/* PE functions using fragment_prev and fragment_next */
Alignment Filter::one_end_anchored_filter(Alignment& aln){
if (aln.fragment_prev().name() != ""){
if (aln.path().name() == "" || aln.fragment_prev().path().name() == ""){
inverse ? Alignment() : aln;
}
else{
inverse ? aln : Alignment();
}
}
else{
return inverse ? aln : Alignment();
}
}
Alignment Filter::interchromosomal_filter(Alignment& aln){
bool fails = aln.path().name() != aln.fragment_prev().path().name();
if (fails){
return inverse ? Alignment() : aln;
}
else{
return inverse ? aln : Alignment();
}
}
Alignment Filter::orientation_filter(Alignment& aln){
bool f_rev = false;
bool s_rev = false;
Path f_path = aln.path();
Path s_path = aln.fragment_prev().path();
for (int i = 0; i < f_path.mapping_size(); i++){
if (f_path.mapping(i).position().is_reverse()){
f_rev = true;
}
}
for (int j = 0; j < s_path.mapping_size(); j++){
if (s_path.mapping(j).position().is_reverse()){
s_rev = true;
}
}
if (f_rev & s_rev){
return inverse ? Alignment() : aln;
}
else{
return inverse ? aln : Alignment();
}
}
