// ----------------------------------------------------------------------------
bool
CVcfReader::x_ProcessMetaLineInfo(
const string& line,
CRef<CSeq_annot> pAnnot )
// ----------------------------------------------------------------------------
{
const string prefix = "##INFO=<";
const string postfix = ">";
if ( ! NStr::StartsWith( line, prefix ) || ! NStr::EndsWith( line, postfix ) ) {
return false;
}
try {
vector<string> fields;
string key, id, numcount, type, description;
string info = line.substr(
prefix.length(), line.length() - prefix.length() - postfix.length() );
NStr::Tokenize( info, ",", fields );
NStr::SplitInTwo( fields[0], "=", key, id );
if ( key != "ID" ) {
throw "Unexpected --- ##INFO: bad ID key!";
}
NStr::SplitInTwo( fields[1], "=", key, numcount );
if ( key != "Number" ) {
throw "Unexpected --- ##INFO: bad number key!";
}
NStr::SplitInTwo( fields[2], "=", key, type );
if ( key != "Type" ) {
throw "Unexpected --- ##INFO: bad type key!";
}
NStr::SplitInTwo( fields[3], "=", key, description );
if ( key != "Description" ) {
throw "Unexpected --- ##INFO: bad description key!";
}
m_InfoSpecs[id] = CVcfInfoSpec( id, numcount, type, description );
}
catch ( ... ) {
return true;
}
return true;
}
// ----------------------------------------------------------------------------
bool
CVcfReader::xProcessMetaLineInfo(
const string& line,
CRef<CSeq_annot> pAnnot,
IMessageListener* pEC)
// ----------------------------------------------------------------------------
{
const string prefix = "##INFO=<";
const string postfix = ">";
if ( ! NStr::StartsWith( line, prefix ) || ! NStr::EndsWith( line, postfix ) ) {
return false;
}
try {
vector<string> fields;
string key, id, numcount, type, description;
string info = line.substr(
prefix.length(), line.length() - prefix.length() - postfix.length() );
NStr::Tokenize( info, ",", fields );
NStr::SplitInTwo( fields[0], "=", key, id );
if ( key != "ID" ) {
AutoPtr<CObjReaderLineException> pErr(
CObjReaderLineException::Create(
eDiag_Error,
0,
"CVcfReader::xProcessMetaLineInfo: ##INFO with bad or missing \"ID\".",
ILineError::eProblem_BadInfoLine) );
pErr->Throw();
}
NStr::SplitInTwo( fields[1], "=", key, numcount );
if ( key != "Number" ) {
AutoPtr<CObjReaderLineException> pErr(
CObjReaderLineException::Create(
eDiag_Error,
0,
"CVcfReader::xProcessMetaLineInfo: ##INFO with bad or missing \"Number\".",
ILineError::eProblem_BadInfoLine) );
pErr->Throw();
}
NStr::SplitInTwo( fields[2], "=", key, type );
if ( key != "Type" ) {
AutoPtr<CObjReaderLineException> pErr(
CObjReaderLineException::Create(
eDiag_Error,
0,
"CVcfReader::xProcessMetaLineInfo: ##INFO with bad or missing \"Type\".",
ILineError::eProblem_BadInfoLine) );
pErr->Throw();
}
NStr::SplitInTwo( fields[3], "=", key, description );
if ( key != "Description" ) {
AutoPtr<CObjReaderLineException> pErr(
CObjReaderLineException::Create(
eDiag_Error,
0,
"CVcfReader::xProcessMetaLineInfo: ##INFO with bad or missing \"Description\".",
ILineError::eProblem_BadInfoLine) );
pErr->Throw();
}
m_InfoSpecs[id] = CVcfInfoSpec( id, numcount, type, description );
}
catch (CObjReaderLineException& err) {
ProcessError(err, pEC);
}
return true;
}