75 lines
3.1 KiB
Java
75 lines
3.1 KiB
Java
|
package edu.mit.broad.picard.util;
|
||
|
|
|
||
|
|
import edu.mit.broad.sam.SAMRecord;
|
||
|
|
|
||
|
|
/**
|
||
|
|
* Utility mthods for pairs of SAMRecords
|
||
|
|
*/
|
||
|
|
public class SamPairUtil {
|
||
|
|
|
||
|
|
// TODO: KT and TF say this is more complicated than what I have here
|
||
|
|
public static boolean isProperPair(final SAMRecord firstEnd, final SAMRecord secondEnd, boolean jumpingLibrary) {
|
||
|
|
if (firstEnd.getReferenceName().equals(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME)) {
|
||
|
|
return false;
|
||
|
|
}
|
||
|
|
if (!firstEnd.getReferenceName().equals(secondEnd.getReferenceName())) {
|
||
|
|
return false;
|
||
|
|
}
|
||
|
|
if (firstEnd.getReadNegativeStrandFlag() == secondEnd.getReadNegativeStrandFlag()) {
|
||
|
|
return false;
|
||
|
|
}
|
||
|
|
final SAMRecord positiveEnd;
|
||
|
|
final SAMRecord negativeEnd;
|
||
|
|
if (firstEnd.getReadNegativeStrandFlag()) {
|
||
|
|
positiveEnd = secondEnd;
|
||
|
|
negativeEnd = firstEnd;
|
||
|
|
} else {
|
||
|
|
positiveEnd = firstEnd;
|
||
|
|
negativeEnd = secondEnd;
|
||
|
|
}
|
||
|
|
if (!jumpingLibrary) {
|
||
|
|
return positiveEnd.getAlignmentStart() < negativeEnd.getAlignmentStart() + negativeEnd.getReadBases().length;
|
||
|
|
} else {
|
||
|
|
return negativeEnd.getAlignmentStart() < positiveEnd.getAlignmentStart() + positiveEnd.getReadBases().length;
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
public static int computeInsertSize(final SAMRecord firstEnd, final SAMRecord secondEnd) {
|
||
|
|
if (firstEnd.getReferenceName().equals(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME)) {
|
||
|
|
return 0;
|
||
|
|
}
|
||
|
|
if (!firstEnd.getReferenceName().equals(secondEnd.getReferenceName())) {
|
||
|
|
return 0;
|
||
|
|
}
|
||
|
|
int firstEnd5PrimePosition = firstEnd.getReadNegativeStrandFlag()? firstEnd.getAlignmentEnd(): firstEnd.getAlignmentStart();
|
||
|
|
int secondEnd5PrimePosition = secondEnd.getReadNegativeStrandFlag()? secondEnd.getAlignmentEnd(): secondEnd.getAlignmentStart();
|
||
|
|
return secondEnd5PrimePosition - firstEnd5PrimePosition;
|
||
|
|
}
|
||
|
|
|
||
|
|
/**
|
||
|
|
* Write the mate info for two SAMRecords
|
||
|
|
*/
|
||
|
|
public static void setMateInfo(final SAMRecord samRecord, final SAMRecord mate) {
|
||
|
|
if (!samRecord.getMateUnmappedFlag()) {
|
||
|
|
samRecord.setMateReferenceName(mate.getReferenceName());
|
||
|
|
samRecord.setMateAlignmentStart(mate.getAlignmentStart());
|
||
|
|
samRecord.setMateNegativeStrandFlag(mate.getReadNegativeStrandFlag());
|
||
|
|
} else {
|
||
|
|
samRecord.setMateReferenceName(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME);
|
||
|
|
samRecord.setMateAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
|
||
|
|
samRecord.setMateUnmappedFlag(true);
|
||
|
|
}
|
||
|
|
if (!mate.getMateUnmappedFlag()) {
|
||
|
|
mate.setMateReferenceName(samRecord.getReferenceName());
|
||
|
|
mate.setMateAlignmentStart(samRecord.getAlignmentStart());
|
||
|
|
mate.setMateNegativeStrandFlag(samRecord.getReadNegativeStrandFlag());
|
||
|
|
} else {
|
||
|
|
mate.setMateReferenceName(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME);
|
||
|
|
mate.setMateAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
|
||
|
|
mate.setMateUnmappedFlag(true);
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
}
|