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Accept PSAM files without FID column #687

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Accept PSAM files without FID column #687

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58 changes: 42 additions & 16 deletions src/Geno.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -940,8 +940,8 @@ uint32_t read_pvar(map<string, vector<uint64>>& index_map, geno_file_info* ext_f

void read_psam(struct in_files* files, struct param* params, mstream& sout) {

int lineread = 0, sex_col = 0;
bool col_found = false;
int lineread = 0, iid_col = 1, sex_col = 0;
bool col_found = false, has_fid = true;
string line, tmp_id, fname;
std::vector<int> sex;
std::vector< string > tmp_str_vec, IDvec;
Expand All @@ -960,15 +960,23 @@ void read_psam(struct in_files* files, struct param* params, mstream& sout) {
if( tmp_str_vec.size() < 1 )
throw "no blank lines should be before the header line in psam file.";

if( tmp_str_vec[0] == "#IID" )
throw "invalid header (must start with #FID [not #IID]).";
if( tmp_str_vec[0] == "#IID" ) {
has_fid = false;
iid_col = 0;
break;
}

if( tmp_str_vec[0] == "#FID" )
if( tmp_str_vec[0] == "#FID" ) {
has_fid = true;
iid_col = 1;
break;
}
}

// check header
if( (tmp_str_vec.size() < 2) || (tmp_str_vec[1] != "IID"))
if( has_fid && ((tmp_str_vec.size() < 2) || (tmp_str_vec[1] != "IID")) )
throw "header does not have the correct format.";
if( !has_fid && ((tmp_str_vec.size() < 1) || (tmp_str_vec[0] != "#IID")) )
throw "header does not have the correct format.";

// find if sex column is present
Expand All @@ -979,19 +987,25 @@ void read_psam(struct in_files* files, struct param* params, mstream& sout) {
while (myfile.readLine(line)) {
tmp_str_vec = string_split(line,"\t ");

if( tmp_str_vec.size() < 3 )
if( has_fid && (tmp_str_vec.size() < 2) )
throw "incorrectly formatted psam file at line " + to_string( lineread + 1 ) ;
if( !has_fid && (tmp_str_vec.size() < 1) )
throw "incorrectly formatted psam file at line " + to_string( lineread + 1 ) ;
if( col_found && ((int)tmp_str_vec.size() <= sex_col) )
throw "incorrectly formatted psam file at line " + to_string( lineread + 1 ) ;

tmp_id = tmp_str_vec[0] + "_" + tmp_str_vec[1];
const string FID = has_fid ? tmp_str_vec[0] : "0";
const string IID = tmp_str_vec[iid_col];
tmp_id = FID + "_" + IID;

// check duplicates -- if not, store in map
if (in_map(tmp_id, params->FID_IID_to_ind))
throw "duplicate individual in fam file : FID_IID=" + tmp_id ;

params->FID_IID_to_ind[ tmp_id ] = lineread;
if(params->write_samples || params->write_masks) {
IDvec[0] = tmp_str_vec[0];
IDvec[1] = tmp_str_vec[1];
IDvec[0] = FID;
IDvec[1] = IID;
params->FIDvec.push_back(IDvec);
}

Expand All @@ -1015,6 +1029,8 @@ void read_psam(struct in_files* files, struct param* params, mstream& sout) {
uint32_t read_psam(struct ext_geno_info& ginfo, geno_file_info* ext_file_info, Ref<ArrayXb> mask, struct param* params, mstream& sout) {

uint32_t position;
int iid_col = 1;
bool has_fid = true;
string line, fname;
std::vector< string > tmp_str_vec, tmp_ids;
Files myfile;
Expand All @@ -1028,21 +1044,31 @@ uint32_t read_psam(struct ext_geno_info& ginfo, geno_file_info* ext_file_info, R
tmp_str_vec = string_split(line,"\t ");
if( tmp_str_vec.size() < 1 )
throw "no blank lines should be before the header line in psam file.";
if( tmp_str_vec[0] == "#IID" )
throw "invalid header (must start with #FID [not #IID]).";
if( tmp_str_vec[0] == "#FID" )
if( tmp_str_vec[0] == "#IID" ) {
has_fid = false;
iid_col = 0;
break;
}
if( tmp_str_vec[0] == "#FID" ) {
has_fid = true;
iid_col = 1;
break;
}
}

// check header
if( (tmp_str_vec.size() < 2) || (tmp_str_vec[1] != "IID"))
if( has_fid && ((tmp_str_vec.size() < 2) || (tmp_str_vec[1] != "IID")) )
throw "header does not have the correct format.";
if( !has_fid && ((tmp_str_vec.size() < 1) || (tmp_str_vec[0] != "#IID")) )
throw "header does not have the correct format.";

while (myfile.readLine(line)) {
tmp_str_vec = string_split(line,"\t ");
if( tmp_str_vec.size() < 2 )
if( has_fid && (tmp_str_vec.size() < 2) )
throw "incorrectly formatted psam file at line " + to_string( tmp_ids.size() + 1 ) ;
tmp_ids.push_back(tmp_str_vec[0] + "_" + tmp_str_vec[1]);
if( !has_fid && (tmp_str_vec.size() < 1) )
throw "incorrectly formatted psam file at line " + to_string( tmp_ids.size() + 1 ) ;
tmp_ids.push_back((has_fid ? tmp_str_vec[0] : "0") + "_" + tmp_str_vec[iid_col]);
}

myfile.closeFile();
Expand Down