bool
CPairedRead::Load(
const CSeqContig& inSC,
CTextIn& inIn,
int inDelimiterChar ) {
__string_vector tWords;
while ( ( ( m_count[0] = inIn.GetLine( inDelimiterChar, m_read[0] ) ) > 0 ) &&
( m_read[0][0] == "@SQ" ) ) {
}
if ( m_count[0] >= 11 &&
( m_count[1] = inIn.GetLine( inDelimiterChar, m_read[1] ) ) >= 11 ) {
if ( m_read[0][0] != m_read[1][0] ) {
std::cerr << "[ERROR] Bad records found at " << m_read[0][0] << " and " << m_read[1][0] << std::endl;
return false;
}
m_mapScore = 0;
for ( int i = 0; i < 2; ++i ) {
if ( ( StringTo( m_read[i][1], m_flag[i] ) && m_flag[i] & 4 ) ||
m_read[i][2] == "*" ) {
++m_mapScore;
}
m_contig[i] = m_read[i][2];
if ( m_contig[i] != "*" ) {
std::string::size_type tBegin, tLast;
if ( ( tBegin = m_contig[i].find( "ref|", 0 ) ) != std::string::npos &&
( tLast = m_contig[i].find( "|", tBegin + 4 ) ) != std::string::npos ) {
m_contig[i] = m_contig[i].substr( tBegin + 4, tLast - tBegin - 4 );
}
m_contigInfo[i] = inSC.GetInfo( m_contig[i] );
if ( m_contigInfo[i] == NULL ) {
std::cerr << "[ERROR] Bad records found at " << m_read[0][0] << " and " << m_read[1][0] << std::endl;
return false;
}
} else {
m_contigInfo[i] = NULL;
}
}
if ( m_mapScore == 0 &&
( m_flag[0] & 8 || m_flag[1] & 8 ) ) {
m_mapScore = 1;
}
if ( m_contig[0] == m_contig[1] ) {
m_sameChr = 1;
} else if ( m_contigInfo[0]->scChr == m_contigInfo[1]->scChr ) {
m_sameChr = 2;
} else {
m_sameChr = 0;
}
m_mapStat = -1;
return true;
}
return false;
}
bool
StringToBool(
const char * src,
size_t len
)
{
bool dest = false;
StringTo( dest, src, len );
return( dest );
}
bool
CSeqContig::Load(
const char* inSeqContigFile )
{
bool tDone = false;
CTextIn tIn;
int tDelimiterChar = CTextIn::TestDelimiterChar( inSeqContigFile );
__string_vector tWords;
ContigInfo tInfo;
if ( tIn.Open( inSeqContigFile ) ) {
while ( tIn.GetLine( tDelimiterChar, tWords ) >= 6 ) {
if ( StringTo( tWords[2], tInfo.scStart ) &&
StringTo( tWords[3], tInfo.scEnd ) ) {
tInfo.scChr = tWords[1];
m_infoMap.insert( ContigInfoMap::value_type( tWords[5], tInfo ) );
}
}
tIn.Close();
tDone = m_infoMap.size() > 0;
}
return tDone;
}
bool
StringTo(
float & dest,
const char * src,
unsigned short baseToUse,
size_t len,
bool stopAtNonDigit
)
{
double value;
if( ! StringTo( value, src, baseToUse, len, stopAtNonDigit ) )
return( false );
dest = value;
return( true );
}
bool
StringTo(
bool & dest,
const char * src,
size_t len
)
{
if( ! src )
return( false );
if( src[0] == 0 )
{
dest = false;
return( true );
}
if( isdigit( src[0] ) )
{
int num = 0;
StringTo( num, src, 0, len );
dest = (num) ? true : false;
return( true );
}
if( ( (len == 1 || (len == NPOS && src[1] == 0 ) ) &&
( tolower( src[0] ) == 't' || tolower( src[0] ) == 'y' ) ) ||
! StringCaseCompare( src, "true", (len && len < 4) ? len : 4 ) ||
! StringCaseCompare( src, "yes", (len && len < 3) ? len : 3 ) ||
! StringCaseCompare( src, "on", (len && len < 2) ? len : 2 ) )
{
dest = true;
return( true );
}
if( ( (len == 1 || (len == NPOS && src[1] == 0 ) ) &&
( tolower( src[0] ) == 'f' ||
tolower( src[0] ) == 'n' ||
tolower( src[0] ) == ' ' ) ) ||
! StringCaseCompare( src, "false", ( (len != NPOS && len < 4) ?
len : 4 ) ) ||
! StringCaseCompare( src, "no", (len != NPOS && len < 2) ? len : 2 ) ||
! StringCaseCompare( src, "off", (len != NPOS && len < 3) ? len : 3 ) )
{
dest = false;
return( true );
}
const char * c = src;
for( ; ((len != NPOS && ((size_t)(c - src)) < len) || *c != 0) &&
*c == ' '; c++ );
if( (len != NPOS && ((size_t)(c - src)) == len ) || *c == 0 )
{
dest = false;
return( true );
}
return( false );
}