Commit 37344ab2 authored by Yannis Duffourd's avatar Yannis Duffourd

Adding control cs improvement

parent 0243b7fc
...@@ -990,11 +990,16 @@ int Vihgo::readRunControl() ...@@ -990,11 +990,16 @@ int Vihgo::readRunControl()
int a = bam_seqi( sequence , i+x ); int a = bam_seqi( sequence , i+x );
char base; char base;
base = this->getBase( a ); base = this->getBase( a );
codon += base; codon += base;
} }
i += 2; i += 2;
if (codon.find( "!" ) != string::npos )
{
continue;
}
// insert the codon in the data // insert the codon in the data
if( !( this->sampleData.count( chr ) > 0) ) if( !( this->sampleData.count( chr ) > 0) )
{ {
...@@ -1659,6 +1664,12 @@ int Vihgo::readSample() ...@@ -1659,6 +1664,12 @@ int Vihgo::readSample()
} }
i += 2; i += 2;
if (codon.find( "!" ) != string::npos )
{
continue;
}
// insert the codon in the data // insert the codon in the data
if( !( this->sampleData.count( chr ) > 0) ) if( !( this->sampleData.count( chr ) > 0) )
{ {
...@@ -1979,6 +1990,7 @@ bool Vihgo::isThereAControl() ...@@ -1979,6 +1990,7 @@ bool Vihgo::isThereAControl()
char Vihgo::getBase( int b ) char Vihgo::getBase( int b )
{ {
// cerr << "inc int base: " << b << " : " << endl;;
switch( b ) switch( b )
{ {
case 1 : case 1 :
...@@ -1996,6 +2008,6 @@ char Vihgo::getBase( int b ) ...@@ -1996,6 +2008,6 @@ char Vihgo::getBase( int b )
case 15 : case 15 :
return 'N'; return 'N';
} }
return 'N'; return '!';
} }
// setters // setters
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