Ejemplo n.º 1
0
bool Locus::operator>( const Locus& rhs ) const
{
    int chrComp = chr_.compare(rhs.chr());
    bool result = ( chrComp > 0 )
               || ( chrComp == 0 && (this->decimalPos() > rhs.decimalPos()) );
    return result;
}
Ejemplo n.º 2
0
void
write_plink_file_gz(const std::vector<Individual> &individuals,
                    const std::vector<Locus> &loci,
                    bool print_header,
                    std::string output_path,
                    std::auto_ptr<DoseWriter> writer)
{
    gz::ogzstream output_file( output_path.c_str( ) );
    output_file << std::fixed << std::setprecision( 3 );

    /* Write header. */
    if( print_header )
    {
        output_file << "SNP\tA1\tA2";
        for(unsigned int i = 0; i < individuals.size( ); i++)
        {
            output_file << "\t" << individuals[ i ].get_fid( ) << " " << individuals[ i ].get_iid( );
        }
        output_file << std::endl;
    }

    /* Write doses */
    for(unsigned int i = 0; i < loci.size( ); i++)
    {
        Locus locus = loci[ i ];

        output_file << locus.get_name( ) << "\t" << locus.get_a1( ) << "\t" << locus.get_a2( );
        for(unsigned int j = 0; j < individuals.size( ); j++)
        {
            writer->write( output_file, individuals[ j ], i );
        }
        output_file << std::endl;
    }
}
Ejemplo n.º 3
0
GenomeTemplate BlanketResolver::resolve(
	std::vector<Genome*> blanketGenomes,
	std::vector<bool> & usedGenomes,
	unsigned int target
) {
	GenomeTemplate resolved;
	GenomeTemplate unresolved = blanketGenomes[target]->getTemplate();

	for (unsigned int i = 0; i < unresolved.genomeLength(); i++) {
		Locus * temp = unresolved.getLocus(i);
		if (!temp->isConstructive()) {
			resolved.add(unresolved.getGene(i));
		} else {
			resolved.add(BlanketResolver::resolve(
				blanketGenomes,
				usedGenomes,
				BlanketResolver::findMetaComponentIndex(
					blanketGenomes,
					usedGenomes,
					((PopulationLocus*)temp)->getNode()
				)
			));
		}
	}

	return resolved;
}
Ejemplo n.º 4
0
void Ladder :: OutputTo (RGTextOutput& xmlFile, LadderInputFile& inputFile) {

	RGString link ("http://www.w3.org/2001/XMLSchema-instance");

	xmlFile << "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n";
	xmlFile << "<KitData xmlns:xsi=\"" << link.GetData () << "\" xsi:noNamespaceSchemaLocation=\"MarkerSet.xsd\">\n";
	xmlFile << "\t<Version>2.0</Version>\n";
	xmlFile << "\t<Kits>\n";
	xmlFile << "\t\t<Set>\n";
	xmlFile << "\t\t\t<Name>" << mMarkerSetName.GetData () << "</Name>\n";
	xmlFile << "\t\t\t<NChannels>" << mNumberOfChannels << "</NChannels>\n";
	xmlFile << "\t\t\t<LS>\n";
	
	OutputILSListTo (xmlFile);

	xmlFile << "\t\t\t\t<ChannelNo>" << mChannelForILS << "</ChannelNo>\n";
	xmlFile << "\t\t\t</LS>\n";
	xmlFile << "\t\t\t<FileNameSuffix>" << mSuffix << "</FileNameSuffix>\n";
	xmlFile << "\t\t\t<GenotypeSuffix>" << mSuffix << "</GenotypeSuffix>\n";
	xmlFile << "\t\t\t<DirectorySearchString>" << mSuffix << "</DirectorySearchString>\n";
	OutputChannelMapTo (xmlFile, inputFile);

	list <Locus*>::const_iterator locusIterator;
	Locus* nextLocus;

	for (locusIterator = mLocusList.begin(); locusIterator != mLocusList.end(); locusIterator++) {

		nextLocus = *locusIterator;
		nextLocus->OutputTo (xmlFile);
	}

	xmlFile << "\t\t</Set>\n";
	xmlFile << "\t</Kits>\n";
	xmlFile << "</KitData>";
}
Ejemplo n.º 5
0
int Ladder :: MergeThisLadderInto (Ladder* ladder) {

	list <Locus*>::const_iterator locusIterator;
	Locus* nextLocus;
	Locus* prevLocus = NULL;
	double prevMax;
	double nextMin;
	double nextOriginal;
	double prevOriginal;

	for (locusIterator = mLocusList.begin(); locusIterator != mLocusList.end(); locusIterator++) {

		nextLocus = *locusIterator;
		ladder->MergeLocusIntoLadder (nextLocus);
	}

	// To do:  test that search regions do not overlap neighboring loci

	for (locusIterator = mLocusList.begin(); locusIterator != mLocusList.end(); locusIterator++) {

		nextLocus = *locusIterator;
		
		if (prevLocus == NULL) {

			prevLocus = nextLocus;
			continue;
		}

		if (nextLocus->GetChannel () != prevLocus->GetChannel ()) {

			prevLocus = nextLocus;
			continue;
		}

		prevMax = prevLocus->GetMaxSearchILSBP ();
		nextMin = nextLocus->GetMinSearchILSBP ();

		if (prevMax <= nextMin) {

			prevLocus = nextLocus;
			continue;
		}

		nextOriginal = nextLocus->GetOriginalMinSearchILSBP () - 0.55;
		prevOriginal = prevLocus->GetOriginalMaxSearchILSBP () + 0.55;

		if (prevOriginal > nextOriginal)
			prevOriginal = nextOriginal = 0.5 * (prevOriginal + nextOriginal);

		if (prevMax >= nextOriginal)
			prevLocus->SetMaxSearhILSBP (nextOriginal);

		if (nextMin <= prevOriginal)
			nextLocus->SetMinSearhILSBP (prevOriginal);

		prevLocus = nextLocus;
	}

	return 0;
}
Ejemplo n.º 6
0
static void
update_dmr_name(Locus &dmr, double lod_sum, double mindiff_sum) {
  ostringstream name_stream;
  name_stream << "dmr:" 
              << lod_sum / dmr.score() << ":" 
              << mindiff_sum / dmr.score();
  dmr.set_name(name_stream.str());
}
Ejemplo n.º 7
0
bool Ladder :: TestAllLociMerged () {

	list <Locus*>::const_iterator locusIterator;
	Locus* nextLocus;

	for (locusIterator = mLocusList.begin(); locusIterator != mLocusList.end(); locusIterator++) {

		nextLocus = *locusIterator;

		if (!nextLocus->GetMerged ())
			return false;
	}

	return true;
}
Ejemplo n.º 8
0
Locus* Ladder :: FindLocusByName (const RGString& locusName) {

	Locus* nextLocus;
	list <Locus*>::const_iterator locusIterator;

	for (locusIterator = mLocusList.begin(); locusIterator != mLocusList.end(); locusIterator++) {

		nextLocus = *locusIterator;

		if (nextLocus->GetName () == locusName)
			return nextLocus;
	}

	return NULL;
}
Ejemplo n.º 9
0
Gene* GaussianMutation::newLocusValue(Gene* current) {
	double addend = HierRNG::gaussian(this->mean, this->stdDev);
	double newIndex = current->getIndex() + addend;

	Locus* locus = current->getLocus();
	if (!this->endReflection)
		return current->copy(locus->closestIndex(newIndex));

	while (locus->outOfRange(newIndex)) {
		double topIndex = locus->topIndex();
		double bottomIndex = locus->bottomIndex();
		if (newIndex > topIndex) {
			newIndex = topIndex - (newIndex - topIndex);
		} else if (newIndex < bottomIndex) {
			newIndex = bottomIndex - (newIndex - bottomIndex);
		}
	}

	return current->copy(newIndex);
}
Ejemplo n.º 10
0
int Ladder :: AddLocus (Locus* newLocus) {

	list <Locus*>::const_iterator locusIterator;
	Locus* nextLocus;
	int status = 0;

	for (locusIterator = mLocusList.begin(); locusIterator != mLocusList.end(); locusIterator++) {

		nextLocus = *locusIterator;

		if (nextLocus->isEqual (newLocus)) {

			status = -1;
			break;
		}
	}

	if (status == 0)
		mLocusList.push_back (newLocus);

	return status;
}
Ejemplo n.º 11
0
Ladder* Bins :: AssembleAllLoci (RGDList& doNotExtend) {

	int nLoci;
	Ladder* newLadder = new Ladder ();
	Locus* nextLocus;
	nLoci = SplitFileIntoLocusStrings ();
	int i;
	int status;
	RGString name;

	if (nLoci <= 0) {

		cout << "Could not complete ladder setup" << endl;
		delete newLadder;
		return NULL;
	}

	for (i=1; i<=nLoci; i++) {

		SplitLocusStringIntoLines (i);
		nextLocus = AssembleLocusFromLineStrings ();
		status = newLadder->AddLocus (nextLocus);

		if (status < 0) {

			cout << "Locus name repeated in bins file:  " << nextLocus->GetName ().GetData () << endl;
			delete newLadder;
			return NULL;
		}

		name = nextLocus->GetName ();

		if (doNotExtend.Contains (&name))
			nextLocus->SetDoNotExtend ();
	}

	return newLadder;
}
Ejemplo n.º 12
0
int Ladder :: MergeLocusIntoLadder (const Locus* locus) {
	
	// This combines info and then computes the rest

	Locus* matchingLocus = FindLocusByName (locus->GetName ());

	if (matchingLocus == NULL) {

		cout << "Could not find locus matching name:  " << locus->GetName ().GetData () << endl;
		return -1;
	}

	matchingLocus->SetFirstCoreLocusBP (locus->GetFirstCoreLocusBP ());
	matchingLocus->SetFirstExtendedAllele (locus->GetFirstExtendedAllele ());
	matchingLocus->SetLastExtendedAllele (locus->GetLastExtendedAllele ());
	matchingLocus->ComputeAllBPs ();
	matchingLocus->SetMinMaxSearchILSBP (locus->GetMinSearchILSBP (), locus->GetMaxSearchILSBP ());
	matchingLocus->AdjustSearchRegion ();
	matchingLocus->SetMerged ();

	return 0;
}
Ejemplo n.º 13
0
int CoreBioComponent :: InitializeSM (SampleData& fileData, PopulationCollection* collection, const RGString& markerSetName, Boolean isGrid) {

	//
	//  This is ladder and sample stage 1
	//

	mTime = fileData.GetCollectionStartTime ();
	mDate = fileData.GetCollectionStartDate ();
	mName = fileData.GetName ();
	mRunStart = mDate.GetOARString () + mTime.GetOARString ();
	mMarkerSet = collection->GetNamedPopulationMarkerSet (markerSetName);
	Progress = 0;

	smMarkerSetNameUnknown noNamedMarkerSet;
	smNamedILSUnknown noNamedILS;
	smChannelIsILS channelIsILS;

	if (mMarkerSet == NULL) {

		ErrorString = "*******COULD NOT FIND MARKER SET NAMED ";
		ErrorString << markerSetName << " IN POPULATION COLLECTION********\n";
		SetMessageValue (noNamedMarkerSet, true);
		AppendDataForSmartMessage (noNamedMarkerSet, markerSetName);
		return -1;
	}

	mLaneStandard = mMarkerSet->GetLaneStandard ();
	mNumberOfChannels = mMarkerSet->GetNumberOfChannels ();

	if ((mLaneStandard == NULL) || !mLaneStandard->IsValid ()) {

		ErrorString = "Could not find named internal lane standard associated with marker set named ";
		ErrorString << markerSetName << "\n";
		cout << "Could not find named internal lane standard associated with marker set named " << (char*)markerSetName.GetData () << endl;
		SetMessageValue (noNamedILS, true);
		AppendDataForSmartMessage (noNamedILS, markerSetName);
		return -1;
	}

	mDataChannels = new ChannelData* [mNumberOfChannels + 1];
	int i;
	const int* fsaChannelMap = mMarkerSet->GetChannelMap ();

	for (i=0; i<=mNumberOfChannels; i++)
		mDataChannels [i] = NULL;

	mLaneStandardChannel = mMarkerSet->GetLaneStandardChannel ();

	for (i=1; i<=mNumberOfChannels; i++) {

		if (i == mLaneStandardChannel)
			mDataChannels [i] = GetNewLaneStandardChannel (i, mLaneStandard);

		else {

			if (isGrid)
				mDataChannels [i] = GetNewGridDataChannel (i, mLaneStandard);

			else
				mDataChannels [i] = GetNewDataChannel (i, mLaneStandard);
		}

		mDataChannels [i]->SetFsaChannel (fsaChannelMap [i]);
	}

	mLSData = mDataChannels [mLaneStandardChannel];
	mLSData->SetMessageValue (channelIsILS, true);
	mMarkerSet->ResetLocusList ();
	Locus* nextLocus;

	while (nextLocus = mMarkerSet->GetNextLocus ())
		mDataChannels [nextLocus->GetLocusChannel ()]->AddLocus (nextLocus);

	Progress = 1;
	return 0;
}
Ejemplo n.º 14
0
void CoreBioComponent :: ReportXMLSmartSampleTableRowWithLinks (RGTextOutput& text, RGTextOutput& tempText) {

	RGString type;

	if (mIsNegativeControl)
		type = "-Control";

	else if (mIsPositiveControl)
		type = "+Control";

	else
		type = "Sample";

	RGString pResult;

	RGString SimpleFileName (mName);
	size_t startPos = 0;
	size_t endPos;
	size_t length = SimpleFileName.Length ();
	
	if (SimpleFileName.FindLastSubstringCaseIndependent (DirectoryManager::GetDataFileType (), startPos, endPos)) {

		if (endPos == length - 1)
			SimpleFileName.ExtractAndRemoveLastCharacters (4);
	}

	SimpleFileName.FindAndReplaceAllSubstrings ("\\", "/");
	startPos = endPos = 0;

	if (SimpleFileName.FindLastSubstring ("/", startPos, endPos)) {

		SimpleFileName.ExtractAndRemoveSubstring (0, startPos);
	}
	
	text << CLevel (1) << "\t\t<Sample>\n";
	text << "\t\t\t<Name>" << xmlwriter::EscAscii (SimpleFileName, &pResult) << "</Name>\n";
	text << "\t\t\t<SampleName>" << xmlwriter::EscAscii (mSampleName, &pResult) << "</SampleName>\n";
	text << "\t\t\t<RunStart>" << mRunStart.GetData () << "</RunStart>\n";
	text << "\t\t\t<Type>" << type.GetData () << "</Type>\n" << PLevel ();

	int trigger = Notice::GetMessageTrigger ();
//	int channelHighestLevel;
//	bool channelAlerts = false;
	int cbcHighestMsgLevel = GetHighestMessageLevelWithRestrictionSM ();
	RGDListIterator it (*mSmartMessageReporters);
	SmartMessageReporter* nextNotice;
	bool includesExportInfo = false;

	while (nextNotice = (SmartMessageReporter*) it ()) {

		if (nextNotice->HasViableExportInfo ()) {

			includesExportInfo = true;
			break;
		}
	}

	if (((cbcHighestMsgLevel > 0) && (cbcHighestMsgLevel <= trigger)) || includesExportInfo) {

//		text << CLevel (1) << "\t\t\t<SampleAlerts>\n" << PLevel ();

		// get message numbers and report
		ReportXMLSmartNoticeObjects (text, tempText, " ");

//		text << CLevel (1) << "\t\t\t</SampleAlerts>\n" << PLevel ();
	}

	mDataChannels [mLaneStandardChannel]->ReportXMLILSSmartNoticeObjects (text, tempText, " ");
	int i;

	//for (i=1; i<=mNumberOfChannels; i++) {

	//	//if (i == mLaneStandardChannel)
	//	//	continue;

	//	channelHighestLevel = mDataChannels [i]->GetHighestMessageLevelWithRestrictionSM ();

	//	if ((channelHighestLevel > 0) && (channelHighestLevel <= trigger)) {

	//		channelAlerts = true;
	//		break;
	//	}
	//}

//	if (channelAlerts) {

		text << CLevel (1) << "\t\t\t<ChannelAlerts>\n" << PLevel ();

		for (i=1; i<=mNumberOfChannels; i++) {

			if (i == mLaneStandardChannel)
				continue;

			mDataChannels [i]->ReportXMLSmartNoticeObjects (text, tempText, " ");
		}

		text << CLevel (1) << "\t\t\t</ChannelAlerts>\n" << PLevel ();
//	}

	mMarkerSet->ResetLocusList ();
	Locus* nextLocus;

	while (nextLocus = mMarkerSet->GetNextLocus ()) {

		nextLocus->ReportXMLSmartSampleTableRowWithLinks (text, tempText, " ");
	}

	if (mIsPositiveControl)
		text << CLevel (1) << "\t\t\t<PositiveControl>" << mPositiveControlName << "</PositiveControl>\n";

	text << CLevel (1) << "\t\t</Sample>\n" << PLevel ();
}
Ejemplo n.º 15
0
Locus* Bins :: AssembleLocusFromLineStrings () {
	
	// uses current values in mLocusLineStrings

	Locus* newLocus = new Locus ();
	int nLines = mLocusLineStrings.Length ();
	SplitLocusLine (mLocusLineStrings [0]);  // This should give us the name field
	RGString name = mLocusLineFieldString [1];
	cout << "Locus name = " << name.GetData () << endl;

	//cout << "Bins locus line 1:  ";
	int i;
	int len = mLocusLineFieldString.Length ();

	//for (i=0; i<len; i++) {

	//	cout << mLocusLineFieldString [i].GetData ();

	//	if (i < len - 1)
	//		cout << ", ";
	//}

	//cout << endl;

	RGString firstAlleleName;
	int firstLocusBP;
	double firstILSBP;
	double lastILSBP;
	RGString firstExtendedAlleleName;
	RGString lastExtendedAlleleName;
	int lineForFirstAllele = 0;

	for (i=1; i<nLines; i++) {

		SplitLocusLine (mLocusLineStrings [i]);

		if (mLocusLineFieldString.Length () < 4) {

			cout << "Could not find first allele for locus " << name.GetData () << endl;
			delete newLocus;
			return NULL;
		}

		if (mLocusLineFieldString.Length () >= 5) {

			if (mLocusLineFieldString [4] == "virtual") {

				if (i == 1) {

					firstExtendedAlleleName = mLocusLineFieldString [0];
				}

				continue;
			}
		}

		firstAlleleName = mLocusLineFieldString [0];
		firstILSBP = mLocusLineFieldString [1].ConvertToDouble ();
		firstLocusBP = (int) floor (firstILSBP + 0.5);
		lineForFirstAllele = i;
		break;
	}

	if (firstExtendedAlleleName.Length () == 0)
		firstExtendedAlleleName = firstAlleleName;

	bool foundLastExtendedAllele = false;

	for (i=nLines-1; i>lineForFirstAllele; i--) {
	
		SplitLocusLine (mLocusLineStrings [i]);

		if (mLocusLineFieldString.Length () < 4)
			continue;

		if (!foundLastExtendedAllele) {
		
			lastExtendedAlleleName = mLocusLineFieldString [0];
			foundLastExtendedAllele = true;
		}

		if ((mLocusLineFieldString.Length () >= 5) && (mLocusLineFieldString [4] == "virtual"))
			continue;

		lastILSBP = mLocusLineFieldString [1].ConvertToDouble ();
		break;
	}

	if (lastExtendedAlleleName.Length () == 0) {

		cout << "Could not locate last extended allele name for locus:  " << name.GetData () << endl;
		delete newLocus;
		return NULL;
	}

	newLocus->SetFirstCoreAllele (firstAlleleName);
	newLocus->SetFirstExtendedAllele (firstExtendedAlleleName);
	newLocus->SetLastExtendedAllele (lastExtendedAlleleName);
	newLocus->SetMinMaxSearchILSBP (firstILSBP, lastILSBP);  // These will have to be adjusted later when core repeat number is known
	newLocus->SetFirstCoreLocusBP (firstLocusBP);
	newLocus->SetName (name);

	//  Need to add to Locus ability to compute first and last extended bp

	return newLocus;
}
Ejemplo n.º 16
0
void
merge(istream &cpg_stream, ostream &dmr_stream, double cutoff) {
  
  bool skipped_last_cpg;
  Locus dmr;
  
  if (!read_next_significant_cpg(cpg_stream, dmr, cutoff, skipped_last_cpg))
    return;
  
  dmr.set_score(1);
  double lod_sum, mindiff_sum, unadjusted_pval;
  extract_scores(dmr.name(), lod_sum, mindiff_sum, unadjusted_pval);
  
  if (unadjusted_pval >= cutoff) {
    lod_sum = 0;
    mindiff_sum = 0;
  }
  
  Locus cpg;
  while(read_next_significant_cpg(cpg_stream, cpg, cutoff, skipped_last_cpg)) {
    double lod, mindiff;
    
    extract_scores(cpg.name(), lod, mindiff, unadjusted_pval);
    
    if (skipped_last_cpg || cpg.chrom() != dmr.chrom()) {
      update_dmr_name(dmr, lod_sum, mindiff_sum);
      
      if (lod_sum != 0) {
        dmr_stream << dmr << std::endl;
      }
      
      dmr = cpg;
      dmr.set_score(1);
      
      if (unadjusted_pval >= cutoff) {
        lod_sum = 0;
        mindiff_sum = 0;
      } else {
        lod_sum = lod;
        mindiff_sum = mindiff;
      }
      
    } else {
      dmr.set_end(cpg.end());
      dmr.set_score(dmr.score() + 1);
      
      if (unadjusted_pval < cutoff) {
        lod_sum += lod;
        mindiff_sum += mindiff;
      }
    }
    
  }
  
  update_dmr_name(dmr, lod_sum, mindiff_sum);
  dmr_stream << dmr << std::endl;
  
}
Ejemplo n.º 17
0
int Ladder :: AmendLadderData (LadderInputFile* inFile, RGString& oldLadderString) {

	RGString newLadderString;

	// Parse oldLadder data into pieces for individual edits
	RGString locusString;
	RGString* newLocusString;
	RGDList locusStrings;
	size_t startPos = 0;
	size_t endPos;
	RGXMLTagSearch locusSearch ("Locus", oldLadderString);
	RGXMLTagSearch searchRegionsSearch ("SearchRegions", oldLadderString);

	RGString* ilsName = (RGString*)inFile->GetILSNameList ().First ();
	endPos = 0;
	oldLadderString.FindNextSubstring (0, "\t\t\t<Locus>", endPos);
	RGString insertBase;
	insertBase << "\t\t\t\t\t<ILSName>" << ilsName->GetData () << "</ILSName>\n";
	insertBase << "\t\t\t\t</LSBases>";
	RGString leadString = oldLadderString.ExtractSubstring (0, endPos - 1);
	//cout << "Lead string = \n" << leadString.GetData () << endl;
	endPos = 0;
	leadString.FindAndReplaceNextSubstring ("\t\t\t\t</LSBases>", insertBase, endPos);
	//cout << "Lead string = \n" << leadString.GetData () << endl;
	newLadderString << leadString;

	startPos = 0;

	while (locusSearch.FindNextTag (startPos, endPos, locusString)) {

		newLocusString = new RGString (locusString);
		locusStrings.Append (newLocusString);
		startPos = endPos;
	}

	if (mLocusList.size () != locusStrings.Entries ()) {

		cout << "Number of loci in bins file does not match number of loci in ladder file" << endl;
		return -152;
	}

	Locus* nextLocus;
	RGString locusInsert;
	RGString currentLocusString;
	RGString nameString;
	RGXMLTagSearch locusNameSearch ("Name", currentLocusString);
	RGXMLTagSearch coreRepeatSearch ("CoreRepeatNumber", currentLocusString);
	double minSearch;
	double maxSearch;
	RGString repeatString;
	int repeatNumber;

	while (locusStrings.Entries () > 0) {

		newLocusString = (RGString*) locusStrings.GetFirst ();
		currentLocusString = *newLocusString;
		locusNameSearch.ResetSearch ();
		coreRepeatSearch.ResetSearch ();

		locusNameSearch.FindNextTag (0, endPos, nameString);
		nextLocus = FindLocusByName (nameString);

		if (nextLocus == NULL) {

			cout << "Could not find locus named " << nameString.GetData () << ".  Exiting..." << endl;
			return -155;
		}

		if (!coreRepeatSearch.FindNextTag (0, endPos, repeatString))
			repeatNumber = 4;

		else
			repeatNumber = repeatString.ConvertToInteger ();

		locusInsert = "";
		minSearch = nextLocus->GetMinSearchILSBP () - repeatNumber + 1;
		maxSearch = nextLocus->GetMaxSearchILSBP () + repeatNumber -1;

		locusInsert << "\t\t\t\t\t<Region>\n";
		locusInsert << "\t\t\t\t\t\t<ILSName>" << ilsName->GetData () << "</ILSName>\n";
		locusInsert << "\t\t\t\t\t\t<MinGrid>" << 0.01 * floor (100.0 * minSearch + 0.5) << "</MinGrid>\n";
		locusInsert << "\t\t\t\t\t\t<MaxGrid>" << 0.01 * floor (100.0 * maxSearch + 0.5) << "</MaxGrid>\n";
		locusInsert << "\t\t\t\t\t</Region>\n";
		locusInsert << "\t\t\t\t</SearchRegions>";
		endPos = 0;
		currentLocusString.FindAndReplaceNextSubstring ("\t\t\t\t</SearchRegions>", locusInsert, endPos);

		newLadderString << "\t\t\t<Locus>" << currentLocusString << "</Locus>\n";
		delete newLocusString;
	}

	newLadderString << "\t\t</Set>\n";
	newLadderString << "\t</Kits>\n";
	newLadderString << "</KitData>\n";

	RGString ladderPath = inFile->GetOutputConfigDirectoryPath () + "/" + inFile->GetLadderFileName ();
	RGTextOutput ladderOutput (ladderPath, FALSE);

	if (!ladderOutput.FileIsValid ()) {

		cout << "Could not open ladder output file:  " << ladderPath.GetData () << endl;
		return -161;
	}

	ladderOutput << newLadderString;

	cout << "Ladder update completed successfully..." << endl;
	return 0;
}