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pbwtImpute.cpp
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pbwtImpute.cpp
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/* File: pbwtImpute.c
* Author: Richard Durbin (rd@sanger.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: phasing and imputation functions in pbwt package,
plus utilities to intentionally corrupt data
* Exported functions:
* HISTORY:
* Last edited: Dec 14 13:52 2015 (rd)
* * Sep 22 23:10 2014 (rd): move to 64 bit arrays
* Created: Thu Apr 4 12:02:56 2013 (rd)
*-------------------------------------------------------------------
*/
#include "pbwt.h"
static void genotypeComparePbwt (PBWT *p, PBWT *q) ; /* forward declaration */
/************************* IMPUTATION AND PHASING *************************/
#include <math.h>
static double fBound[] = {0.1, 0.2, 0.3, 0.5, 0.7, 1, 2, 3, 5, 7, 10, 20, 30, 50, 70, 90, 100.01} ;
void imputeExplore (PBWT *p, int test)
{
int i, j, k, M = p->M, N = p->N, ff ;
uchar *y ;
double xbar, ybar, tot, r2 ;
double f ;
typedef struct {
long n00, n01 ; /* neither neighbour is 1, truth is 0 or 1 */
long n10a, n10b, n11a, n11b ;/* one neighbour is 1; a if d is lower for the 0 neighbour */
long n20, n21 ; /* both neighbours are 1 */
double fsum ;
} TestStat ;
TestStat *testStat = mycalloc (17, TestStat), *t ;
typedef long Counts[4] ;
Array dHist = arrayCreate (1000, Counts) ;
Counts cSimple, cCond0, cCond1 ;
int *n0 = myalloc (M, int), *n1 = myalloc (M, int) ;
uchar *x = myalloc (M, uchar) ;
static long c0[17][5], c1[17][5] ;
pbwtBuildReverse (p) ;
PbwtCursor *u = pbwtCursorCreate (p, TRUE, TRUE) ;
PbwtCursor *uz = pbwtCursorCreate (p, FALSE, FALSE) ;
for (i = 0 ; i < 4 ; ++i) cSimple[i] = cCond0[i] = cCond1[i] = 0 ;
for (k = 0 ; k < N ; ++k)
{ pbwtCursorReadBackwards (uz) ;
if (isCheck)
{ for (i = 0 ; i < M ; ++i)
x[u->a[i]] = u->y[i] ;
for (i = 0 ; i < M ; ++i)
if (x[uz->a[i]] != uz->y[i])
fprintf (logFile, "forward-backward mismatch at k %d i %d\n", k, i) ;
}
if (k > 0.2*N && k < 0.8*N) /* ignore ends */
{ f = (M - u->c) / (double)M ; for (ff = 0 ; f*100 > fBound[ff] ; ++ff) ;
t = &testStat[ff] ;
t->fsum += f ;
memset (n0, 0, M*sizeof(int)) ; memset (n1, 0, M*sizeof(int)) ;
for (i = 1 ; i < M-1 ; ++i)
{ if (u->y[i-1] && u->y[i+1])
if (u->y[i]) ++t->n21 ; else ++t->n20 ;
else if (!u->y[i-1] && !u->y[i+1])
if (u->y[i]) ++t->n01 ; else ++t->n00 ;
else if ((!u->y[i-1] && u->d[i] < u->d[i+1]) ||
(!u->y[i+1] && u->d[i+1] < u->d[i]))
if (u->y[i]) ++t->n11a ; else ++t->n10a ;
else
if (u->y[i]) ++t->n11b ; else ++t->n10b ;
++(array(dHist, u->d[i]/100, Counts)[u->y[i-1] + 2*u->y[i]]) ;
++cSimple[u->y[i-1] + 2*u->y[i]] ;
if (u->y[i+1])
++cCond1[u->y[i-1] + 2*u->y[i]] ;
else
++cCond0[u->y[i-1] + 2*u->y[i]] ;
n0[u->a[i]] += 2 - (u->y[i-1] + u->y[i+1]) ;
n1[u->a[i]] += u->y[i-1] + u->y[i+1] ;
n0[uz->a[i]] += 2 - (uz->y[i-1] + uz->y[i+1]) ;
n1[uz->a[i]] += uz->y[i-1] + uz->y[i+1] ;
x[u->a[i]] = u->y[i] ;
}
for (i = 0 ; i < M ; ++i)
if (n0[i] + n1[i] == 4) /* it wasn't at the end either forwards or backwards */
{ if (x[i]) ++c1[ff][n1[i]] ; else ++c0[ff][n1[i]] ; }
}
pbwtCursorForwardsReadAD (u, k) ;
}
if (test == 1)
for (j = 0 ; j < 17 ; ++j)
{ t = &testStat[j] ;
tot = t->n00 + t->n01 + t->n10a + t->n11a + t->n10b + t->n11b + t->n20 + t->n21 ;
printf ("%-5.1f\t%-7.3f\t00,01\t%ld\t%ld\t10a,11a\t%ld\t%ld\t10b,11b\t%ld\t%ld\t20,21\t%ld\t%ld",
fBound[j], tot ? ((double)testStat[j].fsum) / tot : 0.0,
t->n00, t->n01, t->n10a, t->n11a, t->n10b, t->n11b, t->n20, t->n21) ;
if (tot)
{ xbar = (t->n10b + t->n11b + t->n20 + t->n21)/tot ;
ybar = (t->n01 + t->n11a + t->n11b + t->n21)/tot ;
r2 = ((t->n21 + t->n11b)/tot - xbar*ybar)/sqrt((xbar - xbar*xbar)*(ybar - ybar*ybar)) ;
printf ("\tx,y,r2\t%.4f\t%.4f\t%.4f\n", xbar, ybar, r2) ;
}
else
putchar ('\n') ;
}
else if (test == 2)
for (j = 0 ; j < arrayMax(dHist) ; ++j)
{ long *c ; c = arr(dHist, j, Counts) ;
printf ("%d\t%ld\t%ld\t%ld\t%ld", j, c[0], c[1], c[2], c[3]) ;
if (c[0] + c[2]) printf ("\t%.3f", c[0]/(double)(c[0]+c[2])) ; else printf ("\t0") ;
if (c[1] + c[3]) printf ("\t%.3f", c[3]/(double)(c[1]+c[3])) ; else printf ("\t0") ;
putchar ('\n') ;
}
else if (test == 3)
{ printf ("%.3f %.3f\t", cSimple[0]/(double)(cSimple[0]+cSimple[2]), cSimple[3]/(double)(cSimple[1]+cSimple[3])) ;
printf ("%.3f %.3f\t", cCond0[0]/(double)(cCond0[0]+cCond0[2]), cCond0[3]/(double)(cCond0[1]+cCond0[3])) ;
printf ("%.3f %.3f\n", cCond1[0]/(double)(cCond1[0]+cCond1[2]), cCond1[3]/(double)(cCond1[1]+cCond1[3])) ;
}
else if (test == 4)
for (j = 0 ; j < 17 ; ++j)
{ printf ("%-5.1f", fBound[j]) ;
tot = 0 ;
for (i = 0 ; i < 5 ; ++i) { tot += c0[j][i] + c1[j][i] ; }
printf ("\t%-7.3f", tot ? ((double) testStat[j].fsum) / tot : 0.0) ;
xbar = 0 ; r2 = 0 ;
for (i = 0 ; i < 5 ; ++i)
{ long sum = c0[j][i] + c1[j][i] ;
printf ("\t%ld ", sum) ;
if (sum) printf (" %.3f", c1[j][i]/(double)sum) ; else printf (" 00000") ;
xbar += c1[j][i] ;
if (i == 3 || i == 4) r2 += c1[j][i] ; if (i ==2) r2 += 0.5*c1[j][i] ;
tot += sum ;
}
ybar = c0[j][4] + c1[j][4] + c0[j][3] + c1[j][3] + 0.5*(c0[j][2] + c1[j][2]) ;
if (tot)
{ xbar /= tot ;
ybar /= tot ;
r2 = (r2/tot - xbar*ybar)/sqrt((xbar - xbar*xbar)*(ybar - ybar*ybar)) ;
printf ("\tx,y,r2\t%.4f\t%.4f\t%.4f\n", xbar, ybar, r2) ;
}
else
putchar ('\n') ;
}
pbwtCursorDestroy (u) ;
pbwtCursorDestroy (uz) ;
}
/****************** phasing ****************/
static void phaseCompare (PBWT *p, PBWT *q)
{
int i, k ;
int M = p->M, N = p->N ;
PbwtCursor *up = pbwtCursorCreate (p, TRUE, TRUE) ;
PbwtCursor *uq = pbwtCursorCreate (q, TRUE, TRUE) ;
int *xp = myalloc (M, int), *xq = myalloc (M, int) ;
int *isFirst = myalloc (M, int), *isFlipped = myalloc (M, int) ;
int *lastFlip = mycalloc (M, int), *kHet = mycalloc (M, int) ;
int nSwitch = 0, nHet = 0, nSwitch1 = 0, nSwitch5 = 0 ;
double mFac = 2.0/M ;
int *nSwitchSample = mycalloc (M, int), *nSwitchSite = mycalloc (N, int) ;
if (p->M != q->M || p->N != q->N) die ("size incompatibility in phaseCompare") ;
if (p->M %2) die ("phaseCompare requires that M %d is even", M) ;
memset (isFirst, 1, M*sizeof(int)) ; /* I know this is not 1 - anything non-zero will do */
for (k = 0 ; k < N ; k++)
{ for (i = 0 ; i < M ; ++i)
{ xp[up->a[i]] = up->y[i] ;
xq[uq->a[i]] = uq->y[i] ;
}
for (i = 0 ; i < M ; i += 2)
{ if (xp[i] + xp[i+1] == 1)
{ ++nHet ; ++kHet[i] ;
if (isFirst[i])
{ isFirst[i] = 0 ;
isFlipped[i] = (xp[i] == xq[i+1]) ? 1 : 0 ;
}
else if (xp[i] != xq[i+isFlipped[i]])
{ ++nSwitch ; ++nSwitchSample[i/2] ; ++nSwitchSite[k] ;
if (kHet[i] - lastFlip[i] > 1) ++nSwitch1 ;
if (kHet[i] - lastFlip[i] > 5) ++nSwitch5 ;
isFlipped[i] = 1 - isFlipped[i] ;
lastFlip[i] = kHet[i] ;
}
}
if (isCheck && (xp[i]+xp[i+1] != xq[i]+xq[i+1]))
{ fprintf (logFile, "phaseCompare mismatch k %d sequence %d\np", k, i) ;
uchar **pHaps = pbwtHaplotypes(p), **qHaps = pbwtHaplotypes(q) ;
int kk ;
for (kk = 0 ; kk < 40 ; ++kk)
fprintf (logFile, " %d", pHaps[i][kk] + pHaps[i+1][kk]) ;
fprintf (logFile, "\nq") ;
for (kk = 0 ; kk < 40 ; ++kk)
fprintf (logFile, " %d", qHaps[i][kk] + qHaps[i+1][kk]) ;
fprintf (logFile, "\n") ;
die ("phaseCompare mismatch: k %d, i %d, xp %d|%d, xq %d|%d",
k, i, xp[i], xp[i+1], xq[i], xq[i+1]) ;
}
}
pbwtCursorForwardsRead (up) ;
pbwtCursorForwardsRead (uq) ;
}
fprintf (logFile, "%.1f switches per sample, %.3f per het, %.1f nSwitch1, %.1f nSwitch5\n",
mFac*nSwitch, nSwitch/(double)nHet, mFac*nSwitch1, mFac*nSwitch5) ;
if (isStats)
{ for (i = 0 ; i < M/2 ; ++i)
{ printf ("SAMPLE-SWITCH\t%d\t%d", i, nSwitchSample[i]) ;
if (p->samples)
printf ("\t%s", sampleName(sample (p, 2*i))) ;
putchar ('\n') ;
}
for (k = 0 ; k < N ; ++k)
{ printf ("SITE-SWITCH\t%d\t%d", k, nSwitchSite[k]) ;
if (p->sites)
{ Site *s = arrp(p->sites,k,Site) ;
printf ("\t%s\t%d\t%s", p->chrom, s->x, dictName(variationDict, s->varD)) ;
}
putchar ('\n') ;
}
}
pbwtCursorDestroy (up) ; pbwtCursorDestroy (uq) ;
free (xp) ; free (xq) ; free (isFirst) ; free (isFlipped) ;
free (nSwitchSample) ; free (nSwitchSite) ;
}
/****************************************************************/
static double *scoreBit ;
static double *logisticCache ;
static void phaseInit (int N)
{ int i ;
double z ;
scoreBit = myalloc (N+1, double) ;
for (i = 0 ; i <= N ; ++i) scoreBit[i] = log (i + 1.0) ; /* 1 is simple version */
logisticCache = myalloc (100000, double) ;
for (i = 0 ; i < 100000 ; ++i)
{ z = exp (-i * 0.0001) ; logisticCache[i] = 1.0 / (1.0 + z) ; }
}
static inline double score0 (PbwtCursor *u, double *xp, int i)
{
double s = 0.0 ;
int ubi = u->b[i] ;
if (ubi > 0) s += xp[u->a[ubi-1]] ;
if (ubi < u->M-1) s += xp[u->a[ubi+1]] ;
return s ;
}
static inline double score1 (PbwtCursor *u, double *xp, int i, int k)
{
double s = 0 ;
int ubi = u->b[i] ;
if (ubi > 0) s += xp[u->a[ubi-1]] * scoreBit[(k+1)-u->d[ubi]] ;
if (ubi < u->M-1) s += xp[u->a[ubi+1]] * scoreBit[(k+1)-u->d[ubi+1]] ;
return s ;
}
static inline double logistic (double x)
{ int i = x * 10000 ;
if (i < -99999) return 1.0 - logisticCache[99999] ;
else if (i < 0) return 1.0 - logisticCache[-i] ;
else if (i < 100000) return logisticCache[i] ;
else return logisticCache[99999] ;
}
/******* phase() is phaseOld() rewritten with CNew API and method 3 only ******/
PBWT *phaseSweep (PBWT *p, PBWT *ref, BOOL isStart, PBWT *r, int nSparse)
{
int i, j, k, kk, kr = 0 ;
int M = p->M, N = p->N ;
if (ref && p->M > ref->M) die ("phaseSweep requires ref->M >= p->M") ;
/* initialisation */
PbwtCursor *up = pbwtCursorCreate (p, TRUE, isStart) ;
PBWT *q = pbwtCreate (M, N) ; /* CNew pbwt */
PbwtCursor *ur, *uref ;
if (ref) uref = pbwtCursorCreate (ref, TRUE, isStart) ;
if (r)
{ ur = pbwtCursorCreate (r, TRUE, FALSE) ;
memcpy (ur->b, r->aRend, M*sizeof(int)) ; /* recover stored locations */
// for (i = 0 ; i < M ; ++i) ur->b[ur->a[i]] = i ; /* store inverse a in b */
memcpy (q->aFstart, r->aFend, M*sizeof(int)) ; /* prime uq with final ur */
}
PbwtCursor *uq = pbwtCursorCreate (q, TRUE, TRUE) ;
for (i = 0 ; i < M ; ++i) uq->b[uq->a[i]] = i ; /* store inverse a in b */
PbwtCursor **uqq = myalloc (nSparse, PbwtCursor*) ;
for (kk = 0 ; kk < nSparse ; ++kk)
{ uqq[kk] = pbwtNakedCursorCreate (M, 0) ;
for (i = 0 ; i < M ; ++i) uqq[kk]->b[uqq[kk]->a[i]] = i ;
}
/* now loop through p phasing into q */
uchar *x = myalloc (M, uchar) ; /* actual haplotypes in original order, from p */
double *xp = myalloc(M, double) ; /* 2*p(x=1)-1, so 1 if x=1, -1 if x=0, 0 if unknown */
for (k = 0 ; k < N ; k++)
{ if (!isStart) pbwtCursorReadBackwards (up) ;
for (i = 0 ; i < M ; ++i) x[up->a[i]] = up->y[i] ; /* build x from up->y */
if (isStart) pbwtCursorForwardsRead (up) ;
for (i = 0 ; i < M ; ++i) xp[i] = x[i] ? 1.0 : -1.0 ;
int n2 = 0 ;
for (i = 0 ; i < M ; i += 2) /* go through x in pairs */
if (x[i] != x[i+1]) { ++n2 ; xp[i] = xp[i+1] = 0.0 ; } /* a het */
double s, thresh = ref ? 0.5 : 2*(nSparse + (r?2:1)) + 0.5 ;
while (n2 && thresh > 1.0)
{ int n2Old = n2 ; n2 = 0 ;
for (i = 0 ; i < M ; i += 2) /* loop over genotype pairs in original order */
if (!xp[i]) /* a het to phase */
{ s = score0 (uq, xp, i) - score0 (uq, xp, i+1) ;
if (r) s += score0 (ur, xp,i) - score0 (ur, xp, i+1) ;
for (kk = 0 ; kk < nSparse ; ++kk)
s += score0 (uqq[kk], xp, i) - score0 (uqq[kk], xp, i+1) ;
if (s > thresh) { xp[i] = 1 ; xp[i+1] = -1 ; }
else if (s < -thresh) { xp[i] = -1 ; xp[i+1] = 1 ; }
else ++n2 ;
}
if (n2 == n2Old) { thresh -= 1.0 ; n2Old = M+1 ; }
}
if (n2) /* some unresolved values - phase using length, forwards only for now */
for (i = 0 ; i < M ; i += 2)
if (!xp[i])
{ s = score1 (uq, xp, i, k) - score1 (uq, xp, i+1, k) ;
for (kk = 0 ; kk < nSparse ; ++kk)
s += score1 (uqq[kk], xp, i, k/nSparse) - score1 (uqq[kk], xp, i+1, k/nSparse) ;
if (s > 0) { xp[i] = 1 ; xp[i+1] = -1 ; }
else { xp[i] = -1 ; xp[i+1] = 1 ; }
}
for (i = 0 ; i < M ; ++i) x[i] = (xp[i] > 0.0) ? 1 : 0 ;
for (i = 0 ; i < M ; ++i) uq->y[i] = x[uq->a[i]] ;
pbwtCursorWriteForwardsAD (uq, k) ;
for (i = 0 ; i < M ; ++i) uq->b[uq->a[i]] = i ;
kk = k % nSparse ; /* which of the sparse pbwts to update this time */
for (i = 0 ; i < M ; ++i) uqq[kk]->y[i] = x[uqq[kk]->a[i]] ;
pbwtCursorForwardsAD (uqq[kk], k/nSparse) ;
for (i = 0 ; i < M ; ++i) uqq[kk]->b[uqq[kk]->a[i]] = i ;
if (r)
{ pbwtCursorReadBackwards (ur) ;
for (i = 0 ; i < M ; ++i) ur->b[ur->a[i]] = i ;
}
}
pbwtCursorToAFend (uq, q) ;
/* cache uq->b in aRend so we can retrieve from reverse on forwards pass */
q->aRend = myalloc (q->M, int) ;
for (i = 0 ; i < q->M ; ++i) q->aRend[i] = uq->b[i] ;
/* clean up memory allocated */
free (x) ; free (xp) ;
pbwtCursorDestroy (up) ; pbwtCursorDestroy (uq) ; if (r) pbwtCursorDestroy (ur) ;
for (kk = 0 ; kk < nSparse ; ++kk) pbwtCursorDestroy (uqq[kk]) ; free (uqq) ;
return q ;
}
PBWT *phase (PBWT *p, int nSparse) /* return rephased p */
{
if (p->M % 2) die ("phase requires that M = %d is even", p->M) ;
if (nSparse < 2) nSparse = 2 ;
phaseInit (p->N) ; /* sets up some lookup tables */
if (!p->aFend) pbwtBuildReverse (p) ; /* needed for old PBWT format data */
PBWT *r = phaseSweep (p, 0, FALSE, 0, 2) ; /* always reverse sweep wth nSparse 2 */
if (isCheck) /* flip p->zz round into p->yz and compare to r */
{ Array yzStore = p->yz ; p->yz = p->zz ;
int *aFstartStore = p->aFstart ; p->aFstart = p->aRstart ;
fprintf (logFile, "After reverse pass: ") ; phaseCompare (p, r) ;
p->yz = yzStore ; p->aFstart = aFstartStore ;
}
PBWT *q = phaseSweep (p, 0, TRUE, r, nSparse) ;
/* compare CNew phasing to original and report switch rates */
fprintf (logFile, "After forward pass: ") ; phaseCompare (p, q) ;
pbwtDestroy (p) ;
return q ;
}
/******* reference phase using same strategy as phase **********/
PBWT *referencePhase0 (PBWT *p, PBWT *pRef)
{
int nSparse = 2 ;
phaseInit (pRef->N) ;
if (!pRef->aFend) pbwtBuildReverse (pRef) ; /* needed for oldPBWT format data */
PBWT *r = phaseSweep (p, pRef, FALSE, 0, 2) ; /* always reverse with nSparse 2 */
if (isCheck) /* flip p->zz round into p->yz and compare to r */
{ if (!p->zz) pbwtBuildReverse (p) ;
Array yzStore = p->yz ; p->yz = p->zz ;
int *aFstartStore = p->aFstart ; p->aFstart = p->aRstart ;
fprintf (logFile, "After reverse pass: ") ; phaseCompare (p, r) ;
p->yz = yzStore ; p->aFstart = aFstartStore ;
}
PBWT *q = phaseSweep (p, pRef, TRUE, r, nSparse) ;
return q ;
}
/******* phase a CNew pbwt against the existing one as a reference *******/
typedef struct { int jRef ; int start ; int end ; } MatchSegment ;
/* matches are semi-open [start,end) so length is end-start */
static Array *maxMatch = 0 ; /* of MatchSegment */
static void reportMatch (int iq, int jRef, int start, int end)
{
MatchSegment *ms = arrayp (maxMatch[iq], arrayMax(maxMatch[iq]), MatchSegment) ;
ms->jRef = jRef ; ms->start = start ; ms->end = end ;
}
/**************** referencePhase4 *************************************************/
/* This one keeps track for each position j in the reference pbwt of the (normalised)
probability of generating the data given that the phasing so far sorts at position j,
and also of the other haplotype sort position given that phasing. We keep backtrack
pointers for each j, and prune them back so that only ones connected to the current
values at k are kept live.
As currently implemented this calculates the full likelihood, but gives the most likely
path contributing to that. We could adapt it to full Viterbi, or sampling mode.
*/
/* within this, try different ways to keep the score and extend */
#define EXTEND4
/******** type declarations ********/
typedef unsigned int TraceBackIndex ; /* index into traceBackHeap */
/* #define TRACEBACK_DEBUG */
typedef struct
{ TraceBackIndex back : 28 ; /* index into traceBackHeap for cell at previous het site */
unsigned int value : 1 ; /* 0 or 1 */
unsigned int count : 3 ; /* how many cells at next het site point back to this: 0,1 or 2 */
#ifdef TRACEBACK_DEBUG
int j, k ;
#endif
} TraceBackCell ; /* pack this so it fits into a 4-byte word */
typedef struct {
int j1 ; /* the pair index of j0, which is the index of the cell */
TraceBackIndex back ;
float s ;
#ifdef EXTEND0
float sBest ;
#endif
#ifdef EXTEND1
int dplus0, dminus0, dmax0, dplus1, dminus1, dmax1 ;
#endif
#ifdef EXTEND2
int j0min, j0max, j1min, j1max ;
#endif
#if defined(EXTEND3) || defined(EXTEND4)
int dplus0, dminus0, dplus1, dminus1 ;
#endif
} PhaseCell ;
/********** first the package to manage trace back space efficiently **********/
static Array traceBackHeap = 0 ; /* of TraceBackCell */
static Array traceBackFreeStack = 0 ; /* of TraceBackIndex */
#define traceBackCell(tb) arrp(traceBackHeap, (tb), TraceBackCell)
TraceBackIndex traceBackCreate (TraceBackIndex back, unsigned int value, int j, int k)
{ TraceBackIndex tb ;
TraceBackCell *tc ;
if (!isCheck && arrayMax (traceBackFreeStack))
{ tb = arr (traceBackFreeStack, --arrayMax(traceBackFreeStack), TraceBackIndex) ;
tc = arrp (traceBackHeap, tb, TraceBackCell) ;
}
else
{ tb = arrayMax(traceBackHeap) ;
tc = arrayp (traceBackHeap, tb, TraceBackCell) ;
}
tc->back = back ; tc->value = value ; tc->count = 1 ;
#ifdef TRACEBACK_DEBUG
tc->j = j ; tc->k = k ;
#endif
/* if (isCheck) printf ("traceBackCreate %d at k %d j %d back %d value %d\n", tb, k, j, back, value) ; */
return tb ;
}
inline static void traceBackPrune (TraceBackIndex tb, int k, int j)
{ TraceBackCell *tc = traceBackCell(tb) ;
while (tb && --tc->count == 0) /* i.e. that was the last active link for that cell */
{ array(traceBackFreeStack, arrayMax(traceBackFreeStack), int) = tb ;
/* if (isCheck) printf ("traceBackDestroy %d at k %d j %d\n", tb, k, j) ; */
tb = tc->back ;
tc = traceBackCell(tb) ;
}
}
void traceBackInitialise (void)
{ traceBackHeap = arrayReCreate (traceBackHeap, 4096, TraceBackCell) ;
traceBackFreeStack = arrayReCreate (traceBackFreeStack, 2048, TraceBackIndex) ;
traceBackCreate (0, 0, 0, 0) ; /* make empty first element, so that later back == 0 only at end*/
}
#ifdef TRACEBACK_DEBUG
void traceBackReport (TraceBackIndex tb)
{ while (tb)
{ TraceBackCell *tc = traceBackCell(tb) ;
printf (" %dk%dj%d", tc->value, tc->k, tc->j) ;
tb = tc->back ;
}
}
void traceBackCheck (int jq, int k, PhaseCell *pc, int M) /* beware - very costly */
{
int j ;
int* zCount = mycalloc (arrayMax(traceBackHeap), int) ;
for (j = 0 ; j < arrayMax(traceBackHeap) ; ++j)
{ TraceBackCell *tc = traceBackCell(j) ;
if (tc->count) ++zCount[tc->back] ;
}
for (j = 0 ; j <= M ; ++j) if (pc[j].s) ++zCount[pc[j].back] ;
for (j = 1 ; j < arrayMax(traceBackHeap) ; ++j)
if (zCount[j] && traceBackCell(j)->count != zCount[j])
{ warn ("bad count jq %d, k %d, j %d, zCount[j] %d, traceBackCell(j)->count %d",
jq, k, j, zCount[j], traceBackCell(j)->count) ;
int jj ;
for (jj = 0 ; jj <= M ; ++jj)
if (pc[jj].s && pc[jj].back == j) warn (" back[%d] == %d", jj, j) ;
for (jj = 0 ; jj < arrayMax(traceBackHeap) ; ++jj)
{ TraceBackCell *tc = traceBackCell(jj) ;
if (tc->count && tc->back == j)
warn (" tc[%d]->back %d, tc[%d]->count %d", jj, j, jj, tc->count) ;
}
}
free (zCount) ;
}
#endif // TRACEBACK_DEBUG
/********** next the calculation of how likely to extend from j with value x **********/
#ifdef EXTEND0
/* first version tries to consider all copying haplotypes with weights proportional to shared length */
/* we pre-calculate contributions from above and below in extendPrepare(), caching in extendScore0/1 */
static char *extendMethodText = "EXTEND0" ;
static long *extendScore0 = 0, *extendScore1 = 0 ;
static int extendScoreSize = 0 ;
static Array extendStack = 0 ;
typedef struct {
int d ;
int n0, n1 ; /* number of y[j] == 0/1 so far with this effective dd */
int sum0, sum1 ; /* sum of dd*n up to this element */
} ExtendStruct ;
static ExtendStruct *extendUpdate (int dd, int x)
{
int i, n0 = 0, n1 = 0 ; /* n0 and n1 are # 0s,1s with d > dd */
ExtendStruct *ex ;
if (isCheck && dd < 0) die ("dd %d < 0 in extendUpdate", dd) ;
/* find highest place in stack less than or equal to dd */
for (i = arrayMax(extendStack) ; i-- ; )
{ ex = arrp(extendStack, i, ExtendStruct) ;
if (dd >= ex->d) break ;
n0 += ex->n0 ; n1 += ex->n1 ;
}
arrayMax(extendStack) = i+1 ;
if (dd > ex->d) /* make a CNew exStack element */
{ ex = arrayp(extendStack, i+1, ExtendStruct) ;
ex->d = dd ; ex->n0 = n0 ; ex->n1 = n1 ;
ex->sum0 = ex[-1].sum0 + dd*n0 ; ex->sum1 = ex[-1].sum1 + dd*n1 ;
}
else /* add these things from longer dd to current element */
{ ex->n0 += n0 ; ex->sum0 += dd*n0 ; ex->n1 += n1 ; ex->sum1 += dd*n1 ; }
/* now add the current element on */
if (x) { ++ex->n1 ; ex->sum1 += dd ; } else { ++ex->n0 ; ex->sum0 += dd ; }
return ex ;
}
static void extendPrepare (PbwtCursor *u, int k)
{
int j ;
ExtendStruct *ex ;
if (extendScoreSize != u->M)
{ if (extendScore0) { free (extendScore0) ; free (extendScore1) ; }
extendScore0 = mycalloc (u->M+1, long) ; extendScore1 = mycalloc (u->M+1, long) ;
extendScoreSize = u->M ;
}
/* first run through samples j == 1..M and add scores from top to j */
extendStack = arrayReCreate (extendStack, 512, ExtendStruct) ;
ex = arrayp (extendStack, 0, ExtendStruct) ;
ex->d = 0 ; ex->n0 = 0 ; ex->n1 = 0 ; ex->sum0 = 1 ; ex->sum1 = 1 ;
extendScore0[0] = 0 ; extendScore1[0] = 0 ;
for (j = 0 ; j++ < u->M ; )
{ extendScore0[j] = ex->sum0 ; extendScore1[j] = ex->sum1 ;
int bit = (j < u->M || u->d[j-1] > u->d[j]) ? u->d[j-1] : u->d[j] ;
if (u->y[j-1]) extendScore1[j] += bit ; else extendScore0[j] += bit ;
if (j < u->M) ex = extendUpdate (k - u->d[j], u->y[j-1]) ;
}
/* then reverse j == M-1..0 and add on scores from bottom to j */
extendStack = arrayReCreate (extendStack, 512, ExtendStruct) ;
ex = arrayp (extendStack, 0, ExtendStruct) ;
ex->d = 0 ; ex->n0 = 0 ; ex->n1 = 0 ; ex->sum0 = 1 ; ex->sum1 = 1 ;
for (j = u->M ; j-- > 0 ; )
{ extendScore0[j] += ex->sum0 ; extendScore1[j] += ex->sum1 ;
int bit = (j || u->d[j+1] > u->d[j]) ? u->d[j+1] : u->d[j] ;
if (u->y[j]) extendScore1[j] += bit ; else extendScore0[j] += bit ;
if (j) ex = extendUpdate (k - u->d[j], u->y[j]) ;
}
}
/* To be correct I should calculate the upper score up until but not including the
preceding j-1, and the lower score back until but not including the succeeding j,
because I don't know here the match lengths to the flanking j-1,j. I can know them
during the dynamic programming, because I know the backtrace. But this means
calculating and storing the dplus, dminus values induced by the backtrace, which adds
considerable complexity. Above I assume that they are the greater of d[j] and d[j-1]
(for j-1) and d[j] and d[j+1] (for j), which is a lower bound, taking care not to
query out of bounds at the top and bottom.
*/
static inline double extendScore (int j, int x)
{
double p = extendScore1[j] / (double) (extendScore0[j] + extendScore1[j]) ;
return (x ? p : 1-p) ;
}
static int phaseExtend (int x0, int x1, PbwtCursor *uRef, int j0,
PhaseCell *pcOld, PhaseCell *pcNew, int k)
/* returns the number of CNew back pointers created */
/* change at XXX for sampling or YYY for Viterbi */
/* this code uses extend structure above via extendScore, but did not perform well */
/* so replace with CNew phaseExtend() below, I hope */
{
PhaseCell *old = &pcOld[j0] ;
PhaseCell *CNew = &pcNew[pbwtCursorMap (uRef, x0, j0)] ;
int j1New = pbwtCursorMap (uRef, x1, old->j1) ;
double sBit = old->s * extendScore (j0, x0) * extendScore (old->j1, x1) ;
if (isCheck && k == 51 && (j0 == 1389 || pbwtCursorMap(uRef,x0,j0) == 1370))
printf ("at k %d extend j0 %d j1 %d s %.3g with x %d %d to j0New %d j1New %d sbit %.3g\n",
k, j0, old->j1, old->s, x0, x1, pbwtCursorMap (uRef, x0, j0), j1New, sBit) ;
if (!CNew->s) /* this is the first j to map here */
{ CNew->s = sBit ; CNew->sBest = sBit ;
CNew->j1 = j1New ;
CNew->back = (x0 == x1) ? old->back : traceBackCreate (old->back, x0, j0, k) ;
return 1 ;
}
/* XXX for sampling calculate chance to pick this j rather than
previous here */
if (sBit > CNew->sBest) /* this is better than previous j that mapped here */
{ CNew->s = sBit ; /* YYY originally +=, for Viterbi change to = */
CNew->sBest = sBit ;
CNew->j1 = j1New ;
if (traceBackCell(CNew->back)->back == old->back) /* be careful - edge case! */
{ traceBackCell(CNew->back)->value = x0 ; return 0 ; }
else
{ traceBackPrune (CNew->back, k, j0) ;
CNew->back = (x0 == x1) ? old->back : traceBackCreate (old->back, x0, j0, k) ;
return 1 ;
}
}
/* CNew->s += sBit ; /* include if not Viterbi */
return 0 ;
}
#endif // EXTEND0
#ifdef EXTEND1 /* alternate version minimises number of recombinations */
/* in this version pc->s is -1 minus the number of recombinations */
static char *extendMethodText = "EXTEND1" ;
static void extendPrepare (PbwtCursor *u, int k) {}
static inline int phaseExtend (int x0, int x1, PbwtCursor *uRef, int j0,
PhaseCell *pcOld, PhaseCell *pcNew, int k)
/* returns the number of CNew back pointers created */
{
PhaseCell *old = &pcOld[j0] ;
int j0New = pbwtCursorMap (uRef, x0, j0) ;
PhaseCell *CNew = &pcNew[j0New] ;
if (CNew->s && CNew->s > old->s) return 0 ; /* quick check whether this is possible */
PhaseCell temp ;
temp.s = old->s ;
temp.dplus0 = pbwtCursorMapDplus (uRef, x0, j0, old->dplus0) ;
temp.dminus0 = pbwtCursorMapDminus (uRef, x0, j0, old->dminus0) ;
if (temp.dplus0 > old->dmax0 && temp.dminus0 > old->dmax0) /* need a recombination */
{ --temp.s ; temp.dmax0 = k ; } else temp.dmax0 = old->dmax0 ;
temp.j1 = pbwtCursorMap (uRef, x1, old->j1) ;
temp.dplus1 = pbwtCursorMapDplus (uRef, x1, old->j1, old->dplus1) ;
temp.dminus1 = pbwtCursorMapDminus (uRef, x1, old->j1, old->dminus1) ;
if (temp.dplus1 > old->dmax1 && temp.dminus1 > old->dmax1) /* need a recombination */
{ --temp.s ; temp.dmax1 = k ; } else temp.dmax1 = old->dmax1 ;
if (!CNew->s) /* this is the first j0 to map here */
{ *CNew = temp ;
CNew->back = (x0 == x1) ? old->back : traceBackCreate (old->back, x0, j0, k) ;
return 1 ;
}
else if (temp.s > CNew->s) /* this is better than previous j that mapped here */
{ TraceBackIndex oldNewBack = CNew->back ;
*CNew = temp ; /* originally +=, for Viterbi change to = */
if (traceBackCell(oldNewBack)->back == old->back) /* be careful - edge case! */
{ CNew->back = oldNewBack ; traceBackCell(CNew->back)->value = x0 ; return 0 ; }
else
{ traceBackPrune (oldNewBack, k, j0) ;
CNew->back = (x0 == x1) ? old->back : traceBackCreate (old->back, x0, j0, k) ;
return 1 ;
}
}
else
return 0 ;
}
#endif // EXTEND1
#ifdef EXTEND2 /* alternate version of EXTEND1 that minimises number of recombinations */
/* in this version we track the prefix interval (jmin,jmax) for matches to j0, j1 */
static char *extendMethodText = "EXTEND2" ;
static void extendPrepare (PbwtCursor *u, int k) {}
static inline int phaseExtend (int x0, int x1, PbwtCursor *uRef, int j0,
PhaseCell *pcOld, PhaseCell *pcNew, int k)
/* returns the number of CNew back pointers created */
{
PhaseCell *old = &pcOld[j0] ;
int j0New = pbwtCursorMap (uRef, x0, j0) ;
PhaseCell *CNew = &pcNew[j0New] ;
if (CNew->s && CNew->s > old->s) return 0 ; /* quick check whether this is possible */
PhaseCell temp ;
temp.s = old->s ;
temp.j0min = pbwtCursorMap (uRef, x0, old->j0min) ;
temp.j0max = pbwtCursorMap (uRef, x0, old->j0max) ;
if (temp.j0min == temp.j0max) /* need a recombination */
{ --temp.s ; temp.j0min = x0 ? uRef->c-1 : 0 ; temp.j0max = x0 ? uRef->M : uRef->c ; }
temp.j1 = pbwtCursorMap (uRef, x1, old->j1) ;
temp.j1min = pbwtCursorMap (uRef, x1, old->j1min) ;
temp.j1max = pbwtCursorMap (uRef, x1, old->j1max) ;
if (temp.j1min == temp.j1max) /* need a recombination */
{ --temp.s ; temp.j1min = x1 ? uRef->c-1 : 0 ; temp.j1max = x1 ? uRef->M : uRef->c ; }
if (!CNew->s) /* this is the first j0 to map here */
{ *CNew = temp ;
CNew->back = (x0 == x1) ? old->back : traceBackCreate (old->back, x0, j0, k) ;
return 1 ;
}
else if (temp.s > CNew->s) /* this is better than previous j that mapped here */
{ TraceBackIndex oldNewBack = CNew->back ;
*CNew = temp ; /* originally +=, for Viterbi change to = */
if (traceBackCell(oldNewBack)->back == old->back) /* be careful - edge case! */
{ CNew->back = oldNewBack ; traceBackCell(CNew->back)->value = x0 ; return 0 ; }
else
{ traceBackPrune (oldNewBack, k, j0) ;
CNew->back = (x0 == x1) ? old->back : traceBackCreate (old->back, x0, j0, k) ;
return 1 ;
}
}
else
return 0 ;
}
#endif // EXTEND2
#ifdef EXTEND3 /* like EXTEND1,2 but maximises sum of lengths of maximal matches*/
/* in this version pc->s is 1 + sum of lengths of maximal matches */
static char *extendMethodText = "EXTEND3" ;
static void extendPrepare (PbwtCursor *u, int k) {}
static inline int phaseExtend (int x0, int x1, PbwtCursor *uRef, int j0,
PhaseCell *pcOld, PhaseCell *pcNew, int k)
/* returns the number of CNew back pointers created */
{
PhaseCell *old = &pcOld[j0] ;
int j0New = pbwtCursorMap (uRef, x0, j0) ;
PhaseCell *CNew = &pcNew[j0New] ;
PhaseCell temp ; /* build the potential CNew in this */
temp.s = old->s ;
temp.dplus0 = pbwtCursorMapDplus (uRef, x0, j0, old->dplus0) ;
temp.dminus0 = pbwtCursorMapDminus (uRef, x0, j0, old->dminus0) ;
int j ;
if (old->dplus0 < old->dminus0 && old->dplus0 < temp.dplus0)
for (j = j0 ; j < uRef->M ; )
{ temp.s += (k - old->dplus0) ;
if (uRef->d[++j] > old->dplus0) break ;
}
else if (old->dminus0 < old->dplus0 && old->dminus0 < temp.dminus0)
for (j = j0 ; j < uRef->M ; )
{ temp.s += (k - old->dminus0) ;
if (uRef->d[--j] > old->dminus0) break ;
}
temp.j1 = pbwtCursorMap (uRef, x1, old->j1) ;
temp.dplus1 = pbwtCursorMapDplus (uRef, x1, old->j1, old->dplus1) ;
temp.dminus1 = pbwtCursorMapDminus (uRef, x1, old->j1, old->dminus1) ;
if (old->dplus1 < old->dminus1 && old->dplus1 < temp.dplus1)
for (j = j0 ; j < uRef->M ; )
{ temp.s += (k - old->dplus1) ;
if (uRef->d[++j] > old->dplus1) break ;
}
else if (old->dminus1 < old->dplus1 && old->dminus1 < temp.dminus1)
for (j = j0 ; j < uRef->M ; )
{ temp.s += (k - old->dminus1) ;
if (uRef->d[--j] > old->dminus1) break ;
}
if (!CNew->s) /* this is the first j0 to map here */
{ *CNew = temp ;
CNew->back = (x0 == x1) ? old->back : traceBackCreate (old->back, x0, j0, k) ;
return 1 ;
}
else if (temp.s > CNew->s) /* this is better than previous j that mapped here */
{ TraceBackIndex oldNewBack = CNew->back ;
*CNew = temp ; /* originally +=, for Viterbi change to = */
if (traceBackCell(oldNewBack)->back == old->back) /* be careful - edge case! */
{ CNew->back = oldNewBack ; traceBackCell(CNew->back)->value = x0 ; return 0 ; }
else
{ traceBackPrune (oldNewBack, k, j0) ;
CNew->back = (x0 == x1) ? old->back : traceBackCreate (old->back, x0, j0, k) ;
return 1 ;
}
}
else
return 0 ;
}
#endif // EXTEND3
#ifdef EXTEND4 /* based on diff from neighbours based on -log generative model */
/* in this version pc->s is -1 - sum of lengths of mismatched neighbours */
static char *extendMethodText = "EXTEND4" ;
static void extendPrepare (PbwtCursor *u, int k) {}
static inline int phaseExtend (int x0, int x1, PbwtCursor *uRef, int j0,
PhaseCell *pcOld, PhaseCell *pcNew, int k)
/* returns the number of CNew back pointers created */
{
PhaseCell *old = &pcOld[j0] ;
int j0New = pbwtCursorMap (uRef, x0, j0) ;
PhaseCell *CNew = &pcNew[j0New] ;
PhaseCell temp ; /* build the potential CNew in this */
temp.s = old->s ;
temp.dplus0 = pbwtCursorMapDplus (uRef, x0, j0, old->dplus0) ;
temp.dminus0 = pbwtCursorMapDminus (uRef, x0, j0, old->dminus0) ;
float dS = 0 ;
if (j0)
{ if (x0 == uRef->y[j0-1]) dS += (k-old->dminus0) ; else dS -= (k-old->dminus0) ; }
if (j0 < uRef->M)
{ if (x0 == uRef->y[j0]) dS += (k-old->dplus0) ; else dS -= (k-old->dplus0) ; }
if (dS < 0) temp.s += dS ;
temp.j1 = pbwtCursorMap (uRef, x1, old->j1) ;
temp.dplus1 = pbwtCursorMapDplus (uRef, x1, old->j1, old->dplus1) ;
temp.dminus1 = pbwtCursorMapDminus (uRef, x1, old->j1, old->dminus1) ;
dS = 0 ;
if (old->j1)
{ if (x1 == uRef->y[old->j1-1]) dS += (k-old->dminus1) ; else dS -= (k-old->dminus1) ; }
if (old->j1 < uRef->M)
{ if (x1 == uRef->y[old->j1]) dS += (k-old->dplus1) ; else dS -= (k-old->dplus1) ; }
if (dS < 0) temp.s += dS ;
if (!CNew->s) /* this is the first j0 to map here */
{ *CNew = temp ;
CNew->back = (x0 == x1) ? old->back : traceBackCreate (old->back, x0, j0, k) ;
return 1 ;
}
else if (temp.s > CNew->s) /* this is better than previous j that mapped here */
{ TraceBackIndex oldNewBack = CNew->back ;
*CNew = temp ; /* originally +=, for Viterbi change to = */
if (traceBackCell(oldNewBack)->back == old->back) /* be careful - edge case! */
{ CNew->back = oldNewBack ; traceBackCell(CNew->back)->value = x0 ; return 0 ; }
else
{ traceBackPrune (oldNewBack, k, j0) ;
CNew->back = (x0 == x1) ? old->back : traceBackCreate (old->back, x0, j0, k) ;
return 1 ;
}
}
else
return 0 ;
}
#endif // EXTEND4
/********** finally the main function ********/
static PBWT *referencePhase4 (PBWT *pOld, PBWT *pRef)
{
fprintf (logFile, "Reference phase with extension method %s\n", extendMethodText) ;
int i, j, jq, k ;
PbwtCursor *uOld = pbwtCursorCreate (pOld, TRUE, TRUE) ;
uchar *xOld = myalloc (pOld->M, uchar) ;
PbwtCursor *uRef = pbwtCursorCreate (pRef, TRUE, TRUE) ;
traceBackInitialise() ;
PhaseCell **pcOld = myalloc (pOld->M, PhaseCell*) ;
PhaseCell **pcNew = myalloc (pOld->M, PhaseCell*) ;
for (jq = 0 ; jq < pOld->M ; jq += 2)
{ pcOld[jq] = mycalloc (pRef->M+1, PhaseCell) ;
pcOld[jq][0].back = 0 ;
#if defined(EXTEND0) || defined(EXTEND3)
pcOld[jq][0].s = 1.0 ;
#endif
#if defined(EXTEND1) || defined(EXTEND2) || defined(EXTEND4)
pcOld[jq][0].s = -1.0 ;
#endif
pcNew[jq] = myalloc (pRef->M+1, PhaseCell) ;
}
/* some declarations for checks */
int *checkLiveSum = mycalloc (pOld->M, int) ;
double *checkLikeSum = mycalloc (pOld->M, double) ;
int *checkHets = mycalloc (pOld->M, int) ;
/* here is the main loop through the sites */
for (k = 0 ; k < pOld->N ; ++k)
{ for (j = 0 ; j < pOld->M ; ++j) xOld[uOld->a[j]] = uOld->y[j] ;
#ifdef QUERY0_IS_REF0
if (isCheck)
{ PhaseCell *pc ; TraceBackCell *tc ;
int a0, a1 ;
for (j = 0 ; j < pRef->M ; ++j)
{ if (uRef->a[j] == 0) a0 = j ;
if (uRef->a[j] == 1) a1 = j ;
}
PhaseCell *pc0 = &pcOld[0][a0], *pc1 = &pcOld[0][a1] ;
printf ("at k %4d x0 %d x1 %d", k, xOld[0], xOld[1]) ;
printf ("\n 0 j %4d s %10.3g", a0, pc0->s) ; traceBackReport (pc0->back) ;
printf ("\n 1 j %4d s %10.3g", a1, pc1->s) ; traceBackReport (pc1->back) ;
for (j = 0, pc = pcOld[0] ; j < pRef->M ; ++j, ++pc)
if (pc->s > pc0->s && pc->s > pc1->s)
{ printf ("\n j %4d s %10.3g", j, pc->s) ; traceBackReport (pc->back) ;
die ("done") ;
}
putchar ('\n') ;
}
#endif
if (isCheck && !(k % 100))
{ printf ("check k %d", k) ; int nS = 0 ; PhaseCell *pc ;
for (j = 0, pc = pcOld[0] ; j < pRef->M ; ++j, ++pc) if (pc->s) ++nS ;
printf (" nS %d\n", nS) ;
}
extendPrepare (uRef, k) ;
pbwtCursorCalculateU (uRef) ; /* before pbwtCursorMap()s in phaseExtend() */
/* update each query sample in turn */
for (jq = 0 ; jq < pOld->M ; jq +=2)
{ bzero (pcNew[jq], (pRef->M+1)*sizeof(PhaseCell)) ; /* clear pcNew */
int x0 = xOld[jq], x1 = xOld[jq+1] ;
if (x0 != x1) checkHets[jq]++ ;
for (j = 0 ; j <= pRef->M ; ++j)
if (pcOld[jq][j].s)
{ int countBack ;
if (x0 == x1)
countBack = phaseExtend (x0, x1, uRef, j, pcOld[jq], pcNew[jq], k) ;
else
countBack = phaseExtend (x0, x1, uRef, j, pcOld[jq], pcNew[jq], k) +
phaseExtend (x1, x0, uRef, j, pcOld[jq], pcNew[jq], k) ;
/* now resolve traceback counts on pcOld[jq][j].back */
if (countBack == 0)
traceBackPrune (pcOld[jq][j].back, k, j) ;
else if (countBack == 2 && pcOld[jq][j].back) /* don't increment tb cell 0 */
traceBackCell(pcOld[jq][j].back)->count++ ;
/* else leave count at default of 1 */
++checkLiveSum[jq] ;
}
/* now update pcOld from pcNew to be ready for next column */
double sum = 0 ; for (j = 0 ; j <= pRef->M ; ++j) sum += pcNew[jq][j].s ;
if (!sum) die ("sum is 0 at k %d jq %d", k, jq) ;
checkLikeSum[jq] += log (sum) ;
for (j = 0 ; j <= pRef->M ; ++j)
{ pcOld[jq][j] = pcNew[jq][j] ;
#ifdef EXTEND0
if (!isCheck) pcOld[jq][j].s /= sum ; /* normalise */
#endif
}
}
#ifdef TRACEBACK_DEBUG
if (isCheck) traceBackCheck (jq, k, pcOld[0], pRef->M) ; /* check traceback counters */
printf ("%d%d %d", xOld[0], xOld[1], uRef->y[0]) ;
for (j = 1 ; j <= pRef->M ; ++j) printf (" %d", uRef->y[j]) ; putchar ('\n') ;
for (j = 0 ; j <= pRef->M ; ++j) printf (" %6.1f", pcOld[0][j].s) ; putchar ('\n') ;
for (j = 0 ; j <= pRef->M ; ++j) printf (" %6d", pcOld[0][j].j1) ; putchar ('\n') ;
#endif