/**
* Returns the mate for a paired-end read. Please note that this method will return an unmapped
* mate for any single end read as well. Do check if the read is paired before calling getMate().
*
* @return The mate, or a constant unmapped mate (for single end reads, or paired end where the
* mate is not found).
*/
public ReadMate getMate() {
if (entry.hasPairAlignmentLink()) {
Alignments.RelatedAlignmentEntry link = entry.getPairAlignmentLink();
String mateChr = getChromosome(link.getTargetIndex());
int mateStart = link.getPosition();
boolean mateNegativeStrand = EntryFlagHelper.isMateReverseStrand(entry);
boolean isReadUnmappedFlag = EntryFlagHelper.isReadUnmapped(entry);
final ReadMate mate =
new ReadMate(mateChr, mateStart, mateNegativeStrand, isReadUnmappedFlag);
return mate;
} else {
return unmappedMate;
}
}
public boolean isPaired() {
if (entry.hasPairFlags()) {
return EntryFlagHelper.isPaired(entry);
} else return false;
}
public String getPairOrientation() {
// LOG.info("getPairOrientation");
String pairOrientation = "";
if (EntryFlagHelper.isPaired(entry)
&& !EntryFlagHelper.isMateUnmapped(entry)
&& entry.getTargetIndex() == entry.getPairAlignmentLink().getTargetIndex()) {
char s1 = EntryFlagHelper.isReadReverseStrand(entry) ? 'R' : 'F';
char s2 = EntryFlagHelper.isMateReverseStrand(entry) ? 'R' : 'F';
char o1 = ' ';
char o2 = ' ';
char[] tmp = new char[4];
if (EntryFlagHelper.isFirstInPair(entry)) {
o1 = '1';
o2 = '2';
} else if (EntryFlagHelper.isSecondInPair(entry)) {
o1 = '2';
o2 = '1';
}
if (getInferredInsertSize() > 0) {
tmp[0] = s1;
tmp[1] = o1;
tmp[2] = s2;
tmp[3] = o2;
} else {
tmp[2] = s1;
tmp[3] = o1;
tmp[0] = s2;
tmp[1] = o2;
}
pairOrientation = new String(tmp);
}
return pairOrientation;
}
/**
* Return true if this alignment is marked "second in pair". Added to suppor bisulfite sequencing
* mode.
*/
public boolean isSecondOfPair() {
return EntryFlagHelper.isSecondInPair(entry);
}
/**
* Return true if this alignment is marked "first in pair". Added to suppor bisulfite sequencing
* mode.
*/
public boolean isFirstOfPair() {
return EntryFlagHelper.isFirstInPair(entry);
}