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Clove.java
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Clove.java
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package au.edu.wehi.clove;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.StringTokenizer;
import java.util.Map.Entry;
import java.util.TreeSet;
import htsjdk.samtools.util.Tuple;
import htsjdk.samtools.*;
import htsjdk.samtools.util.Interval;
import htsjdk.samtools.util.IntervalList;
import htsjdk.samtools.util.SamLocusIterator;
class EventIterator implements Iterator<Event> {
private Iterator<GenomicNode> myNodeIterator;
private GenomicNode currentNode;
private int nextEventIndex;
private HashSet<Event> skipEvents;
private Event currentEvent;
public EventIterator(Iterator<GenomicNode> nodeIterator, HashSet<Event> skip){
myNodeIterator = nodeIterator;
currentNode = nodeIterator.next();
nextEventIndex = 0;
skipEvents = skip;
}
@Override
public boolean hasNext() {
System.err.println("Method in EventIterator should not be used!");
return false;
}
@Override
public Event next() {
if(currentNode == null){
return null;
}
if(nextEventIndex < currentNode.getEvents().size()) {
currentEvent = currentNode.getEvents().get(nextEventIndex);
nextEventIndex ++;
if(skipEvents.contains(currentEvent))
return this.next();
else
return currentEvent;
}
nextEventIndex = 0;
currentNode = (myNodeIterator.hasNext()? myNodeIterator.next() : null);
while(currentNode!=null && currentNode.getEvents().size() == 0){
if (myNodeIterator.hasNext())
currentNode = myNodeIterator.next();
else
currentNode = null;
}
if(currentNode != null)
return this.next();
else
return null;
}
public GenomicCoordinate getInsertionCoordinate() {
if(currentEvent.getNode(true) == currentNode){
return currentEvent.getC1();
} else {
return currentEvent.getC2();
}
}
@Override
public void remove() {
System.err.println("Method in EventIterator should not be used!");
}
}
public class Clove {
private static int softclipLength5prime(SAMRecord s){
int sc_start = s.getAlignmentStart() - s.getUnclippedStart();
return sc_start;
}
private static int softclipLength3prime(SAMRecord s){
int sc_end = s.getUnclippedEnd() - s.getAlignmentEnd();
return sc_end;
}
private static boolean isInteresingSoftclip(SAMRecord s, int start, int end, String orientation){
if(orientation.equals("+") && s.getAlignmentEnd() <= end + 2 && softclipLength5prime(s) > 4){
return true;
}
if(orientation.equals("-") && s.getAlignmentStart() >= start -2 && softclipLength3prime(s) > 4) {
return true;
}
// if(s.getAlignmentStart()-2 <= breakpoint && s.getAlignmentEnd()+2>=breakpoint && (softclipLength3prime(s) > 4 || softclipLength5prime(s) > 4))
// return true;
return false;
}
private static boolean isAlignedAcrossBreakpoint(SAMRecord s, int breakpointPosition){
if(s.getAlignmentStart() < breakpointPosition-5 && s.getAlignmentEnd() > breakpointPosition+5 && s.getAlignmentStart() - s.getUnclippedStart() < 10 && s.getUnclippedEnd() - s.getAlignmentEnd() < 10)
return true;
return false;
}
private static double fetchStuff(
String chr, int start, int end, String orientation, SAMFileReader bamFile) {
SAMRecordIterator iter = bamFile.queryOverlapping(chr, start, end);
int properAlignment = 0, softclipped = 0;
int breakpointPosition = (start + end)/2;
for(SAMRecord s; iter.hasNext();){
s = iter.next();
if(isInteresingSoftclip(s, start, end, orientation)){
softclipped ++;
} else if (isAlignedAcrossBreakpoint(s, breakpointPosition)){
properAlignment++;
}
}
return (double)softclipped/(softclipped+properAlignment);
}
private static void addEventToNodeList(Event e, Hashtable<String, TreeSet<GenomicNode>> genomicNodes, boolean useFirstCoordinate){
GenomicCoordinate coordinate = (useFirstCoordinate? e.getC1() : e.getC2());
TreeSet<GenomicNode> nodeSet;
if(! genomicNodes.containsKey(coordinate.getChr())){
nodeSet = new TreeSet<GenomicNode>();
genomicNodes.put(coordinate.getChr(), nodeSet);
} else {
nodeSet = genomicNodes.get(coordinate.getChr()) ;
}
GenomicNode newNode = new GenomicNode(coordinate, e);
e.setNode(newNode, useFirstCoordinate);
nodeSet.add(newNode);
}
private static String generateNodeLabel(GenomicNode n){
return n.getStart().getChr()+"_"+n.getStart().getPos()+"_"+n.getEnd().getPos();
}
private static void graphVisualisation(String outputFilename, Hashtable<String, TreeSet<GenomicNode>> genomicNodes) throws IOException{
HashSet<Event> eventsWritten = new HashSet<Event>();
FileWriter output = new FileWriter(outputFilename);
output.write("digraph g {\n");
for(Entry<String, TreeSet<GenomicNode>> tableEntry: genomicNodes.entrySet()) {
if(!tableEntry.getKey().equals("ecoli"))
continue;
output.write("{rank=same; ");
for(GenomicNode n : tableEntry.getValue()){
output.write(generateNodeLabel(n)+"; ");
}
output.write("}\n");
for(GenomicNode n : tableEntry.getValue()){
for(Event e: n.getEvents()) {
if(eventsWritten.contains(e))
continue;
else
eventsWritten.add(e);
String l1 = generateNodeLabel(e.getNode(true)), l2 = generateNodeLabel(e.getNode(false));
switch(e.getType()){
case DEL: output.write(l1+"->"+l2+"[label=\"DEL\"];\n"); break;
case TAN: output.write(l1+"->"+l2+"[label=\"TAN\" arrowtail=normal arrowhead=none dir=both];\n"); break;
case COMPLEX_INVERSION:
Event ee = ((ComplexEvent)e).getEventsInvolvedInComplexEvent()[0];
l1 = generateNodeLabel(ee.getNode(true));
l2 = generateNodeLabel(ee.getNode(false));
//if (l1.equals("ecoli_28204143_28204160")){
//if (l1.equals("ecoli_24118329_24118583")){
System.out.println("COMPLEX_INV:");
System.out.println("l1:\t"+generateNodeLabel(ee.getNode(true))+"\t");
System.out.println("l2:\t"+generateNodeLabel(ee.getNode(false))+"\t");
//}
output.write(l1+"->"+l2+"[label=\"COMPLEX_INV\" dir=both];\n"); break;//should we differentiate COMPLEX_INV and INV?
case COMPLEX_TRANSLOCATION:
case COMPLEX_DUPLICATION:
GenomicNode insNode = e.getNode(true);
String label = (e.getType() == EVENT_TYPE.COMPLEX_DUPLICATION? "DUP" : "TRANS");
l1 = generateNodeLabel(insNode);
Event[] allEvents = ((ComplexEvent)e).getEventsInvolvedInComplexEvent();
for(int i=0;i<allEvents.length;i++){
if(allEvents[i].getNode(true) == insNode){
l2 = generateNodeLabel(allEvents[i].getNode(false));
output.write(l1+"->"+l2+"[label=\""+label+"\" arrowtail=odiamond arrowhead=normal dir=both];\n");
} else if(allEvents[i].getNode(false) == insNode){
l2 = generateNodeLabel(allEvents[i].getNode(true));
output.write(l1+"->"+l2+"[label=\""+label+"\" arrowtail=odiamond arrowhead=normal dir=both];\n");
}
}
break;
default: output.write(l1+"->"+l2+"[label=\""+e.getType()+"\"];\n");
}
}
}
}
output.write("}\n");
output.flush();
output.close();
}
private static void compareToGoldStandard(String goldFileName, Hashtable<String, TreeSet<GenomicNode>> genomicNodes, int margin, boolean compareStrictly) throws IOException {
boolean checkAgain = true;
if(oldFns.size() == 0){
checkAgain = false;
}
BufferedReader gold = new BufferedReader(new FileReader(goldFileName));
String goldLine = gold.readLine();
String currentChromosome = goldLine.replace(":","\t").split( "\t")[1];
System.out.println("Working on first chromosome: "+currentChromosome);
//Iterator<GenomicNode> iter = genomicNodes.get("gi|260447279|gb|CP001637.1|").iterator();
HashSet<Event> skip = new HashSet<Event>();
HashSet<Event> tryAgain = new HashSet<Event>();
HashSet<String> recalledOnce = new HashSet<String>();
Iterator<GenomicNode> iter = genomicNodes.get(currentChromosome).iterator();
EventIterator events = new EventIterator(iter, skip);
Event e = events.next();
Hashtable<EVENT_TYPE, int[]> statsByType = new Hashtable<EVENT_TYPE, int[]>();
for(EVENT_TYPE t: EVENT_TYPE.values()){
//the convention used below is: TP index 0, FP 1, and FN 2
statsByType.put(t, new int[4]);
}
//static conversion table
Hashtable<String, EVENT_TYPE> typeConversion = new Hashtable<String, EVENT_TYPE>();
{
typeConversion.put("INVERSION", EVENT_TYPE.COMPLEX_INVERSION);
typeConversion.put("DELETION", EVENT_TYPE.DEL);
typeConversion.put("TANDEM", EVENT_TYPE.TAN);
//typeConversion.put("INSERTION", EVENT_TYPE.INS);
typeConversion.put("INSERTION", EVENT_TYPE.COMPLEX_DUPLICATION);
typeConversion.put("TRANSLOCATION", EVENT_TYPE.COMPLEX_TRANSLOCATION);
typeConversion.put("INVERTED_TRANSLOCATION", EVENT_TYPE.COMPLEX_INVERTED_TRANSLOCATION);
typeConversion.put("INVERTED_INSERTION", EVENT_TYPE.COMPLEX_INVERTED_DUPLICATION);
typeConversion.put("DUPLICATION", EVENT_TYPE.COMPLEX_DUPLICATION);
typeConversion.put("INVERTED_DUPLICATION", EVENT_TYPE.COMPLEX_INVERTED_DUPLICATION);
typeConversion.put("INTERCHROMOSOMAL_TRANSLOCATION", EVENT_TYPE.COMPLEX_INTERCHROMOSOMAL_TRANSLOCATION);
typeConversion.put("INTERCHROMOSOMAL_INVERTED_TRANSLOCATION", EVENT_TYPE.COMPLEX_INTERCHROMOSOMAL_INVERTED_TRANSLOCATION);
typeConversion.put("INTERCHROMOSOMAL_DUPLICATION", EVENT_TYPE.COMPLEX_INTERCHROMOSOMAL_DUPLICATION);
typeConversion.put("INTERCHROMOSOMAL_INVERTED_DUPLICATION", EVENT_TYPE.COMPLEX_INTERCHROMOSOMAL_INVERTED_DUPLICATION);
}
while(goldLine != null ){
StringTokenizer st = new StringTokenizer(goldLine, ":-\t ");
String type = st.nextToken();
String chr = st.nextToken();
//TODO: what if the SVs are on a different chromosome?
if(!currentChromosome.equals(chr)) {
while(e!=null){
if(tryAgain.contains(e)){
System.out.println("FPFPFPFP: "+e);
statsByType.get(e.getType())[1]++;
} else {
tryAgain.add(e);
}
e = events.next();
}
currentChromosome = chr;
System.out.println("Working on chromosome: "+currentChromosome);
if(!genomicNodes.containsKey(chr)){
e = null;
continue;
}
iter = genomicNodes.get(currentChromosome).iterator();
events = new EventIterator(iter, skip);
e = events.next();
}
int start = Integer.parseInt(st.nextToken());
//int end = Integer.parseInt(st.nextToken());
if(type.equals("SNP") || type.equals("JOIN") || type.equals("TRANSLOCATION_DELETION")){
goldLine = gold.readLine();
continue;
}
if(e==null){
//System.out.println("DEFINITE FN: "+goldLine);
statsByType.get(typeConversion.get(type))[2]++;
goldLine = gold.readLine();
continue;
}
GenomicCoordinate compare;
if(e.getType() == EVENT_TYPE.COMPLEX_INVERTED_TRANSLOCATION || e.getType() == EVENT_TYPE.COMPLEX_INVERTED_DUPLICATION
|| e.getType() == EVENT_TYPE.COMPLEX_DUPLICATION || e.getType() == EVENT_TYPE.COMPLEX_TRANSLOCATION
|| e.getType() == EVENT_TYPE.COMPLEX_INTERCHROMOSOMAL_INVERTED_TRANSLOCATION || e.getType() == EVENT_TYPE.COMPLEX_INTERCHROMOSOMAL_INVERTED_DUPLICATION
|| e.getType() == EVENT_TYPE.COMPLEX_INTERCHROMOSOMAL_DUPLICATION || e.getType() == EVENT_TYPE.COMPLEX_INTERCHROMOSOMAL_TRANSLOCATION) {
compare = ((ComplexEvent)e).getInsertionPoint();
tryAgain.add(e); // do not attempt single coordinate events twice.
} else if(tryAgain.contains(e)){
compare = events.getInsertionCoordinate();
} else {
compare = events.getInsertionCoordinate();
}
if(!compare.getChr().equals(chr)) {
//Fusion on different chr than goldLine
if(compare.getChr().compareTo(chr) < 0){
System.out.println("DEFAULT FP? "+e);
e = events.next();
continue;
} else {
System.out.println("DEFAULT FN?");
goldLine= gold.readLine();
continue;
}
}
//GenomicCoordinate compare = (e.getType() == EVENT_TYPE.COMPLEX_INVERTED_TRANSLOCATION || e.getType() == EVENT_TYPE.COMPLEX_INVERTED_DUPLICATION || e.getType() == EVENT_TYPE.COMPLEX_DUPLICATION || e.getType() == EVENT_TYPE.COMPLEX_TRANSLOCATION? ((ComplexEvent)e).getInsertionPoint() : e.getC1());
if(compare.distanceTo(new GenomicCoordinate(chr, start)) > margin) {
if(compare.compareTo(new GenomicCoordinate(chr, start)) < 0) {
//half TP?
if(tryAgain.contains(e) || compareStrictly){
//System.out.println("FP: "+e);
statsByType.get(e.getType())[1]++;
} else {
tryAgain.add(e);
}
e = events.next();
} else {
if(!recalledOnce.contains(goldLine) || compareStrictly){
System.out.println("FN: "+goldLine);
if(checkAgain && !oldFns.contains(goldLine)){
System. out.println("New FN: "+goldLine);
} else if (!checkAgain){
oldFns.add(goldLine);
}
statsByType.get(typeConversion.get(type))[2]++;
}
goldLine = gold.readLine();
continue;
}
} else {
if(typeConversion.get(type) == e.getType()){
// if(type.equals("INVERSION") && e.getType()==EVENT_TYPE.COMPLEX_INVERSION || type.equals("DELETION") && e.getType()==EVENT_TYPE.DEL
// || type.equals("TANDEM") && e.getType()==EVENT_TYPE.TAN || type.equals("INSERTION") && e.getType()==EVENT_TYPE.COMPLEX_DUPLICATION
// || type.equals("TRANSLOCATION") && e.getType()==EVENT_TYPE.COMPLEX_TRANSLOCATION || type.equals("INSERTION") && e.getType()==EVENT_TYPE.INS) {
//System.out.println("TP: "+e+" "+goldLine);
if(recalledOnce.contains(goldLine)){
//redundant TP?
System.out.println("Redundant TP!");
} else {
statsByType.get(e.getType())[0]++;
}
//goldLine = gold.readLine();
} else {
//System.out.println("Half TP: Type mismatch: "+e+" "+goldLine);
if(recalledOnce.contains(goldLine)){
//redundant HTP?
System.out.println("Redundant HTP!");
} else {
statsByType.get(e.getType())[3]++;
}
}
recalledOnce.add(goldLine);
skip.add(e);
e = events.next();
}
}
while(goldLine!=null){
if(! goldLine.contains("SNP") && ! goldLine.contains("TRANSLOCATION_DELETION") && (!recalledOnce.contains(goldLine) || compareStrictly)){
String type = (new StringTokenizer(goldLine)).nextToken();
System.out.println("FN: "+goldLine);
statsByType.get(typeConversion.get(type))[2]++;
}
goldLine = gold.readLine();
}
e = events.next();
int tps=0, fps=0, fns=0, htps=0;
System.out.println("Stats:\tTP\tHalf TP\tFP\tFN\tSen\tSpe");
for(EVENT_TYPE t: EVENT_TYPE.values()){
int[] stats = statsByType.get(t);
double sen = (stats[0]+stats[2]==0? 0: (double)stats[0]/(stats[0]+stats[2]));
double spe = (stats[0]+stats[1]==0? 0: (double)stats[0]/(stats[0]+stats[1]));
System.out.println(t+"\t"+stats[0]+"\t"+stats[3]+"\t"+stats[1]+"\t"+stats[2]+"\t"+sen+"\t"+spe);
tps+=stats[0]; fps+=stats[1]; fns+=stats[2]; htps +=stats[3];
}
System.out.println("Total\t"+tps+"\t"+htps+"\t"+fps+"\t"+fns+"\t"+((double)(tps+htps)/(tps+htps+fns))+"\t"+((double)(tps+htps)/(tps+htps+fps)));
System.out.println("Accuracy:\t"+((double)tps/(tps+fps+fns))+"\t"+((double)(tps+htps)/(tps+fps+fns+htps)));
gold.close();
}
private static void reportEventComposition(Hashtable<String, TreeSet<GenomicNode>> genomicNodes) {
Hashtable<EVENT_TYPE, Integer> eventCounts = new Hashtable<EVENT_TYPE, Integer>();
int selfRef = 0;
for(EVENT_TYPE t: EVENT_TYPE.values()){
eventCounts.put(t, 0);
}
HashSet<Event> skipEvents = new HashSet<Event>();
for(Entry<String, TreeSet<GenomicNode>> tableEntry: genomicNodes.entrySet()) {
for(GenomicNode n: tableEntry.getValue()){
for(Event e: n.getEvents()){
if(skipEvents.contains(e))
continue;
Integer i = eventCounts.get(e.getType()) + 1;
eventCounts.put(e.getType(), i);
if(e.otherNode(n) == n){
selfRef++;
} else
skipEvents.add(e);
}
}
}
for(EVENT_TYPE t: EVENT_TYPE.values()){
System.out.println(t+": "+eventCounts.get(t));
}
System.out.println("Self refs: "+selfRef);
}
//private static double getReadDepth(String str, String chr, int start, int end){
private static double getReadDepth(SAMFileReader samReader, String chr, int start, int end){
if(start >= end){
return -1;
}
//SAMFileReader samReader=new SAMFileReader(new File(str));
String chromId=chr;
int chromStart=start;
int chromEnd=end;
int pos=0;
int depth=0;
int total=0;
int count=0;
Interval interval=new Interval(chromId,chromStart,chromEnd);
IntervalList iL=new IntervalList(samReader.getFileHeader());
iL.add(interval);
SamLocusIterator sli=new SamLocusIterator(samReader,iL,true);
for(Iterator<SamLocusIterator.LocusInfo> iter=sli.iterator(); iter.hasNext();){
SamLocusIterator.LocusInfo locusInfo=iter.next();
//pos = locusInfo.getPosition();
depth = locusInfo.getRecordAndPositions().size();
total+=depth;
count++;
//System.out.println("POS="+pos+" depth:"+depth);
}
//System.out.println("total: "+total+"\tcount: "+count);
sli.close();
//samReader.close();
return (double)total/count;
}
public static void createVCFHeader(PrintWriter output) throws IOException{
//file format
output.write("##fileformat=VCFv4.2\n");
//fileDate
DateFormat dateFormat = new SimpleDateFormat ("yyyyMMdd");
Date date = new Date();
output.write("##fileDate="+dateFormat.format(date)+"\n");
//INFO
output.write("##INFO=<ID=CIEND,Number=2,Type=Integer,Description=\"PE confidence interval around END\">\n");
output.write("##INFO=<ID=CIPOS,Number=2,Type=Integer,Description=\"PE confidence interval around POS\">\n");
output.write("##INFO=<ID=CHR2,Number=1,Type=String,Description=\"Chromosome for END coordinate in case of a translocation\">\n");
output.write("##INFO=<ID=START>,Number=1,Type=Integer,Description=\"Start position of the interval (for certain types only)\">\n");
output.write("##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the structural variant\">\n");
output.write("##INFO=<ID=PE,Number=1,Type=Integer,Description=\"Paired-end support of the structural variant\">\n");
output.write("##INFO=<ID=MAPQ,Number=1,Type=Integer,Description=\"Median mapping quality of paired-ends\">\n");
output.write("##INFO=<ID=SR,Number=1,Type=Integer,Description=\"Split-read support\">\n");
output.write("##INFO=<ID=SRQ,Number=1,Type=Float,Description=\"Split-read consensus alignment quality\">\n");
output.write("##INFO=<ID=CONSENSUS,Number=1,Type=String,Description=\"Split-read consensus sequence\">\n");
output.write("##INFO=<ID=CT,Number=1,Type=String,Description=\"Paired-end signature induced connection type\">\n");
output.write("##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description=\"Imprecise structural variation\">\n");
output.write("##INFO=<ID=PRECISE,Number=0,Type=Flag,Description=\"Precise structural variation\">\n");
output.write("##INFO=<ID=SVTYPE,Number=1,Type=String,Description=\"Type of structural variant\">\n");
output.write("##INFO=<ID=SVMETHOD,Number=1,Type=String,Description=\"Type of approach used to detect SV\">\n");
output.write("##INFO=<ID=ADP,Number=1,Type=Integer,Description=\"Average Read Depth\">\n");
output.write("##INFO=<ID=SUPPORT,Number=2,Type=Integer,Description=\"SV support by (i) number of aligners, and (ii) number of calls between all aligners\">\n");
//FILTER
output.write("##FILTER=<ID=LowQual,Description=\"PE support below 3 or mapping quality below 20.\">\n");
//FORMAT
output.write("##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n");
output.write("##FORMAT=<ID=GL,Number=G,Type=Float,Description=\"Log10-scaled genotype likelihoods for RR,RA,AA genotypes\">\n");
output.write("##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\n");
output.write("##FORMAT=<ID=FT,Number=1,Type=String,Description=\"Per-sample genotype filter\">\n");
output.write("##FORMAT=<ID=RC,Number=1,Type=Integer,Description=\"Raw high-quality read counts for the SV\">\n");
output.write("##FORMAT=<ID=DR,Number=1,Type=Integer,Description=\"# high-quality reference pairs\">\n");
output.write("##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"# high-quality variant pairs\">\n");
output.write("##FORMAT=<ID=RR,Number=1,Type=Integer,Description=\"# high-quality reference junction reads\">\n");
output.write("##FORMAT=<ID=RV,Number=1,Type=Integer,Description=\"# high-quality variant junction reads\">\n");
//ALT
output.write("##ALT=<ID=DEL,Description=\"Deletion\">\n");
output.write("##ALT=<ID=TAN,Description=\"Tandem Duplication\">\n");
output.write("##ALT=<ID=INV,Description=\"Inversion\">\n");
output.write("##ALT=<ID=INS,Description=\"Insertion\">\n");
output.write("##ALT=<ID=DUP,Description=\"Complex Duplication\">\n");
output.write("##ALT=<ID=TRA,Description=\"Complex Translocation\">\n");
output.write("##ALT=<ID=CIV,Description=\"Complex Inversion\">\n");
output.write("##ALT=<ID=CVT,Description=\"Complex Inverted Translocation\">\n");
output.write("##ALT=<ID=CVD,Description=\"Complex Inverted Duplication\">\n");
output.write("##ALT=<ID=CIT,Description=\"Complex Interchromosomal Translocation\">\n");
output.write("##ALT=<ID=CID,Description=\"Complex Interchromosomal Duplication\">\n");
output.write("##ALT=<ID=IVT,Description=\"Complex Inverted Interchromosomal Translocation\">\n");
output.write("##ALT=<ID=IVD,Description=\"Complex Inverted Interchromosomal Duplication\">\n");
//Header Line
output.write("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\n");
}
enum SV_ALGORITHM {SOCRATES, DELLY, CREST, GUSTAF, BEDPE};
static ArrayList<String> oldFns = new ArrayList<String>();
/**
* @param args
* @throws IOException
*/
public static void main(String[] args) throws IOException {
//Start Time
long startTime = System.nanoTime();
if(args.length < 8){
System.err.println("Options (all mandatory -- input can be specified more than once):" +
"\n\t-i <list of breakpoints> <algorithm (Socrates/Delly/Crest/Gustaf/BEDPE)>" +
"\n\t-b <BAM file> \n\t-c <mean coverage> <coverage>" +
"\n\t-o <output filename> [default: CLOVE.vcf]");
System.exit(0);
}
/*parse the options from the command line */
int argindex = 0;
ArrayList<Tuple<BufferedReader, SV_ALGORITHM>> inputs = new ArrayList<Tuple<BufferedReader,SV_ALGORITHM>>();
SAMFileReader samReader = null;
double mean = 0;
double interval= 0;
String goldStandard = null;
String outputVCF = "CLOVE.vcf";
while (argindex < args.length){
if (args[argindex].equals("-i")){
try{
BufferedReader input = new BufferedReader(new FileReader(args[argindex + 1]));
SV_ALGORITHM algorithm = SV_ALGORITHM.valueOf(args[argindex + 2].toUpperCase());
inputs.add(new Tuple<BufferedReader, Clove.SV_ALGORITHM>(input, algorithm));
argindex += 3;
} catch (IllegalArgumentException e){
System.err.println("Unable to parse input breakpoints.");
System.exit(1);
}
} else if (args[argindex].equals("-b")){
try {
samReader=new SAMFileReader(new File(args[argindex + 1]));
argindex += 2;
} catch (Exception e){
System.err.println("Unable to load bam file.");
System.exit(1);
}
} else if(args[argindex].equals("-c")){
try{
mean = Double.parseDouble(args[argindex + 1]);
interval = Double.parseDouble(args[argindex + 2]);
argindex += 3;
} catch (IllegalArgumentException e){
System.err.println("Unable to parse coverage and std.");
System.exit(1);
}
} else if (args[argindex].equals("-d")){
goldStandard = args[argindex + 1];
argindex += 2;
} else if(args[argindex].equals("-o")){
outputVCF = args[argindex + 1];
argindex += 2;
}
else {
System.err.println("Unknown option: "+args[argindex]);
throw new IllegalArgumentException();
}
}
/*
* parse the entire input file and collect all events in list
*/
ArrayList<Event> allEvents = new ArrayList<Event>();
String line;
int count = 0;
for(Tuple<BufferedReader, SV_ALGORITHM> input_tuple : inputs){
System.out.println("Reading input...");
BufferedReader input = input_tuple.a;
SV_ALGORITHM algorithm = input_tuple.b;
while ((line = input.readLine()) != null){
//TODO: make # check algorithm specific?
if(line.startsWith("#"))
continue;
Event e;
switch(algorithm){
case SOCRATES: e = Event.createNewEventFromSocratesOutputLatest(line, count++); break;
case DELLY: e = Event.createNewEventFromDellyOutputLatest(line);break;
case CREST: e = Event.createNewEventFromCrestOutputLatest(line, count++); break;
case GUSTAF: e = Event.createNewEventFromGustafOutput(line); if(e.size()<50) continue; break;
case BEDPE: e = Event.createNewEventFromBEDPE(line); break;
default: e = null;
}
allEvents.add(e);
}
input.close();
}
System.out.println("Total events: "+allEvents.size());
/*VCF Header*/
//PrintWriter writer = new PrintWriter("/Users/schroeder/Downloads/VCF.txt", "UTF-8");
//PrintWriter writer = new PrintWriter("/home/adrianto/Downloads/VCF.txt", "UTF-8");
//PrintWriter writer = new PrintWriter("/home/users/allstaff/schroeder/tools/GenotypeBreakpoints/VCF.txt", "UTF-8");
PrintWriter writer = new PrintWriter(outputVCF, "UTF-8");
createVCFHeader(writer);
/*
* Create nodes data structure that combines close events into the same
* genomic node
*/
Hashtable<String, TreeSet<GenomicNode>> genomicNodes = new Hashtable<String, TreeSet<GenomicNode>>();
//parse all events and create new nodes
for (Event e: allEvents){
addEventToNodeList(e, genomicNodes, true);
addEventToNodeList(e, genomicNodes, false);
}
//establish distance for "close" events according to algorithm
int maxDistanceForNodeMerge = 15;
// switch(algorithm){
// case SOCRATES: maxDistanceForNodeMerge = 15; break;
// case DELLY: maxDistanceForNodeMerge = 100; break;
// case CREST: maxDistanceForNodeMerge = 15; break;
// case GUSTAF: maxDistanceForNodeMerge = 15; break;
// default: System.err.println("Node merge distance set to 0!");
// }
//static parameter to classify single inversions as FP or TP
final boolean classifySimpleInversion = false;
//iterate through node sets and merge nodes where necessary
//also checks each node for redundant members
//TODO: handle redundant members
for(Entry<String, TreeSet<GenomicNode>> tableEntry: genomicNodes.entrySet()) {
int nodesMerged = 0;
GenomicNode[] staticList = new GenomicNode[tableEntry.getValue().size()];
tableEntry.getValue().toArray(staticList);
if(staticList.length == 0)
break;
GenomicNode lastNode = staticList[0], currentNode = null;
for(int i = 1; i < staticList.length; i++){
currentNode = staticList[i];
if(currentNode.getStart().distanceTo(lastNode.getEnd()) < maxDistanceForNodeMerge){
// System.out.println("Merging Node at "+lastNode.getStart()+" with node at "+currentNode.getStart());
// for(Event e:lastNode.getEvents()){
// System.out.println(e);
// }
// System.out.println("----");
// for(Event e:currentNode.getEvents()){
// System.out.println(e);
// }
lastNode.mergeWithNode(currentNode);
if(!tableEntry.getValue().remove(currentNode))
System.out.println("NO CAN DO");
nodesMerged++;
} else {
lastNode.checkForRedundantEvents(maxDistanceForNodeMerge);
lastNode = currentNode;
}
}
lastNode.checkForRedundantEvents(maxDistanceForNodeMerge);
System.out.println("Nodes merged: "+nodesMerged);
}
System.out.println("Events merged: "+GenomicNode.global_event_merge_counter);
//String goldStandard = args[1].substring(0, 22)+"_2.fa";
//String goldStandard = "/home/users/allstaff/schroeder/GenotypeBreakpoints/data/ecoli/SV_list_2.txt";
//compareToGoldStandard(goldStandard, genomicNodes, 150, true);
if(goldStandard != null)
compareToGoldStandard(goldStandard, genomicNodes, 150, false);
String tempInfo = null;
//iterate through node sets again, and genotype events
for(Entry<String, TreeSet<GenomicNode>> tableEntry: genomicNodes.entrySet()) {
System.out.println("Nodes on chr:"+tableEntry.getValue().size());
for(GenomicNode currentNode: tableEntry.getValue()){
//iterate through all event-event pairing in this node and assess for complex events
Event e1, e2;
HashSet<Event> removeEvents = new HashSet<Event>();
HashSet<ComplexEvent> newComplexEvents = new HashSet<ComplexEvent>();
ComplexEvent newComplexEvent = null;
for(int i=0; i<currentNode.getEvents().size(); i++){
e1 = currentNode.getEvents().get(i);
for(int j=0; j<currentNode.getEvents().size(); j++){
e2 = currentNode.getEvents().get(j);
if(e1 == e2 || removeEvents.contains(e2) || removeEvents.contains(e1)
|| e1.otherNode(currentNode) == currentNode || e2.otherNode(currentNode) == currentNode)
continue;
switch(e1.getType()){
//inversions
case INV1: {
if(e2.getType() == EVENT_TYPE.INV2 && Event.sameNodeSets(e1, e2)){
//System.out.println("Complex inversion between "+e1+" and "+e2);
GenomicCoordinate invstart = (e1.getC1().compareTo(e1.getC2()) < 0? e1.getC1() : e1.getC2());
GenomicCoordinate invend = (e2.getC2().compareTo(e2.getC1()) < 0? e2.getC1() : e2.getC2());
//System.out.println(e1.getC1()+"\t"+e1.getC2()+"\t"+e2.getC1()+"\t"+e2.getC2()+"\t"+invstart+"\t"+invend);
newComplexEvent = new ComplexEvent(invstart, invend, EVENT_TYPE.COMPLEX_INVERSION, (new Event[] {e1, e2}), currentNode);
//newComplexEvent.setId(e1.getId());
newComplexEvent.setCoord(invstart);
newComplexEvent.setId(e1.getId()+"+"+e2.getId());
newComplexEvent.setRef(e1.getRef());
newComplexEvent.setAlt("<CIV>");
newComplexEvent.setFilter(e1.getFilter());
newComplexEvent.setQual(e1.getQual());
// tempInfo = e1.getInfo();
// //System.out.println(tempInfo+"\n");
// if (tempInfo.contains("SVTYPE")){
// tmpOld = tempInfo.substring(tempInfo.indexOf("SVTYPE=")+7, tempInfo.indexOf("SVTYPE=")+10);
// tmpNew = newComplexEvent.getAlt();
// tempInfo=tempInfo.replace(tmpOld, tmpNew);
// tmpOld = tempInfo.substring(tempInfo.indexOf("CHR2=")+5, tempInfo.indexOf(";",tempInfo.indexOf("CHR2=")));
// tmpNew = invend.getChr();
// tempInfo=tempInfo.replace(tmpOld, tmpNew);
// tmpOld = tempInfo.substring(tempInfo.indexOf(";END=")+5, tempInfo.indexOf(";CT",tempInfo.indexOf(";END=")));
// tmpNew = Integer.toString(invend.getPos());
// tempInfo.replace(tmpOld, tmpNew);
// newComplexEvent.setInfo(tempInfo);
// }
double readDepth = getReadDepth(samReader, invstart.getChr(), invstart.getPos(), invend.getPos());
//tempInfo="SVTYPE="+newComplexEvent.getAlt().substring(1, 4)+"; CHR2="+invend.getChr()+"; END="+Integer.toString(invend.getPos());
tempInfo="SVTYPE="+newComplexEvent.getAlt().substring(1, 4)+";CHR2="+invend.getChr()+";END="+Integer.toString(invend.getPos())+";ADP="+readDepth;
newComplexEvent.setInfo(tempInfo);
//writer.write(newComplexEvent.getC1().getChr()+"\t"+invstart+"\t"+newComplexEvent.getId()+"\t"+newComplexEvent.getRef()+"\t"+newComplexEvent.getAlt()+"\t"+newComplexEvent.getQual()+"\t"+newComplexEvent.getFilter()+"\t"+newComplexEvent.getInfo()+"\n");
//currentNode?
//System.out.println(currentNode.getStart().toString());
// System.out.println(currentNode.getEnd().toString());
}
else if(e2.getType() == EVENT_TYPE.INV2 ){
GenomicNode other1 = e1.otherNode(currentNode), other2 = e2.otherNode(currentNode);
if(other1.compareTo(other2) > 0){
Event e3 = other1.existsDeletionEventTo(other2);
if(e3 != null){
GenomicCoordinate invstart = (e2.getNode(true) == currentNode ? e2.getC2() : e2.getC1() ),
invend = (e1.getNode(true) == currentNode ? e1.getC2() : e1.getC1() ),
insert = (e1.getNode(true) == currentNode ? e1.getC1() : e1.getC2() );
newComplexEvent = new ComplexEvent(invstart, invend, EVENT_TYPE.COMPLEX_INVERTED_TRANSLOCATION, (new Event[] {e1, e2, e3}), currentNode, insert);
//newComplexEvent.setId(e1.getId());
newComplexEvent.setCoord(invstart);
newComplexEvent.setId(e1.getId()+"+"+e2.getId());
newComplexEvent.setRef(e1.getRef());
newComplexEvent.setAlt("<CVT>");
newComplexEvent.setFilter(e1.getFilter());
newComplexEvent.setQual(e1.getQual());
// tempInfo = e1.getInfo();
// //System.out.println(tempInfo+"\n");
// if (tempInfo.contains("SVTYPE")){
// tmpOld = tempInfo.substring(tempInfo.indexOf("SVTYPE=")+7, tempInfo.indexOf("SVTYPE=")+10);
// tmpNew = newComplexEvent.getAlt();
// tempInfo=tempInfo.replace(tmpOld, tmpNew);
// tmpOld = tempInfo.substring(tempInfo.indexOf("CHR2=")+5, tempInfo.indexOf(";",tempInfo.indexOf("CHR2=")));
// tmpNew = invend.getChr();
// tempInfo=tempInfo.replace(tmpOld, tmpNew);
// tmpOld = tempInfo.substring(tempInfo.indexOf(";END=")+5, tempInfo.indexOf(";CT",tempInfo.indexOf(";END=")));
// tmpNew = Integer.toString(invend.getPos());
// tempInfo.replace(tmpOld, tmpNew);
// newComplexEvent.setInfo(tempInfo);
// }
double readDepth = getReadDepth(samReader, invstart.getChr(), invstart.getPos(), invend.getPos());
//tempInfo="SVTYPE="+newComplexEvent.getAlt().substring(1, 4)+"; CHR2="+invend.getChr()+"; END="+Integer.toString(invend.getPos());
tempInfo="SVTYPE="+newComplexEvent.getAlt().substring(1, 4)+";CHR2="+invend.getChr()+";END="+Integer.toString(invend.getPos())+";ADP="+readDepth;
newComplexEvent.setInfo(tempInfo);
//writer.write(newComplexEvent.getC1().getChr()+"\t"+invstart+"\t"+newComplexEvent.getId()+"\t"+newComplexEvent.getRef()+"\t"+newComplexEvent.getAlt()+"\t"+newComplexEvent.getQual()+"\t"+newComplexEvent.getFilter()+"\t"+newComplexEvent.getInfo()+"\n");
} else {
//System.out.println("INVDUP!"+e1+e2);
GenomicCoordinate invstart = (e2.getNode(true) == currentNode ? e2.getC2() : e2.getC1() ),
invend = (e1.getNode(true) == currentNode ? e1.getC2() : e1.getC1() ),
insert = (e1.getNode(true) == currentNode ? e1.getC1() : e1.getC2() );
newComplexEvent = new ComplexEvent(invstart, invend, EVENT_TYPE.COMPLEX_INVERTED_DUPLICATION, (new Event[] {e1, e2}), currentNode, insert);
//newComplexEvent.setId(e1.getId());
newComplexEvent.setCoord(invstart);
newComplexEvent.setId(e1.getId()+"+"+e2.getId());
newComplexEvent.setRef(e1.getRef());
newComplexEvent.setAlt("<CVD>");
newComplexEvent.setFilter(e1.getFilter());
newComplexEvent.setQual(e1.getQual());
// tempInfo = e1.getInfo();
// //System.out.println(tempInfo+"\n");
// if (tempInfo.contains("SVTYPE")){
// tmpOld = tempInfo.substring(tempInfo.indexOf("SVTYPE=")+7, tempInfo.indexOf("SVTYPE=")+10);
// tmpNew = newComplexEvent.getAlt();
// tempInfo=tempInfo.replace(tmpOld, tmpNew);
// tmpOld = tempInfo.substring(tempInfo.indexOf("CHR2=")+5, tempInfo.indexOf(";",tempInfo.indexOf("CHR2=")));
// tmpNew = invend.getChr();
// tempInfo=tempInfo.replace(tmpOld, tmpNew);
// tmpOld = tempInfo.substring(tempInfo.indexOf(";END=")+5, tempInfo.indexOf(";CT",tempInfo.indexOf(";END=")));
// tmpNew = Integer.toString(invend.getPos());
// tempInfo.replace(tmpOld, tmpNew);
// newComplexEvent.setInfo(tempInfo);
// }
double readDepth = getReadDepth(samReader, invstart.getChr(), invstart.getPos(), invend.getPos());
//tempInfo="SVTYPE="+newComplexEvent.getAlt().substring(1, 4)+"; CHR2="+invend.getChr()+"; END="+Integer.toString(invend.getPos());
// tempInfo="SVTYPE="+newComplexEvent.getAlt().substring(1, 4)+"; CHR2="+invend.getChr()+"; END="+Integer.toString(invend.getPos())+"; ADP="+readDepth;
tempInfo="SVTYPE="+newComplexEvent.getAlt().substring(1, 4)+";CHR2="+invstart.getChr()+";START="+Integer.toString(invstart.getPos())+";END="+Integer.toString(invend.getPos())+";ADP="+readDepth;
newComplexEvent.setInfo(tempInfo);
newComplexEvent.setCoord(insert);
//writer.write(newComplexEvent.getC1().getChr()+"\t"+invstart+"\t"+newComplexEvent.getId()+"\t"+newComplexEvent.getRef()+"\t"+newComplexEvent.getAlt()+"\t"+newComplexEvent.getQual()+"\t"+newComplexEvent.getFilter()+"\t"+newComplexEvent.getInfo()+"\n");
}
}
}
else {
//unknown pairing
}
break;
}
//duplications and translocations
case DEL: {
if(e2.getType() == EVENT_TYPE.TAN){
GenomicNode other1 = e1.otherNode(currentNode), other2 = e2.otherNode(currentNode);
if(other1.compareTo(other2) < 0 && currentNode.compareTo(other1) < 0
|| other2.compareTo(other1) < 0 && other1.compareTo(currentNode) < 0){
Event e3 = other1.existsDeletionEventTo(other2);
if(e3 != null){
//System.out.println("Translocation between "+e1+ " and "+ e2);
//intrachromosomal translocations are actually ambiguous as to where they come from and got to
//as a convention, we call the smaller bit the translocated one inserted into the larger bit.
if(e1.size() < e3.size()) {
//area under e1 is translocated
GenomicCoordinate transtart, tranend;
if(e1.getC1().compareTo(e1.getC2()) < 0) { // don't assume ordered coordinates
transtart = e1.getC1();
tranend = e1.getC2();
} else {
transtart = e1.getC2();
tranend = e1.getC1();
}
GenomicCoordinate traninsert = (e2.getNode(true) == currentNode? e2.getC2() : e2.getC1());
GenomicNode hostingNode = (e2.getNode(true) == currentNode? e2.getNode(false) : e2.getNode(true));
newComplexEvent = new ComplexEvent(transtart, tranend, EVENT_TYPE.COMPLEX_TRANSLOCATION, (new Event[] {e1, e2, e3}), hostingNode, traninsert);
//newComplexEvent.setId(e1.getId());
newComplexEvent.setCoord(transtart);
newComplexEvent.setId(e1.getId()+"+"+e2.getId()+"+"+e3.getId());
newComplexEvent.setRef(e1.getRef());
newComplexEvent.setAlt("<TRA>");
newComplexEvent.setFilter(e1.getFilter());
newComplexEvent.setQual(e1.getQual());
// tempInfo = e1.getInfo();
// //System.out.println(tempInfo+"\n");
// if (tempInfo.contains("SVTYPE")){
// tmpOld = tempInfo.substring(tempInfo.indexOf("SVTYPE=")+7, tempInfo.indexOf("SVTYPE=")+10);
// tmpNew = newComplexEvent.getAlt();
// tempInfo=tempInfo.replace(tmpOld, tmpNew);
// tmpOld = tempInfo.substring(tempInfo.indexOf("CHR2=")+5, tempInfo.indexOf(";",tempInfo.indexOf("CHR2=")));
// tmpNew = tranend.getChr();
// tempInfo=tempInfo.replace(tmpOld, tmpNew);
// tmpOld = tempInfo.substring(tempInfo.indexOf(";END=")+5, tempInfo.indexOf(";CT",tempInfo.indexOf(";END=")));
// tmpNew = Integer.toString(tranend.getPos());
// tempInfo.replace(tmpOld, tmpNew);
// newComplexEvent.setInfo(tempInfo);
// }
double readDepth = getReadDepth(samReader, transtart.getChr(), transtart.getPos(), tranend.getPos());
//tempInfo="SVTYPE="+newComplexEvent.getAlt().substring(1, 4)+"; CHR2="+tranend.getChr()+"; END="+Integer.toString(tranend.getPos());
tempInfo="SVTYPE="+newComplexEvent.getAlt().substring(1, 4)+";CHR2="+transtart.getChr()+";START="+Integer.toString(transtart.getPos())+";END="+Integer.toString(tranend.getPos())+";ADP="+readDepth;
newComplexEvent.setInfo(tempInfo);
newComplexEvent.setCoord(traninsert);
//writer.write(newComplexEvent.getC1().getChr()+"\t"+newComplexEvent.getC1().getPos()+"\t"+newComplexEvent.getId()+"\t"+newComplexEvent.getRef()+"\t"+newComplexEvent.getAlt()+"\t"+newComplexEvent.getQual()+"\t"+newComplexEvent.getFilter()+"\t"+newComplexEvent.getInfo()+"\n");
} else {
//area under e3 is translocated
GenomicCoordinate transtart, tranend;
if(e3.getC1().compareTo(e3.getC2()) < 0) {
transtart = e3.getC1();
tranend = e3.getC2();
} else {
transtart = e3.getC2();
tranend = e3.getC1();
}
GenomicCoordinate traninsert = (e2.getNode(true) == currentNode? e2.getC1() : e2.getC2());
newComplexEvent = new ComplexEvent(transtart, tranend, EVENT_TYPE.COMPLEX_TRANSLOCATION, (new Event[] {e1, e2, e3}), currentNode, traninsert);
newComplexEvent.setCoord(transtart);
//newComplexEvent.setId(e1.getId());
newComplexEvent.setId(e1.getId()+"+"+e2.getId()+"+"+e3.getId());
newComplexEvent.setRef(e1.getRef());
newComplexEvent.setAlt("<TRA>");
newComplexEvent.setFilter(e1.getFilter());
newComplexEvent.setQual(e1.getQual());
// tempInfo = e1.getInfo();
// //System.out.println(tempInfo+"\n");
// if (tempInfo.contains("SVTYPE")){
// tmpOld = tempInfo.substring(tempInfo.indexOf("SVTYPE=")+7, tempInfo.indexOf("SVTYPE=")+10);
// tmpNew = newComplexEvent.getAlt();
// tempInfo=tempInfo.replace(tmpOld, tmpNew);
// tmpOld = tempInfo.substring(tempInfo.indexOf("CHR2=")+5, tempInfo.indexOf(";",tempInfo.indexOf("CHR2=")));
// tmpNew = tranend.getChr();
// tempInfo=tempInfo.replace(tmpOld, tmpNew);
// tmpOld = tempInfo.substring(tempInfo.indexOf(";END=")+5, tempInfo.indexOf(";CT",tempInfo.indexOf(";END=")));
// tmpNew = Integer.toString(tranend.getPos());
// tempInfo.replace(tmpOld, tmpNew);
// newComplexEvent.setInfo(tempInfo);
// }
double readDepth = getReadDepth(samReader, transtart.getChr(), transtart.getPos(), tranend.getPos());
//tempInfo="SVTYPE="+newComplexEvent.getAlt().substring(1, 4)+"; CHR2="+tranend.getChr()+"; END="+Integer.toString(tranend.getPos());
tempInfo="SVTYPE="+newComplexEvent.getAlt().substring(1, 4)+";CHR2="+transtart.getChr()+";START="+Integer.toString(transtart.getPos())+";END="+Integer.toString(tranend.getPos())+";ADP="+readDepth;
newComplexEvent.setInfo(tempInfo);
newComplexEvent.setCoord(traninsert);
//writer.write(newComplexEvent.getC1().getChr()+"\t"+newComplexEvent.getC1().getPos()+"\t"+newComplexEvent.getId()+"\t"+newComplexEvent.getRef()+"\t"+newComplexEvent.getAlt()+"\t"+newComplexEvent.getQual()+"\t"+newComplexEvent.getFilter()+"\t"+newComplexEvent.getInfo()+"\n");
}
}
else {
//System.out.println("Duplication between "+e1+ " and "+ e2);
GenomicCoordinate dupstart, dupend, insert;
if(other1.compareTo(other2) < 0){
//duplicated bit is downstream of currentNode
dupstart = (e1.getNode(true) == currentNode? e1.getC2() : e1.getC1());
dupend = (e2.getNode(true) == currentNode? e2.getC2() : e2.getC1());
insert = (e1.getNode(true) == currentNode? e1.getC1() : e1.getC2());
newComplexEvent = new ComplexEvent(dupstart, dupend, EVENT_TYPE.COMPLEX_DUPLICATION, (new Event[] {e1, e2}), currentNode, insert);
newComplexEvent.setCoord(dupstart);
//newComplexEvent.setId(e1.getId());
newComplexEvent.setId(e1.getId()+"+"+e2.getId());
newComplexEvent.setRef(e1.getRef());
newComplexEvent.setAlt("<DUP>");
newComplexEvent.setFilter(e1.getFilter());
newComplexEvent.setQual(e1.getQual());
// tempInfo = e1.getInfo();
// //System.out.println(tempInfo+"\n");
// if (tempInfo.contains("SVTYPE")){
// tmpOld = tempInfo.substring(tempInfo.indexOf("SVTYPE=")+7, tempInfo.indexOf("SVTYPE=")+10);
// tmpNew = newComplexEvent.getAlt();
// tempInfo=tempInfo.replace(tmpOld, tmpNew);
// tmpOld = tempInfo.substring(tempInfo.indexOf("CHR2=")+5, tempInfo.indexOf(";",tempInfo.indexOf("CHR2=")));
// tmpNew = dupend.getChr();
// tempInfo=tempInfo.replace(tmpOld, tmpNew);
// tmpOld = tempInfo.substring(tempInfo.indexOf(";END=")+5, tempInfo.indexOf(";CT",tempInfo.indexOf(";END=")));
// tmpNew = Integer.toString(dupend.getPos());
// tempInfo.replace(tmpOld, tmpNew);
// newComplexEvent.setInfo(tempInfo);
// }
double readDepth = getReadDepth(samReader, dupstart.getChr(), dupstart.getPos(), dupend.getPos());
//tempInfo="SVTYPE="+newComplexEvent.getAlt().substring(1, 4)+"; CHR2="+dupend.getChr()+"; END="+Integer.toString(dupend.getPos());
tempInfo="SVTYPE="+newComplexEvent.getAlt().substring(1, 4)+";CHR2="+dupstart.getChr()+";START="+Integer.toString(dupstart.getPos())+";END="+Integer.toString(dupend.getPos())+";ADP="+readDepth;
newComplexEvent.setInfo(tempInfo);
newComplexEvent.setCoord(insert);
//writer.write(newComplexEvent.getC1().getChr()+"\t"+newComplexEvent.getC1().getPos()+"\t"+newComplexEvent.getId()+"\t"+newComplexEvent.getRef()+"\t"+newComplexEvent.getAlt()+"\t"+newComplexEvent.getQual()+"\t"+newComplexEvent.getFilter()+"\t"+newComplexEvent.getInfo()+"\n");
} else {
//duplication upstream of currentNode
dupstart = (e2.getNode(true) == currentNode? e2.getC2() : e2.getC1());
dupend = (e1.getNode(true) == currentNode? e1.getC2() : e1.getC1());
insert = (e2.getNode(true) == currentNode? e2.getC1() : e2.getC2());
newComplexEvent = new ComplexEvent(dupstart, dupend, EVENT_TYPE.COMPLEX_DUPLICATION, (new Event[] {e1, e2}), currentNode, insert);
newComplexEvent.setCoord(dupstart);
//newComplexEvent.setId(e1.getId());
newComplexEvent.setId(e1.getId()+"+"+e2.getId());
newComplexEvent.setRef(e1.getRef());
newComplexEvent.setAlt("<DUP>");
newComplexEvent.setFilter(e1.getFilter());
newComplexEvent.setQual(e1.getQual());
// tempInfo = e1.getInfo();
// //System.out.println(tempInfo+"\n");
// if (tempInfo.contains("SVTYPE")){
// tmpOld = tempInfo.substring(tempInfo.indexOf("SVTYPE=")+7, tempInfo.indexOf("SVTYPE=")+10);
// tmpNew = newComplexEvent.getAlt();
// tempInfo=tempInfo.replace(tmpOld, tmpNew);
// tmpOld = tempInfo.substring(tempInfo.indexOf("CHR2=")+5, tempInfo.indexOf(";",tempInfo.indexOf("CHR2=")));
// tmpNew = dupend.getChr();
// tempInfo=tempInfo.replace(tmpOld, tmpNew);
// tmpOld = tempInfo.substring(tempInfo.indexOf(";END=")+5, tempInfo.indexOf(";CT",tempInfo.indexOf(";END=")));
// tmpNew = Integer.toString(dupend.getPos());
// tempInfo.replace(tmpOld, tmpNew);
// newComplexEvent.setInfo(tempInfo);
// }
double readDepth = getReadDepth(samReader, dupstart.getChr(), dupstart.getPos(), dupend.getPos());
//tempInfo="SVTYPE="+newComplexEvent.getAlt().substring(1, 4)+"; CHR2="+dupend.getChr()+"; END="+Integer.toString(dupend.getPos());
tempInfo="SVTYPE="+newComplexEvent.getAlt().substring(1, 4)+";CHR2="+dupstart.getChr()+";START="+Integer.toString(dupstart.getPos())+";END="+Integer.toString(dupend.getPos())+";ADP="+readDepth;
newComplexEvent.setInfo(tempInfo);