PBWT *pbwtSubRange (PBWT *pOld, int start, int end) { int M = pOld->M ; PBWT *pNew = pbwtCreate (M) ; int i, j, k ; uchar *x ; PbwtCursor *uOld = pbwtCursorCreate (pOld, TRUE, TRUE) ; pNew->yz = arrayCreate (pNew->N*8, uchar) ; PbwtCursor *uNew = pbwtCursorCreate (pNew, TRUE, TRUE) ; if (!pOld || !pOld->yz) die ("subrange without an existing pbwt") ; if (start < 0 || end > pOld->N || end <= start) die ("subrange invalid start %d, end %d", start, end) ; x = myalloc (M, uchar) ; if (pOld->sites) pNew->sites = arrayCreate (4096, Site) ; for (i = 0 ; i < end ; ++i) { if (i >= start) { for (j = 0 ; j < M ; ++j) x[uOld->a[j]] = uOld->y[j] ; for (j = 0 ; j < M ; ++j) uNew->y[j] = x[uNew->a[j]] ; pbwtCursorWriteForwards (uNew) ; if (pOld->sites) array(pNew->sites, pNew->N, Site) = arr(pOld->sites, i, Site) ; ++pNew->N ; } pbwtCursorForwardsRead (uOld) ; } pNew->aFend = myalloc (pNew->M, int) ; memcpy (pNew->aFend, uNew->a, pNew->M*sizeof(int)) ; pbwtDestroy (pOld) ; pbwtCursorDestroy (uOld) ; pbwtCursorDestroy (uNew) ; free(x) ; return pNew ; }
PBWT *pbwtSubSites (PBWT *pOld, double fmin, double frac) { int M = pOld->M ; PBWT *pNew = pbwtCreate (M, 0) ; int i, j, k, thresh = M*(1-fmin) ; double bit = 0.0 ; uchar *x ; PbwtCursor *uOld = pbwtCursorCreate (pOld, TRUE, TRUE) ; PbwtCursor *uNew = pbwtCursorCreate (pNew, TRUE, TRUE) ; if (!pOld || !pOld->yz) die ("subsites without an existing pbwt") ; if (fmin < 0 || fmin >= 1 || frac <= 0 || frac > 1) die ("fmin %f, frac %f for subsites out of range\n", fmin, frac) ; x = myalloc (M, uchar) ; if (pOld->sites) pNew->sites = arrayCreate (4096, Site) ; for (i = 0 ; i < pOld->N ; ++i) { if ((uOld->c < thresh) && ((bit += frac) > 1.0)) { for (j = 0 ; j < M ; ++j) x[uOld->a[j]] = uOld->y[j] ; for (j = 0 ; j < M ; ++j) uNew->y[j] = x[uNew->a[j]] ; pbwtCursorWriteForwards (uNew) ; if (pOld->sites) array(pNew->sites, pNew->N, Site) = arr(pOld->sites, i, Site) ; ++pNew->N ; bit -= 1.0 ; } pbwtCursorForwardsRead (uOld) ; } pbwtCursorToAFend (uNew, pNew) ; fprintf (logFile, "subsites with fmin %f, frac %f leaves %d sites\n", fmin, frac, pNew->N) ; pNew->chrom = pOld->chrom ; pOld->chrom = 0 ; pNew->samples = pOld->samples ; pOld->samples = 0 ; pNew->missingOffset = pOld->missingOffset ; pOld->missingOffset = 0 ; pNew->zMissing = pOld->zMissing ; pOld->zMissing = 0 ; pbwtDestroy (pOld) ; pbwtCursorDestroy (uOld) ; pbwtCursorDestroy (uNew) ; free(x) ; return pNew ; }
PBWT *pbwtSubRange (PBWT *pOld, int start, int end) { int M = pOld->M ; PBWT *pNew = pbwtCreate (M, 0) ; int i, j, k ; uchar *x ; PbwtCursor *uOld = pbwtCursorCreate (pOld, TRUE, TRUE) ; PbwtCursor *uNew = pbwtCursorCreate (pNew, TRUE, TRUE) ; if (!pOld || !pOld->yz) die ("subrange without an existing pbwt") ; if (start < 0 || end > pOld->N || end <= start) die ("subrange invalid start %d, end %d", start, end) ; x = myalloc (M, uchar) ; if (pOld->sites) pNew->sites = arrayCreate (4096, Site) ; for (i = 0 ; i < end ; ++i) { if (i >= start) { for (j = 0 ; j < M ; ++j) x[uOld->a[j]] = uOld->y[j] ; for (j = 0 ; j < M ; ++j) uNew->y[j] = x[uNew->a[j]] ; pbwtCursorWriteForwards (uNew) ; if (pOld->sites) array(pNew->sites, pNew->N, Site) = arr(pOld->sites, i, Site) ; ++pNew->N ; } pbwtCursorForwardsRead (uOld) ; } pbwtCursorToAFend (uNew, pNew) ; pNew->chrom = pOld->chrom ; pOld->chrom = 0 ; pNew->samples = pOld->samples ; pOld->samples = 0 ; pNew->missingOffset = pOld->missingOffset ; pOld->missingOffset = 0 ; pNew->zMissing = pOld->zMissing ; pOld->zMissing = 0 ; pbwtDestroy (pOld) ; pbwtCursorDestroy (uOld) ; pbwtCursorDestroy (uNew) ; free(x) ; return pNew ; }
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; }