static void flush_viterbi(args_t *args)
{
int i,j;
if ( !args->nsites ) return;
if ( !args->vi_training )
{
// single viterbi pass, one chromsome
hmm_run_viterbi(args->hmm, args->nsites, args->eprob, args->sites);
hmm_run_fwd_bwd(args->hmm, args->nsites, args->eprob, args->sites);
double *fwd = hmm_get_fwd_bwd_prob(args->hmm);
const char *chr = bcf_hdr_id2name(args->hdr,args->prev_rid);
uint8_t *vpath = hmm_get_viterbi_path(args->hmm);
for (i=0; i<args->nsites; i++)
{
int state = vpath[i*2]==STATE_AZ ? 1 : 0;
double *pval = fwd + i*2;
printf("%s\t%d\t%d\t%.1f\n", chr,args->sites[i]+1, state, phred_score(1.0-pval[state]));
}
return;
}
// viterbi training, multiple chromosomes
double t2az_prev, t2hw_prev;
double deltaz, delthw;
int niter = 0;
do
{
double *tprob_arr = hmm_get_tprob(args->hmm);
t2az_prev = MAT(tprob_arr,2,1,0); //args->t2AZ;
t2hw_prev = MAT(tprob_arr,2,0,1); //args->t2HW;
double tcounts[] = { 0,0,0,0 };
for (i=0; i<args->nrids; i++)
{
// run viterbi for each chromosomes. eprob and sites contain
// multiple chromosomes, rid_offs mark the boundaries
int ioff = args->rid_offs[i];
int nsites = (i+1==args->nrids ? args->nsites : args->rid_offs[i+1]) - ioff;
hmm_run_viterbi(args->hmm, nsites, args->eprob+ioff*2, args->sites+ioff);
// what transitions were observed: add to the total counts
uint8_t *vpath = hmm_get_viterbi_path(args->hmm);
for (j=1; j<nsites; j++)
{
// count the number of transitions
int prev_state = vpath[2*(j-1)];
int curr_state = vpath[2*j];
MAT(tcounts,2,curr_state,prev_state) += 1;
}
}
// update the transition matrix tprob
for (i=0; i<2; i++)
{
int n = 0;
for (j=0; j<2; j++) n += MAT(tcounts,2,i,j);
if ( !n) error("fixme: state %d not observed\n", i+1);
for (j=0; j<2; j++) MAT(tcounts,2,i,j) /= n;
}
if ( args->genmap_fname || args->rec_rate > 0 )
hmm_set_tprob(args->hmm, tcounts, 0);
else
hmm_set_tprob(args->hmm, tcounts, 10000);
tprob_arr = hmm_get_tprob(args->hmm);
deltaz = fabs(MAT(tprob_arr,2,1,0)-t2az_prev);
delthw = fabs(MAT(tprob_arr,2,0,1)-t2hw_prev);
niter++;
fprintf(pysamerr,"%d: %f %f\n", niter,deltaz,delthw);
}
while ( deltaz > 0.0 || delthw > 0.0 );
fprintf(pysamerr, "Viterbi training converged in %d iterations to", niter);
double *tprob_arr = hmm_get_tprob(args->hmm);
for (i=0; i<2; i++) for (j=0; j<2; j++) fprintf(pysamerr, " %f", MAT(tprob_arr,2,i,j));
fprintf(pysamerr, "\n");
// output the results
for (i=0; i<args->nrids; i++)
{
int ioff = args->rid_offs[i];
int nsites = (i+1==args->nrids ? args->nsites : args->rid_offs[i+1]) - ioff;
hmm_run_viterbi(args->hmm, nsites, args->eprob+ioff*2, args->sites+ioff);
uint8_t *vpath = hmm_get_viterbi_path(args->hmm);
const char *chr = bcf_hdr_id2name(args->hdr,args->rids[i]);
for (j=0; j<nsites; j++)
{
printf("%s\t%d\t%d\t..\n", chr,args->sites[ioff+j]+1,vpath[j*2]==STATE_AZ ? 1 : 0);
}
}
}
void flush_viterbi(args_t *args)
{
const char *s1, *s2, *s3 = NULL;
if ( args->mode==C_UNRL )
{
s1 = bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,args->isample);
s2 = bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,args->jsample);
}
else if ( args->mode==C_TRIO )
{
s1 = bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,args->imother);
s3 = bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,args->ifather);
s2 = bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,args->ichild);
}
if ( !args->fp )
{
kstring_t str = {0,0,0};
kputs(args->prefix, &str);
kputs(".dat", &str);
args->fp = fopen(str.s,"w");
if ( !args->fp ) error("%s: %s\n", str.s,strerror(errno));
free(str.s);
fprintf(args->fp,"# SG, shared segment\t[2]Chromosome\t[3]Start\t[4]End\t[5]%s:1\t[6]%s:2\n",s2,s2);
fprintf(args->fp,"# SW, number of switches\t[3]Sample\t[4]Chromosome\t[5]nHets\t[5]nSwitches\t[6]switch rate\n");
}
hmm_run_viterbi(args->hmm,args->nsites,args->eprob,args->sites);
uint8_t *vpath = hmm_get_viterbi_path(args->hmm);
int i, iprev = -1, prev_state = -1, nstates = hmm_get_nstates(args->hmm);
int nswitch_mother = 0, nswitch_father = 0;
for (i=0; i<args->nsites; i++)
{
int state = vpath[i*nstates];
if ( state!=prev_state || i+1==args->nsites )
{
uint32_t start = iprev>=0 ? args->sites[iprev]+1 : 1, end = i>0 ? args->sites[i-1] : 1;
const char *chr = bcf_hdr_id2name(args->hdr,args->prev_rid);
if ( args->mode==C_UNRL )
{
switch (prev_state)
{
case UNRL_0x0x:
fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:1\t-\n", chr,start,end,s1); break;
case UNRL_0xx0:
fprintf(args->fp,"SG\t%s\t%d\t%d\t-\t%s:1\n", chr,start,end,s1); break;
case UNRL_x00x:
fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:2\t-\n", chr,start,end,s1); break;
case UNRL_x0x0:
fprintf(args->fp,"SG\t%s\t%d\t%d\t-\t%s:2\n", chr,start,end,s1); break;
case UNRL_0101:
fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:1\t%s:2\n", chr,start,end,s1,s1); break;
case UNRL_0110:
fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:2\t%s:1\n", chr,start,end,s1,s1); break;
}
}
else if ( args->mode==C_TRIO )
{
switch (prev_state)
{
case TRIO_AC:
fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:1\t%s:1\n", chr,start,end,s1,s3); break;
case TRIO_AD:
fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:1\t%s:2\n", chr,start,end,s1,s3); break;
case TRIO_BC:
fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:2\t%s:1\n", chr,start,end,s1,s3); break;
case TRIO_BD:
fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:2\t%s:2\n", chr,start,end,s1,s3); break;
case TRIO_CA:
fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:1\t%s:1\n", chr,start,end,s3,s1); break;
case TRIO_DA:
fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:2\t%s:1\n", chr,start,end,s3,s1); break;
case TRIO_CB:
fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:1\t%s:2\n", chr,start,end,s3,s1); break;
case TRIO_DB:
fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:2\t%s:2\n", chr,start,end,s3,s1); break;
}
if ( hap_switch[state][prev_state] & SW_MOTHER ) nswitch_mother++;
if ( hap_switch[state][prev_state] & SW_FATHER ) nswitch_father++;
}
iprev = i-1;
}
prev_state = state;
}
float mrate = args->nhet_mother>1 ? (float)nswitch_mother/(args->nhet_mother-1) : 0;
float frate = args->nhet_father>1 ? (float)nswitch_father/(args->nhet_father-1) : 0;
fprintf(args->fp,"SW\t%s\t%s\t%d\t%d\t%f\n", s1,bcf_hdr_id2name(args->hdr,args->prev_rid),args->nhet_mother,nswitch_mother,mrate);
fprintf(args->fp,"SW\t%s\t%s\t%d\t%d\t%f\n", s3,bcf_hdr_id2name(args->hdr,args->prev_rid),args->nhet_father,nswitch_father,frate);
args->nsites = 0;
args->nhet_father = args->nhet_mother = 0;
}
