void deconv3(void *g, int gx, int gy, int gz, void *f, int fx, int fy, int fz, void *out) {
double *g2 = unpack3(g, gx, gy, gz, gy, gz);
double *f2 = unpack3(f, fx, fy, fz, gy, gz);
double ff[(gx - fx + 1) * gy * gz];
deconv(g2, gx * gy * gz, f2, fx * gy * gz, ff, gy * gz);
pack3(ff, gx - fx + 1, gy, gz, gy - fy + 1, gz - fz + 1, out);
free(g2);
free(f2);
}
PBWT *pbwtMerge(const char **fnames, int nfiles)
{
pbwt_reader_t *reader = pbwt_reader_init(fnames, nfiles);
int nhaps = 0, i;
for (i=0; i<nfiles; i++) nhaps += reader->pbwt[i]->M;
PBWT *out_pbwt = pbwtCreate(nhaps, 0);
PbwtCursor *cursor = pbwtNakedCursorCreate(nhaps, 0);
uchar *yseq = myalloc(nhaps, uchar);
out_pbwt->yz = arrayCreate (1<<20, uchar) ;
out_pbwt->sites = arrayReCreate(out_pbwt->sites, reader->pbwt[0]->N, Site);
out_pbwt->chrom = strdup(reader->pbwt[0]->chrom);
int pos, j;
while ( (pos=pbwt_reader_next(reader, nfiles)) )
{
// Merge only records shared by all files
for (i=0; i<nfiles; i++)
{
PBWT *p = reader->pbwt[i];
Site *site = arrp(p->sites, reader->cpos[i], Site);
// Both position and alleles must match. This requires that the records are sorted by alleles.
if ( site->x!=pos ) break;
char *als = dictName(variationDict, site->varD);
if ( strcmp(als,reader->mals) ) break;
}
if ( i!=nfiles )
{
// intersection: skip records which are not present in all files
for (i=0; i<nfiles; i++)
{
PBWT *p = reader->pbwt[i];
Site *site = arrp(p->sites, reader->cpos[i], Site);
if ( site->x!=pos ) continue;
char *als = dictName(variationDict, site->varD);
if ( strcmp(als,reader->mals) ) continue;
PbwtCursor *c = reader->cursor[i];
reader->unpacked[i] += unpack3(arrp(p->yz,reader->unpacked[i],uchar), p->M, c->y, 0);
pbwtCursorForwardsA(c);
}
continue;
}
// read and merge
int ihap = 0;
for (i=0; i<nfiles; i++)
{
PbwtCursor *c = reader->cursor[i];
PBWT *p = reader->pbwt[i];
Site *site = arrp(p->sites, reader->cpos[i], Site);
reader->unpacked[i] += unpack3(arrp(p->yz,reader->unpacked[i],uchar), p->M, c->y, 0);
for (j=0; j<p->M; j++) yseq[ihap + c->a[j]] = c->y[j];
pbwtCursorForwardsA(c);
ihap += p->M;
}
// pack merged haplotypes
for (j=0; j<nhaps; j++)
cursor->y[j] = yseq[cursor->a[j]];
pack3arrayAdd(cursor->y, out_pbwt->M, out_pbwt->yz);
pbwtCursorForwardsA(cursor);
// insert new site
arrayExtend(out_pbwt->sites, out_pbwt->N+1);
Site *site = arrayp(out_pbwt->sites, out_pbwt->N, Site);
site->x = pos;
dictAdd(variationDict, reader->mals, &site->varD);
out_pbwt->N++;
}
pbwtCursorToAFend (cursor, out_pbwt) ;
free(yseq);
pbwtCursorDestroy(cursor);
pbwt_reader_destroy(reader);
return out_pbwt;
}
