcf_sweep_bwd(bcf_sweep_t *sw)
{
    if ( sw->direction==SW_FWD ) sw_seek(sw, SW_BWD);
    if ( !sw->nrec ) sw_fill_buffer(sw);
    if ( !sw->nrec ) return NULL;
    return &sw->rec[ --sw->nrec ];
}

bcf_hdr_t *bcf_sweep_hdr(bcf_sweep_t *sw) { return sw->hdr; }