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cleanup clang compiler warnings
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cleanup `tautological-constant-out-of-range-compare` and `unused function` warnings.
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@mcshane
mcshane committed Feb 23, 2017
1 parent d17235b commit eaf74ca
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Showing 3 changed files with 37 additions and 37 deletions.
26 changes: 13 additions & 13 deletions mcall.c
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Original file line number Diff line number Diff line change
Expand Up @@ -547,19 +547,19 @@ float calc_HOB(int nref, int nalt, int nhets, int ndiploid)
/**
* log(sum_i exp(a_i))
*/
static inline double logsumexp(double *vals, int nvals)
{
int i;
double max_exp = vals[0];
for (i=1; i<nvals; i++)
if ( max_exp < vals[i] ) max_exp = vals[i];

double sum = 0;
for (i=0; i<nvals; i++)
sum += exp(vals[i] - max_exp);

return log(sum) + max_exp;
}
// static inline double logsumexp(double *vals, int nvals)
// {
// int i;
// double max_exp = vals[0];
// for (i=1; i<nvals; i++)
// if ( max_exp < vals[i] ) max_exp = vals[i];

// double sum = 0;
// for (i=0; i<nvals; i++)
// sum += exp(vals[i] - max_exp);

// return log(sum) + max_exp;
// }
/** log(exp(a)+exp(b)) */
static inline double logsumexp2(double a, double b)
{
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30 changes: 15 additions & 15 deletions vcfgtcheck.c
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Original file line number Diff line number Diff line change
Expand Up @@ -520,21 +520,21 @@ static void check_gt(args_t *args)
}
}

static inline int is_hom_most_likely(int nals, int *pls)
{
int ia, ib, idx = 1, min_is_hom = 1, min_pl = pls[0];
for (ia=1; ia<nals; ia++)
{
for (ib=0; ib<ia; ib++)
{
if ( pls[idx] < min_pl ) { min_pl = pls[idx]; min_is_hom = 0; }
idx++;
}
if ( pls[idx] < min_pl ) { min_pl = pls[idx]; min_is_hom = 1; }
idx++;
}
return min_is_hom;
}
// static inline int is_hom_most_likely(int nals, int *pls)
// {
// int ia, ib, idx = 1, min_is_hom = 1, min_pl = pls[0];
// for (ia=1; ia<nals; ia++)
// {
// for (ib=0; ib<ia; ib++)
// {
// if ( pls[idx] < min_pl ) { min_pl = pls[idx]; min_is_hom = 0; }
// idx++;
// }
// if ( pls[idx] < min_pl ) { min_pl = pls[idx]; min_is_hom = 1; }
// idx++;
// }
// return min_is_hom;
// }

int process_GT(args_t *args, bcf1_t *line, uint32_t *ntot, uint32_t *ndif)
{
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18 changes: 9 additions & 9 deletions vcfroh.c
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Original file line number Diff line number Diff line change
Expand Up @@ -740,9 +740,9 @@ int estimate_AF_from_PL(args_t *args, bcf_fmt_t *fmt_pl, int ial, double *alt_fr
if ( p[irr]<0 || p[ira]<0 || p[iaa]<0 ) continue; /* missing value */ \
if ( p[irr]==p[ira] && p[irr]==p[iaa] ) continue; /* all values are the same */ \
double prob[3], norm = 0; \
prob[0] = p[irr] < 256 ? args->pl2p[ p[irr] ] : args->pl2p[255]; \
prob[1] = p[ira] < 256 ? args->pl2p[ p[ira] ] : args->pl2p[255]; \
prob[2] = p[iaa] < 256 ? args->pl2p[ p[iaa] ] : args->pl2p[255]; \
prob[0] = p[irr] < (type_t)256 ? args->pl2p[ p[irr] ] : args->pl2p[255]; \
prob[1] = p[ira] < (type_t)256 ? args->pl2p[ p[ira] ] : args->pl2p[255]; \
prob[2] = p[iaa] < (type_t)256 ? args->pl2p[ p[iaa] ] : args->pl2p[255]; \
for (j=0; j<3; j++) norm += prob[j]; \
for (j=0; j<3; j++) prob[j] /= norm; \
af += 0.5*prob[1] + prob[2]; \
Expand Down Expand Up @@ -770,9 +770,9 @@ int estimate_AF_from_PL(args_t *args, bcf_fmt_t *fmt_pl, int ial, double *alt_fr
if ( p[irr]<0 || p[ira]<0 || p[iaa]<0 ) continue; /* missing value */ \
if ( p[irr]==p[ira] && p[irr]==p[iaa] ) continue; /* all values are the same */ \
double prob[3], norm = 0; \
prob[0] = p[irr] < 256 ? args->pl2p[ p[irr] ] : args->pl2p[255]; \
prob[1] = p[ira] < 256 ? args->pl2p[ p[ira] ] : args->pl2p[255]; \
prob[2] = p[iaa] < 256 ? args->pl2p[ p[iaa] ] : args->pl2p[255]; \
prob[0] = p[irr] < (type_t)256 ? args->pl2p[ p[irr] ] : args->pl2p[255]; \
prob[1] = p[ira] < (type_t)256 ? args->pl2p[ p[ira] ] : args->pl2p[255]; \
prob[2] = p[iaa] < (type_t)256 ? args->pl2p[ p[iaa] ] : args->pl2p[255]; \
for (j=0; j<3; j++) norm += prob[j]; \
for (j=0; j<3; j++) prob[j] /= norm; \
af += 0.5*prob[1] + prob[2]; \
Expand Down Expand Up @@ -916,9 +916,9 @@ int process_line(args_t *args, bcf1_t *line, int ial)
type_t *p = (type_t*)fmt_pl->p + fmt_pl->n*ismpl; \
if ( p[irr]<0 || p[ira]<0 || p[iaa]<0 ) continue; /* missing value */ \
if ( p[irr]==p[ira] && p[irr]==p[iaa] ) continue; /* all values are the same */ \
pdg[0] = p[irr] < 256 ? args->pl2p[ p[irr] ] : args->pl2p[255]; \
pdg[1] = p[ira] < 256 ? args->pl2p[ p[ira] ] : args->pl2p[255]; \
pdg[2] = p[iaa] < 256 ? args->pl2p[ p[iaa] ] : args->pl2p[255]; \
pdg[0] = p[irr] < (type_t)256 ? args->pl2p[ p[irr] ] : args->pl2p[255]; \
pdg[1] = p[ira] < (type_t)256 ? args->pl2p[ p[ira] ] : args->pl2p[255]; \
pdg[2] = p[iaa] < (type_t)256 ? args->pl2p[ p[iaa] ] : args->pl2p[255]; \
}
switch (fmt_pl->type) {
case BCF_BT_INT8: BRANCH(int8_t); break;
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