Skip to content

Commit

Permalink
new handling of complex events, events composition and different VCF
Browse files Browse the repository at this point in the history 
output.
  • Loading branch information
@jibsch
jibsch committed Jan 12, 2017
1 parent 9cb5f62 commit 467032f
Show file tree
Hide file tree
Showing 5 changed files with 77 additions and 26 deletions.
2 changes: 1 addition & 1 deletion pom.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
<groupId>au.edu.wehi</groupId>
<artifactId>clove</artifactId>
<packaging>jar</packaging>
<version>0.11</version>
<version>0.12</version>
<name>clove</name>
<url>http://github.com/PapenfussLab/clove</url>
<properties>
Expand Down
43 changes: 25 additions & 18 deletions src/main/java/au/edu/wehi/clove/Clove.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -276,6 +276,10 @@ private static void compareToGoldStandard(String goldFileName, Hashtable<String,

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();
Expand All @@ -289,6 +293,7 @@ private static void compareToGoldStandard(String goldFileName, Hashtable<String,
}
if(e==null){
//System.out.println("DEFINITE FN: "+goldLine);
statsByType.get(typeConversion.get(type))[2]++;
goldLine = gold.readLine();
continue;
}
Expand Down Expand Up @@ -488,6 +493,7 @@ public static void createVCFHeader(PrintWriter output) throws IOException{
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");
Expand Down Expand Up @@ -565,7 +571,7 @@ public static void main(String[] args) throws IOException {
try {
samReader=new SAMFileReader(new File(args[argindex + 1]));
argindex += 2;
} catch (IllegalArgumentException e){
} catch (Exception e){
System.err.println("Unable to load bam file.");
System.exit(1);
}
Expand Down Expand Up @@ -748,7 +754,7 @@ public static void main(String[] args) throws IOException {
// }
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="+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");
Expand Down Expand Up @@ -788,7 +794,7 @@ else if(e2.getType() == EVENT_TYPE.INV2 ){
// }
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="+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 {
Expand Down Expand Up @@ -821,7 +827,7 @@ else if(e2.getType() == EVENT_TYPE.INV2 ){
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;
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");
Expand Down Expand Up @@ -859,7 +865,7 @@ else if(e2.getType() == EVENT_TYPE.INV2 ){
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());
newComplexEvent.setId(e1.getId()+"+"+e2.getId()+"+"+e3.getId());
newComplexEvent.setRef(e1.getRef());
newComplexEvent.setAlt("<TRA>");
newComplexEvent.setFilter(e1.getFilter());
Expand All @@ -880,7 +886,7 @@ else if(e2.getType() == EVENT_TYPE.INV2 ){
// }
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;
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");
Expand All @@ -898,7 +904,7 @@ else if(e2.getType() == EVENT_TYPE.INV2 ){
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());
newComplexEvent.setId(e1.getId()+"+"+e2.getId()+"+"+e3.getId());
newComplexEvent.setRef(e1.getRef());
newComplexEvent.setAlt("<TRA>");
newComplexEvent.setFilter(e1.getFilter());
Expand All @@ -919,7 +925,7 @@ else if(e2.getType() == EVENT_TYPE.INV2 ){
// }
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;
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");
Expand Down Expand Up @@ -957,7 +963,7 @@ else if(e2.getType() == EVENT_TYPE.INV2 ){
// }
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;
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");
Expand Down Expand Up @@ -990,7 +996,7 @@ else if(e2.getType() == EVENT_TYPE.INV2 ){
// }
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;
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");
Expand Down Expand Up @@ -1026,7 +1032,7 @@ else if(e2.getType() == EVENT_TYPE.INV2 ){
newComplexEvent = new ComplexEvent(eventStart, eventEnd, EVENT_TYPE.COMPLEX_INTERCHROMOSOMAL_TRANSLOCATION, new Event[] {e1, e2, e3}, currentNode, eventInsert);
newComplexEvent.setCoord(eventStart);
//newComplexEvent.setId(e1.getId());
newComplexEvent.setId(e1.getId()+"+"+e2.getId());
newComplexEvent.setId(e1.getId()+"+"+e2.getId()+"+"+e3.getId());
newComplexEvent.setRef(e1.getRef());
newComplexEvent.setAlt("<CIT>");
newComplexEvent.setFilter(e1.getFilter());
Expand All @@ -1046,7 +1052,7 @@ else if(e2.getType() == EVENT_TYPE.INV2 ){
// newComplexEvent.setInfo(tempInfo);
// }
double readDepth = getReadDepth(samReader, eventStart.getChr(), eventStart.getPos(), eventEnd.getPos());
tempInfo="SVTYPE="+newComplexEvent.getAlt().substring(1, 4)+"; CHR2="+eventStart.getChr()+"; START="+Integer.toString(eventStart.getPos())+"; END="+Integer.toString(eventEnd.getPos())+"; ADP="+readDepth;
tempInfo="SVTYPE="+newComplexEvent.getAlt().substring(1, 4)+"; CHR2="+eventStart.getChr()+"; START="+Integer.toString(eventStart.getPos())+"; END="+Integer.toString(eventEnd.getPos())+";ADP="+readDepth;
newComplexEvent.setInfo(tempInfo);
newComplexEvent.setCoord(eventInsert);
//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");
Expand Down Expand Up @@ -1074,7 +1080,7 @@ else if(e2.getType() == EVENT_TYPE.INV2 ){
// newComplexEvent.setInfo(tempInfo);
// }
double readDepth = getReadDepth(samReader, eventStart.getChr(), eventStart.getPos(), eventEnd.getPos());
tempInfo="SVTYPE="+newComplexEvent.getAlt().substring(1, 4)+"; CHR2="+eventStart.getChr()+"; START="+Integer.toString(eventStart.getPos())+"; END="+Integer.toString(eventEnd.getPos())+"; ADP="+readDepth;
tempInfo="SVTYPE="+newComplexEvent.getAlt().substring(1, 4)+";CHR2="+eventStart.getChr()+";START="+Integer.toString(eventStart.getPos())+";END="+Integer.toString(eventEnd.getPos())+";ADP="+readDepth;
newComplexEvent.setInfo(tempInfo);
newComplexEvent.setCoord(eventInsert);
//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");
Expand Down Expand Up @@ -1117,7 +1123,7 @@ else if(e2.getType() == EVENT_TYPE.INV2 ){
// newComplexEvent.setInfo(tempInfo);
// }
double readDepth = getReadDepth(samReader, eventStart.getChr(), eventStart.getPos(), eventEnd.getPos());
tempInfo="SVTYPE="+newComplexEvent.getAlt().substring(1, 4)+"; CHR2="+eventStart.getChr()+"; START="+Integer.toString(eventStart.getPos())+"; END="+Integer.toString(eventEnd.getPos())+"; ADP="+readDepth;
tempInfo="SVTYPE="+newComplexEvent.getAlt().substring(1, 4)+";CHR2="+eventStart.getChr()+";START="+Integer.toString(eventStart.getPos())+";END="+Integer.toString(eventEnd.getPos())+";ADP="+readDepth;
newComplexEvent.setInfo(tempInfo);
newComplexEvent.setCoord(eventInsert);
//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");
Expand Down Expand Up @@ -1145,7 +1151,7 @@ else if(e2.getType() == EVENT_TYPE.INV2 ){
// newComplexEvent.setInfo(tempInfo);
// }
double readDepth = getReadDepth(samReader, eventStart.getChr(), eventStart.getPos(), eventEnd.getPos());
tempInfo="SVTYPE="+newComplexEvent.getAlt().substring(1, 4)+"; CHR2="+eventStart.getChr()+"; START="+Integer.toString(eventStart.getPos())+"; END="+Integer.toString(eventEnd.getPos())+"; ADP="+readDepth;
tempInfo="SVTYPE="+newComplexEvent.getAlt().substring(1, 4)+";CHR2="+eventStart.getChr()+";START="+Integer.toString(eventStart.getPos())+";END="+Integer.toString(eventEnd.getPos())+";ADP="+readDepth;
newComplexEvent.setInfo(tempInfo);
newComplexEvent.setCoord(eventInsert);
//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");
Expand Down Expand Up @@ -1231,7 +1237,7 @@ else if(e2.getType() == EVENT_TYPE.INV2 ){
//System.out.print("read depth for event: "+readDepth+"\t");
}
e.setAlt("<DEL>");
e.setInfo(e.getInfo()+"; ADP="+readDepth );
e.setInfo(e.getInfo()+";ADP="+readDepth );
break;
case TAN:
//double readDepth = meanReadDepth(reader, e.getC1().getPos()+1, e.getC2().getPos()-1);
Expand All @@ -1246,7 +1252,7 @@ else if(e2.getType() == EVENT_TYPE.INV2 ){
//System.out.print("read depth for event: "+readDepth+"\t");
}
e.setAlt("<DUP>");
e.setInfo(e.getInfo()+"; ADP="+readDepth );
e.setInfo(e.getInfo()+";ADP="+readDepth );
break;
case COMPLEX_DUPLICATION:
case COMPLEX_INVERTED_DUPLICATION:
Expand Down Expand Up @@ -1315,6 +1321,7 @@ else if(e2.getType() == EVENT_TYPE.INV2 ){
writer.write(e.toVcf()+"\n");
} catch (NullPointerException npe) {
System.out.println("VCF fail");
System.err.println(npe);
}
}
}
Expand All @@ -1324,7 +1331,7 @@ else if(e2.getType() == EVENT_TYPE.INV2 ){
samReader.close();
//End Time
long endTime = System.nanoTime();
System.out.println("Took "+(endTime - startTime) + " ns");
System.out.println("Took "+(endTime - startTime)/1000000000 + " seconds");
}


Expand Down
13 changes: 12 additions & 1 deletion src/main/java/au/edu/wehi/clove/ComplexEvent.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,12 +11,23 @@ public ComplexEvent(GenomicCoordinate c1, GenomicCoordinate c2,
this.eventsInvolvedInComplexEvent = involvedEvents;
super.setNode(hostingNode, true);
super.setNode(hostingNode, false);

// String[] ids = new String[involvedEvents.length];
// for (int i=0; i<ids.length;i++){ ids[i] = involvedEvents[i].getId();}
// String newId = String.join("+", ids) ;
// super.setId(newId);
for(Event e: involvedEvents){
super.addCaller(e.getCalledBy());
super.increaseCalls(e.getCalledTimes());
}
}
public ComplexEvent(GenomicCoordinate c1, GenomicCoordinate c2,
EVENT_TYPE type, Event[] involvedEvents, GenomicNode hostingNode, GenomicCoordinate insertionPoint) {
this(c1,c2,type,involvedEvents,hostingNode);
this.insertionPoint = insertionPoint;
// String[] ids = new String[involvedEvents.length];
// for (int i=0; i<ids.length;i++){ ids[i] = involvedEvents[i].getId();}
// String newId = String.join("+", ids) ;
// super.setId(newId);
}

public Event[] getEventsInvolvedInComplexEvent(){
Expand Down

0 comments on commit 467032f

Please sign in to comment.