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pbwtPaint.cpp
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pbwtPaint.cpp
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/* File: pbwtPaint.c
* Author: Richard Durbin (rd@sanger.ac.uk) and Daniel Lawson (dan.lawson@bristol.ac.uk)
* Copyright (C) Genome Research Limited, 2013-
*-------------------------------------------------------------------
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*-------------------------------------------------------------------
* Description: tools for chromosome painting as in ChromoPainter, FineStructure etc.
* Exported functions:
* HISTORY:
* Last edited: Aug 7 16:24 2015 (rd)
* Created: Tue Apr 1 11:34:41 2014 (rd)
*-------------------------------------------------------------------
*/
//#define LEGACY_MATRIX
#include "zlib.h"
#include "pbwt.h"
//#include "dynamiclist.h"
typedef struct { int j ; int start ; int end ; } MatchSegment ;
/* matches are semi-open [start,end) so length is end-start */
static Array *maxMatch = 0 ; /* arrays of MatchSegment */
static void reportMatch (int i, int j, int start, int end)
{ MatchSegment *ms = arrayp (maxMatch[i], arrayMax(maxMatch[i]), MatchSegment) ;
ms->j = j ; ms->start = start ; ms->end = end ;
}
static inline int isprevind(int i,int *map_indhap){
if(i==0) return(0);
return(map_indhap[i]==map_indhap[i-1]);
}
static inline void printAll(int ii,int Ninds,
double *t_counts,double *t_counts2,double *t_counts3,double *t_totlengths,double nregions,
gzFile fc,gzFile fc2,gzFile fc3,gzFile fl,gzFile fr){
int jj ; for (jj = 0 ; jj < Ninds ; ++jj) {
if(t_counts[jj]){
gzprintf (fc, "IND%i IND%i %.4f\n", ii+1,jj+1,t_counts[jj]) ;
gzprintf (fl, "IND%i IND%i %.4f\n", ii+1,jj+1,t_totlengths[jj]) ;
gzprintf (fc2,"IND%i IND%i %.4f\n", ii+1,jj+1,t_counts2[jj]) ;
gzprintf (fc3,"IND%i IND%i %.4f\n", ii+1,jj+1,t_counts3[jj]) ;
}
}
gzprintf (fr,"IND%i %.2f\n",ii+1, nregions) ;
}
void paintAncestryMatrix (PBWT *p, char* fileRoot,int chunksperregion)
{
int ploidy=2;
int Ninds=p->M/ploidy;
double **totlengths = 0 ;
double **counts = 0 ;
double **counts2 = 0 ; /* store sums of squares of counts in 100 block bins */
double **counts3 = 0 ; /* store sums of counts in 100 block bins */
double *nregions = 0; /* store number of regions found */
int i, j, k ;
int *map_indhap = mycalloc (p->M,int);
for (i = 0 ; i < p->M ; ++i) map_indhap[i]=i/ploidy;
double *totCounts = mycalloc (Ninds, double) ;
nregions = mycalloc (Ninds,double);
counts = myalloc (Ninds, double*) ; counts2 = myalloc (Ninds, double*) ; counts3 = myalloc (Ninds, double*) ; totlengths= myalloc (Ninds, double*);
for (i = 0 ; i < Ninds ; ++i)
{
counts[i] = mycalloc (Ninds, double) ;
counts2[i] = mycalloc (Ninds, double) ;
counts3[i] = mycalloc (Ninds, double) ;
totlengths[i] = mycalloc (Ninds, double) ;
}
memset (nregions, 0, sizeof(double)*Ninds) ;
maxMatch = myalloc (p->M, Array) ;
for (i = 0 ; i < p->M ; ++i) maxMatch[i] = arrayCreate (1024, MatchSegment) ;
matchMaximalWithin (p, reportMatch) ; /* store maximal matches in maxMatch */
double *partCounts = myalloc (Ninds, double) ;
/* now weight per site based on distance from ends */
for (i = 0 ; i < p->M ; ++i)
{
// printf("Processing individual %i (haplotype %i)\n",i/ploidy,i);
MatchSegment *m1 = arrp(maxMatch[i],0,MatchSegment), *m ;
int n1 = 1 ; /* so don't have an empty chunk to start with! */
MatchSegment *mStop = arrp(maxMatch[i], arrayMax(maxMatch[i])-1, MatchSegment) ;
memset (partCounts, 0, sizeof(double)*Ninds) ;
for (k = 1 ; k < p->N ; k++)
{ double sum = 0 ;
while (m1->end <= k && m1 < mStop)
{ if ((n1 % chunksperregion)==0)
{ int jj ; for (jj = 0 ; jj < Ninds ; ++jj) {
counts2[map_indhap[i]][jj] += partCounts[jj]*partCounts[jj] ;
counts3[map_indhap[i]][jj] += partCounts[jj] ;
}
memset (partCounts, 0, sizeof(double)*Ninds) ;
nregions[map_indhap[i]]+=1.0;
}
++m1 ; ++n1 ;
}
for (m = m1 ; m->start < k && m <= mStop ; ++m)
sum += (k - m->start) * (m->end - k) ;
if (sum)
for (m = m1 ; m->start < k && m <= mStop ; ++m) {
totlengths[map_indhap[i]][map_indhap[m->j]] += (k - m->start) * (m->end - k) / sum;
double thiscount=(k - m->start) * (m->end - k) / sum/(m->end - m->start);
counts[map_indhap[i]][map_indhap[m->j]] += thiscount;
partCounts[map_indhap[m->j]] += thiscount;
}
}
}
free(map_indhap);
free (partCounts) ;
/* report results */
FILE *fc = fopenTag (fileRoot, "chunkcounts.out", "w") ;
FILE *fl = fopenTag (fileRoot, "chunklengths.out", "w") ;
FILE *fc2 = fopenTag (fileRoot, "regionsquaredchunkcounts.out", "w") ;
FILE *fc3 = fopenTag (fileRoot, "regionchunkcounts.out", "w") ;
fprintf (fc,"RECIPIENT") ;
fprintf (fl,"RECIPIENT") ;
fprintf (fc2,"RECIPIENT nregions") ;
fprintf (fc3,"RECIPIENT nregions") ;
for (i = 0 ; i < Ninds ; ++i) {
fprintf (fc," IND%i",i+1) ;
fprintf (fl," IND%i",i+1) ;
fprintf (fc2," IND%i",i+1) ;
fprintf (fc3," IND%i",i+1) ;
}
fputc ('\n', fc) ;
fputc ('\n', fl) ;
fputc ('\n', fc2) ;
fputc ('\n', fc3) ;
for (i = 0 ; i < Ninds ; ++i) {
fprintf (fc3,"IND%i %.2f",i+1, nregions[i]) ;
fprintf (fc2,"IND%i %.2f",i+1, nregions[i]) ;
fprintf (fl,"IND%i",i+1) ;
fprintf (fc,"IND%i",i+1) ;
for (j = 0 ; j < Ninds ; ++j)
{
fprintf (fc, " %.4f", counts[i][j]) ;
fprintf (fl, " %.4f", totlengths[i][j]) ;
fprintf (fc2," %.4f", counts2[i][j]) ;
fprintf (fc3," %.4f", counts3[i][j]) ;
totCounts[i] += counts[i][j] ;
}
fputc ('\n', fc) ;
fputc ('\n', fl) ;
fputc ('\n', fc2) ;
fputc ('\n', fc3) ;
if (isCheck && (i%2) && p->samples)
fprintf (logFile, "%s %8.4g %8.4g\n",
sampleName (sample(p,i-1)), totCounts[i-1], totCounts[i]) ;
}
fclose (fc) ; fclose (fl) ; fclose (fc2) ;fclose (fc3) ;
timeUpdate(logFile);
/* clean up */
for (i = 0 ; i < Ninds ; ++i) { free (counts[i]) ; free (counts2[i]) ; }
free (counts) ; free (counts2) ; free (counts3) ; free (totCounts) ; free (nregions); free(totlengths);
}
void paintAncestryMatrixSparse (PBWT *p, char* fileRoot,int chunksperregion,int cutoff)
{
int i, j, k ;
int ploidy=2;
int Ninds=p->M/ploidy;
int *map_indhap = mycalloc (p->M,int);
for (i = 0 ; i < p->M ; ++i) map_indhap[i]=i/ploidy;
double *nregions = 0; /* store number of regions found */
nregions = mycalloc (Ninds,double);
// double *totCounts = mycalloc (Ninds, double) ;
gzFile fr = gzopenTag (fileRoot, "nregions.s.out.gz", "w") ;
gzFile fc = gzopenTag (fileRoot, "chunkcounts.s.out.gz", "w") ;
gzFile fl = gzopenTag (fileRoot, "chunklengths.s.out.gz", "w") ;
gzFile fc2 = gzopenTag (fileRoot, "regionsquaredchunkcounts.s.out.gz", "w") ;
gzFile fc3 = gzopenTag (fileRoot, "regionchunkcounts.s.out.gz", "w") ;
/// The dynamic structure storing the sparse matrices
int *t_obs = myalloc (Ninds,int);
double *t_counts = myalloc (Ninds,double);
double *t_counts2 = myalloc (Ninds,double);
double *t_counts3 = myalloc (Ninds,double);
double *t_totlengths = myalloc (Ninds,double);
maxMatch = myalloc (p->M, Array) ;
for (i = 0 ; i < p->M ; ++i) maxMatch[i] = arrayCreate (1024, MatchSegment) ;
matchMaximalWithin (p, reportMatch) ; /* store maximal matches in maxMatch */
double *partCounts = myalloc (Ninds, double) ;
/* now weight per site based on distance from ends */
/// i =1 .. M is each SNP
for (i = 0 ; i < p->M ; ++i)
{
// printf("Processing Individual %i in haplotype %i\n",i/ploidy,i);
MatchSegment *m1 = arrp(maxMatch[i],0,MatchSegment); // m1 is a SEGMENT that matches at SNP i
MatchSegment *m ;// m is another segment
int n1 = 1 ; // number of chunks found so far. 1 so don't have an empty chunk to start with!
MatchSegment *mStop = arrp(maxMatch[i], arrayMax(maxMatch[i])-1, MatchSegment) ;//
// Clear records if we have a new individual
if(!isprevind(i,map_indhap)){
if(i>0) printAll(map_indhap[i-1],Ninds,t_counts,t_counts2,t_counts3,t_totlengths,nregions[map_indhap[i-1]],fc,fc2,fc3,fl,fr);
memset (t_obs, 0, sizeof(int)*Ninds) ;
memset (partCounts, 0, sizeof(double)*Ninds) ;
memset (t_counts, 0, sizeof(double)*Ninds) ;
memset (t_counts2, 0, sizeof(double)*Ninds) ;
memset (t_counts3, 0, sizeof(double)*Ninds) ;
memset (t_totlengths, 0, sizeof(double)*Ninds) ;
}
for (k = 1 ; k < p->N ; k++)
{ double sum = 0 ;
while (m1->end <= k && m1 < mStop)
{ if ((n1 % chunksperregion)==0) {
int jj ; for (jj = 0 ; jj < Ninds ; ++jj) {
if(partCounts[jj]){
t_counts2[jj] += partCounts[jj]*partCounts[jj] ;
t_counts3[jj] += partCounts[jj] ;
}
}
memset (partCounts, 0, sizeof(double)*Ninds) ;
nregions[map_indhap[i]]+=1.0;
}
++m1 ; ++n1 ;
}
// for every individual who has a sufficiently long match
for (m = m1 ; m->start < k && m <= mStop ; ++m)
sum += (k - m->start) * (m->end - k) ;
if (sum)
for (m = m1 ; m->start < k && m <= mStop ; ++m) {
double thislengths = (k - m->start) * (m->end - k) / sum;
double thiscount=(k - m->start) * (m->end - k) / sum/(m->end - m->start);
t_obs[map_indhap[m->j]] = 1;
t_totlengths[map_indhap[m->j]] += thislengths;
t_counts[map_indhap[m->j]] += thiscount;
partCounts[map_indhap[m->j]] += thiscount;
// dynamicListSet(usedinds,map_indhap[m->j],1);
}
} // end loop over the N loci
}// end loop over individuals
printAll(map_indhap[p->M-1],Ninds,
t_counts,t_counts2,t_counts3,t_totlengths,nregions[map_indhap[p->M-1]],
fc,fc2,fc3,fl,fr);
/* clean up */
free (t_obs) ;
free (t_counts) ;
free (t_counts2) ;
free (t_counts3) ;
free (t_totlengths) ;
free (partCounts) ;
free (nregions) ;
free(map_indhap);
gzclose (fc) ; gzclose (fl) ; gzclose (fc2) ;gzclose (fc3) ; gzclose(fr);
}
/* end of file */