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-rw-r--r--src/io.cpp85
1 files changed, 42 insertions, 43 deletions
diff --git a/src/io.cpp b/src/io.cpp
index 3a4bc3c..3bf6a9e 100644
--- a/src/io.cpp
+++ b/src/io.cpp
@@ -114,7 +114,7 @@ std::istream& safeGetline(std::istream& is, std::string& t) {
sb->sbumpc();
return is;
case EOF:
-
+
// Also handle the case when the last line has no line
// ending.
if(t.empty())
@@ -312,7 +312,7 @@ bool ReadFile_column (const string &file_pheno, vector<int> &indicator_idv,
if (strcmp(ch_ptr, "NA")==0) {
indicator_idv.push_back(0);
pheno.push_back(-9);
- }
+ }
else {
// Pheno is different from pimass2.
@@ -800,7 +800,7 @@ bool ReadFile_bed (const string &file_bed, const set<string> &setSnps,
for (size_t t=0; t<ns_total; ++t) {
// n_bit, and 3 is the number of magic numbers.
- infile.seekg(t*n_bit+3);
+ infile.seekg(t*n_bit+3);
if (setSnps.size()!=0 &&
setSnps.count(snpInfo[t].rs_number) == 0) {
@@ -978,7 +978,7 @@ void Plink_ReadOneSNP (const int pos, const vector<int> &indicator_idv,
else {n_bit=ni_total/4+1;}
// n_bit, and 3 is the number of magic numbers.
- infile.seekg(pos*n_bit+3);
+ infile.seekg(pos*n_bit+3);
// Read genotypes.
char ch[1];
@@ -993,7 +993,7 @@ void Plink_ReadOneSNP (const int pos, const vector<int> &indicator_idv,
b=ch[0];
// Minor allele homozygous: 2.0; major: 0.0.
- for (size_t j=0; j<4; ++j) {
+ for (size_t j=0; j<4; ++j) {
if ((i==(n_bit-1)) && c==ni_total) {break;}
if (indicator_idv[c]==0) {c++; continue;}
c++;
@@ -1406,7 +1406,7 @@ bool PlinkKin (const string &file_bed, vector<int> &indicator_snp,
if (indicator_snp[t]==0) {continue;}
// n_bit, and 3 is the number of magic numbers.
- infile.seekg(t*n_bit+3);
+ infile.seekg(t*n_bit+3);
// Read genotypes.
geno_mean=0.0; n_miss=0; ci_total=0; geno_var=0.0;
@@ -1415,7 +1415,7 @@ bool PlinkKin (const string &file_bed, vector<int> &indicator_snp,
b=ch[0];
// Minor allele homozygous: 2.0; major: 0.0.
- for (size_t j=0; j<4; ++j) {
+ for (size_t j=0; j<4; ++j) {
if ((i==(n_bit-1)) && ci_total==ni_total) {
break;
}
@@ -1734,7 +1734,7 @@ bool ReadFile_bed (const string &file_bed, vector<int> &indicator_idv,
if (indicator_snp[t]==0) {continue;}
// n_bit, and 3 is the number of magic numbers.
- infile.seekg(t*n_bit+3);
+ infile.seekg(t*n_bit+3);
// Read genotypes.
c_idv=0; geno_mean=0.0; n_miss=0; c=0;
@@ -1855,7 +1855,7 @@ bool ReadFile_bed (const string &file_bed, vector<int> &indicator_idv,
if (indicator_snp[t]==0) {continue;}
// n_bit, and 3 is the number of magic numbers.
- infile.seekg(t*n_bit+3);
+ infile.seekg(t*n_bit+3);
// Read genotypes.
c_idv=0; geno_mean=0.0; n_miss=0; c=0;
@@ -1864,7 +1864,7 @@ bool ReadFile_bed (const string &file_bed, vector<int> &indicator_idv,
b=ch[0];
// Minor allele homozygous: 2.0; major: 0.0.
- for (size_t j=0; j<4; ++j) {
+ for (size_t j=0; j<4; ++j) {
if ((i==(n_bit-1)) && c==ni_total) {break;}
if (indicator_idv[c]==0) {c++; continue;}
c++;
@@ -2113,7 +2113,7 @@ bool ReadFile_sample (const string &file_sample,
vector<map<uint32_t, size_t> > cvt_factor_levels;
char col_type[num_cols];
-
+
// Read header line2.
if(!safeGetline(infile, line).eof()) {
ch_ptr=strtok ((char *)line.c_str(), " \t");
@@ -2168,7 +2168,7 @@ bool ReadFile_sample (const string &file_sample,
}
if(col_type[i]=='D')
{
-
+
// NOTE THIS DOES NOT CHECK TO BE SURE LEVEL
// IS INTEGRAL i.e for atoi error.
if (strcmp(ch_ptr, "NA")!=0) {
@@ -2189,7 +2189,7 @@ bool ReadFile_sample (const string &file_sample,
pheno.push_back(pheno_row);
}
-
+
// Close and reopen the file.
infile.close();
infile.clear();
@@ -2202,7 +2202,7 @@ bool ReadFile_sample (const string &file_sample,
file_sample<<endl;
return false;
}
-
+
// Skip header.
safeGetline(infile2, line);
safeGetline(infile2, line);
@@ -2220,16 +2220,16 @@ bool ReadFile_sample (const string &file_sample,
size_t fac_cvt_i=0;
size_t num_fac_levels;
while (i<num_cols) {
-
+
if(col_type[i]=='C') {
if (strcmp(ch_ptr, "NA")==0) {flag_na=1; d=-9;}
else {d=atof(ch_ptr);}
-
+
v_d.push_back(d);
}
-
+
if(col_type[i]=='D') {
-
+
// NOTE THIS DOES NOT CHECK TO BE SURE
// LEVEL IS INTEGRAL i.e for atoi error.
num_fac_levels=cvt_factor_levels[fac_cvt_i].size();
@@ -2251,7 +2251,7 @@ bool ReadFile_sample (const string &file_sample,
}
fac_cvt_i++;
}
-
+
ch_ptr=strtok (NULL, " \t");
i++;
}
@@ -2321,7 +2321,7 @@ bool ReadFile_bgen(const string &file_bgen, const set<string> &setSnps,
int sig;
LUDecomp (WtW, pmt, &sig);
LUInvert (WtW, pmt, WtWi);
-
+
// Read in header.
uint32_t bgen_snp_block_offset;
uint32_t bgen_header_length;
@@ -2373,7 +2373,7 @@ bool ReadFile_bgen(const string &file_bgen, const set<string> &setSnps,
size_t ni_total=indicator_idv.size();
// Number of samples to use in test.
- size_t ni_test=0;
+ size_t ni_test=0;
uint32_t bgen_N;
uint16_t bgen_LS;
@@ -2434,7 +2434,7 @@ bool ReadFile_bgen(const string &file_bgen, const set<string> &setSnps,
if (setSnps.size()!=0 && setSnps.count(rs)==0) {
SNPINFO sInfo={"-9", rs, -9, -9, minor, major,
static_cast<size_t>(-9), -9, (long int) -9};
-
+
snpInfo.push_back(sInfo);
indicator_snp.push_back(0);
if(CompressedSNPBlocks)
@@ -2476,7 +2476,7 @@ bool ReadFile_bgen(const string &file_bgen, const set<string> &setSnps,
c_idv=0;
gsl_vector_set_zero (genotype_miss);
for (size_t i=0; i<bgen_N; ++i) {
-
+
// CHECK this set correctly!
if (indicator_idv[i]==0) {continue;}
@@ -2665,7 +2665,7 @@ bool bgenKin (const string &file_oxford, vector<int> &indicator_snp,
infile.read(reinterpret_cast<char*>(&bgen_LB),4);
bgen_B_allele.resize(bgen_LB);
infile.read(&bgen_B_allele[0], bgen_LB);
-
+
uint16_t unzipped_data[3*bgen_N];
if (indicator_snp[t]==0) {
@@ -2683,11 +2683,11 @@ bool bgenKin (const string &file_oxford, vector<int> &indicator_snp,
{
infile.read(reinterpret_cast<char*>(&bgen_P),4);
uint8_t zipped_data[bgen_P];
-
+
unzipped_data_size=6*bgen_N;
-
+
infile.read(reinterpret_cast<char*>(zipped_data),bgen_P);
-
+
int result=
uncompress(reinterpret_cast<Bytef*>(unzipped_data),
reinterpret_cast<uLongf*>(&unzipped_data_size),
@@ -2698,7 +2698,7 @@ bool bgenKin (const string &file_oxford, vector<int> &indicator_snp,
}
else
{
-
+
bgen_P=6*bgen_N;
infile.read(reinterpret_cast<char*>(unzipped_data),bgen_P);
}
@@ -2708,7 +2708,7 @@ bool bgenKin (const string &file_oxford, vector<int> &indicator_snp,
for (size_t i=0; i<bgen_N; ++i) {
-
+
bgen_geno_prob_AA=
static_cast<double>(unzipped_data[i*3])/32768.0;
bgen_geno_prob_AB=
@@ -2723,13 +2723,13 @@ bool bgenKin (const string &file_oxford, vector<int> &indicator_snp,
n_miss++;
}
else {
-
+
bgen_geno_prob_AA/=bgen_geno_prob_non_miss;
bgen_geno_prob_AB/=bgen_geno_prob_non_miss;
bgen_geno_prob_BB/=bgen_geno_prob_non_miss;
-
+
genotype=2.0*bgen_geno_prob_BB+bgen_geno_prob_AB;
-
+
gsl_vector_set(geno, i, genotype);
gsl_vector_set(geno_miss, i, 1.0);
geno_mean+=genotype;
@@ -2936,8 +2936,7 @@ bool ReadHeader_io (const string &line, HEADER &header)
header.n_col=header.coln+1;
} else {
cout<<"error! more than two n_total columns in the file."<<endl;
- n_
- error++;}
+ n_error++;}
} else if (nmis_set.count(type)!=0) {
if (header.nmis_col==0) {header.nmis_col=header.coln+1;} else {
cout<<"error! more than two n_mis columns in the file."<<endl;
@@ -2988,7 +2987,7 @@ bool ReadHeader_io (const string &line, HEADER &header)
} else {
string str = ch_ptr;
string cat = str.substr(str.size()-2, 2);
-
+
if(cat == "_c" || cat =="_C"){
// continuous
@@ -2999,7 +2998,7 @@ bool ReadHeader_io (const string &line, HEADER &header)
header.catd_col.insert(header.coln+1);
}
}
-
+
ch_ptr=strtok (NULL, " , \t");
header.coln++;
}
@@ -3396,7 +3395,7 @@ bool PlinkKin (const string &file_bed, const int display_pace,
for (size_t j=0; j<4; ++j) {
if ((i==(n_bit-1)) && ci_total==ni_total) {break;}
if (indicator_idv[ci_total]==0) {ci_total++; continue;}
-
+
if (b[2*j]==0) {
if (b[2*j+1]==0) {
gsl_vector_set(geno, ci_test, 2.0);
@@ -3412,7 +3411,7 @@ bool PlinkKin (const string &file_bed, const int display_pace,
if (b[2*j+1]==1) {gsl_vector_set(geno, ci_test, 0.0); }
else {gsl_vector_set(geno, ci_test, -9.0); n_miss++; }
}
-
+
ci_test++;
ci_total++;
}
@@ -3561,7 +3560,7 @@ bool MFILEKin (const size_t mfile_mode, const string &file_mfile,
} else {
BimbamKin (file_name, display_pace, indicator_idv, mindicator_snp[l], mapRS2weight, mapRS2cat, msnpInfo[l], W, kin_tmp, ns_tmp);
}
-
+
// Add ns.
gsl_vector_add(vector_ns, ns_tmp);
@@ -3647,7 +3646,7 @@ bool ReadFile_wsnp (const string &file_wcat, const size_t n_vc,
}
string line, rs, chr, a1, a0, pos, cm;
-
+
// Read header.
HEADER header;
!safeGetline(infile, line).eof();
@@ -3978,7 +3977,7 @@ void Calcq (const size_t n_block, const vector<size_t> &vec_cat,
// Compute q and s.
for (size_t i=0; i<vec_cat.size(); i++) {
-
+
// Extract quantities.
cat=vec_cat[i];
n_total=vec_ni[i];
@@ -4017,7 +4016,7 @@ void Calcq (const size_t n_block, const vector<size_t> &vec_cat,
// Record values.
for (size_t i=0; i<vec_cat.size(); i++) {
-
+
// Extract quantities.
cat=vec_cat[i];
n_total=vec_ni[i];
@@ -4369,7 +4368,7 @@ void ReadFile_mref (const string &file_mref, gsl_matrix *S_mat,
if (i!=j) {gsl_matrix_set(Svar_mat, j, i, d);}
}
}
-
+
// Free matrices.
gsl_matrix_free(S_sub);
gsl_matrix_free(Svar_sub);
generated by cgit v1.2.3 (git 2.44.0) at 2025-01-19 02:20:20 +0000