Skip to content

Fix off-by-one in HMM forward-backward posterior indexing #2519

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
sirus20x6 wants to merge 1 commit into from
+5 −4
Closed

Fix off-by-one in HMM forward-backward posterior indexing #2519

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 3 additions & 2 deletions HMM.c
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -215,11 +215,12 @@ void hmm_reset(hmm_t *hmm, void *_snapshot)

void hmm_set_tprob(hmm_t *hmm, double *tprob, int ntprob)
{
int old_ntprob_arr = hmm->ntprob_arr;
hmm->ntprob_arr = ntprob;
if ( ntprob<=0 ) ntprob = 1;

if ( !hmm->tprob_arr )
hmm->tprob_arr = (double*) malloc(sizeof(double)*hmm->nstates*hmm->nstates*ntprob);
if ( !hmm->tprob_arr || ntprob != old_ntprob_arr )
hmm->tprob_arr = (double*) realloc(hmm->tprob_arr, sizeof(double)*hmm->nstates*hmm->nstates*ntprob);

memcpy(hmm->tprob_arr,tprob,sizeof(double)*hmm->nstates*hmm->nstates);

Expand Down
2 changes: 1 addition & 1 deletion vcfcnv.c
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1037,7 +1037,7 @@ static void cnv_flush_viterbi(args_t *args)
for (isite=0; isite<args->nsites; isite++)
{
int state = vpath[args->nstates*isite];
double *pval = fwd + isite*args->nstates;
double *pval = fwd + (isite+1)*args->nstates;

qual += pval[start_cn];

Expand Down
2 changes: 1 addition & 1 deletion vcfroh.c
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -525,7 +525,7 @@ static void flush_viterbi(args_t *args, int ismpl)
for (i=0; i<end; i++)
{
int state = vpath[i*2]==STATE_AZ ? 1 : 0;
double qual = phred_score(1.0 - fwd[i*2 + state]);
double qual = phred_score(1.0 - fwd[(i+1)*2 + state]);
if ( args->output_type & OUTPUT_ST )
{
args->str.l = 0;
Expand Down