//------------------------------------------------------------------------------
void CheckDuplicates( const vector< string > & input,
const string & infmt,
const CWinMaskUtil::CIdSet * ids,
const CWinMaskUtil::CIdSet * exclude_ids )
{
typedef vector< string >::const_iterator input_iterator;
dup_lookup_table table;
CRef<CObjectManager> om(CObjectManager::GetInstance());
for( input_iterator i( input.begin() ); i != input.end(); ++i )
{
Uint4 seqnum( 0 );
for(CWinMaskUtil::CInputBioseq_CI bs_iter(*i, infmt); bs_iter; ++bs_iter)
{
CBioseq_Handle bsh = *bs_iter;
if( CWinMaskUtil::consider( bsh, ids, exclude_ids ) )
{
TSeqPos data_len = bsh.GetBioseqLength();
if( data_len < MIN_SEQ_LENGTH )
continue;
string id;
sequence::GetId(bsh, sequence::eGetId_Best)
.GetSeqId()->GetLabel(&id);
data_len -= SAMPLE_SKIP;
tracker track( table, id );
string index;
CSeqVector data =
bsh.GetSeqVector(CBioseq_Handle::eCoding_Iupac);
for( TSeqPos i = 0; i < data_len; ++i )
{
index.erase();
data.GetSeqData(i, i + SAMPLE_LENGTH, index);
const dup_lookup_table::sample * sample( table[index] );
if( sample != 0 )
track( index, seqnum, i, sample->begin(), sample->end() );
}
table.add_seq_info( id, data );
++seqnum;
}
}
}
}
//-------------------------------------------------------------------------
int CWinMaskApplication::Run (void)
{
SetDiagPostLevel( eDiag_Warning );
CWinMaskConfig aConfig( GetArgs() );
// Branch away immediately if the converter is called.
//
// if( GetArgs()["convert"].AsBoolean() ) {
if( aConfig.AppType() == CWinMaskConfig::eConvertCounts )
{
if( aConfig.Output() == "-" ) {
CWinMaskCountsConverter converter(
aConfig.Input(),
NcbiCout,
aConfig.SFormat(),
aConfig.GetMetaData() );
return converter();
}
else {
CWinMaskCountsConverter converter(
aConfig.Input(),
aConfig.Output(),
aConfig.SFormat(),
aConfig.GetMetaData() );
return converter();
}
}
CRef<CObjectManager> om(CObjectManager::GetInstance());
if(aConfig.InFmt() == "seqids")
CGBDataLoader::RegisterInObjectManager(
*om, 0, CObjectManager::eDefault );
// Read and validate configuration values.
if( aConfig.AppType() == CWinMaskConfig::eComputeCounts )
{
if( aConfig.Output() == "-" ) {
CWinMaskCountsGenerator cg( aConfig.Input(),
NcbiCout,
aConfig.InFmt(),
aConfig.SFormat(),
aConfig.Th(),
aConfig.Mem(),
aConfig.UnitSize(),
aConfig.GenomeSize(),
aConfig.MinScore(),
aConfig.MaxScore(),
aConfig.CheckDup(),
aConfig.FaList(),
aConfig.Ids(),
aConfig.ExcludeIds(),
aConfig.UseBA(),
aConfig.GetMetaData() );
cg();
}
else {
CWinMaskCountsGenerator cg( aConfig.Input(),
aConfig.Output(),
aConfig.InFmt(),
aConfig.SFormat(),
aConfig.Th(),
aConfig.Mem(),
aConfig.UnitSize(),
aConfig.GenomeSize(),
aConfig.MinScore(),
aConfig.MaxScore(),
aConfig.CheckDup(),
aConfig.FaList(),
aConfig.Ids(),
aConfig.ExcludeIds(),
aConfig.UseBA(),
aConfig.GetMetaData() );
cg();
}
return 0;
}
if(aConfig.InFmt() == "seqids"){
LOG_POST(Error << "windowmasker with seqids input not implemented yet");
return 1;
}
CMaskReader & theReader = aConfig.Reader();
CMaskWriter & theWriter = aConfig.Writer();
CSeqMasker theMasker( aConfig.LStatName(),
aConfig.WindowSize(),
aConfig.WindowStep(),
aConfig.UnitStep(),
aConfig.Textend(),
aConfig.CutoffScore(),
aConfig.MaxScore(),
aConfig.MinScore(),
aConfig.SetMaxScore(),
aConfig.SetMinScore(),
aConfig.MergePass(),
aConfig.MergeCutoffScore(),
aConfig.AbsMergeCutoffDist(),
aConfig.MeanMergeCutoffDist(),
aConfig.MergeUnitStep(),
aConfig.Trigger(),
aConfig.TMin_Count(),
aConfig.Discontig(),
aConfig.Pattern(),
aConfig.UseBA() );
CRef< CSeq_entry > aSeqEntry( 0 );
Uint4 total = 0, total_masked = 0;
CSDustMasker * duster( 0 );
const CWinMaskConfig::CIdSet * ids( aConfig.Ids() );
const CWinMaskConfig::CIdSet * exclude_ids( aConfig.ExcludeIds() );
if( aConfig.AppType() == CWinMaskConfig::eGenerateMasksWithDuster )
duster = new CSDustMasker( aConfig.DustWindow(),
aConfig.DustLevel(),
aConfig.DustLinker() );
while( (aSeqEntry = theReader.GetNextSequence()).NotEmpty() )
{
if( aSeqEntry->Which() == CSeq_entry::e_not_set ) continue;
CScope scope(*om);
CSeq_entry_Handle seh = scope.AddTopLevelSeqEntry(*aSeqEntry);
Uint4 masked = 0;
CBioseq_CI bs_iter(seh, CSeq_inst::eMol_na);
for ( ; bs_iter; ++bs_iter) {
CBioseq_Handle bsh = *bs_iter;
if (bsh.GetBioseqLength() == 0) {
continue;
}
if( CWinMaskUtil::consider( bsh, ids, exclude_ids ) )
{
TSeqPos len = bsh.GetBioseqLength();
total += len;
_TRACE( "Sequence length " << len );
CSeqVector data =
bsh.GetSeqVector(CBioseq_Handle::eCoding_Iupac);
auto_ptr< CSeqMasker::TMaskList > mask_info( theMasker( data ) );
CSeqMasker::TMaskList dummy;
if( duster != 0 ) // Dust and merge with mask_info
{
auto_ptr< CSeqMasker::TMaskList > dust_info(
(*duster)( data, *mask_info.get() ) );
CSeqMasker::MergeMaskInfo( mask_info.get(), dust_info.get() );
}
// theWriter.Print( bsh, *mask_info, aConfig.MatchId() );
theWriter.Print( bsh, *mask_info, GetArgs()["parse_seqids"] );
for( CSeqMasker::TMaskList::const_iterator i = mask_info->begin();
i != mask_info->end(); ++i )
masked += i->second - i->first + 1;
total_masked += masked;
_TRACE( "Number of positions masked: " << masked );
}
}
}
_TRACE( "Total number of positions: " << total );
_TRACE( "Total number of positions masked: " << total_masked );
return 0;
}
