public interface PairedReads
SequenceAlignmentDocument, the expected distance now refers to where a sequence expects to find its mate. If a sequence is placed in the alignment without reverse-complementing, then its expected distance will remain the same as specified above. If the sequence is placed in an alignment reverse-complemented, then its expected distance will be negated (postive <-> negative). So, no matter what the sequencing technology used, when reads are correctly orientated in the alignment, the left-hand read will have a positive expected distance and the right-hand read will have a negative expected distance. For example, if aligned pairs are:
SequenceAlignmentDocumentsimplements this interface. A
SequenceListDocumentcan optionally implement this interface to provide paired read data.
getMateIndex(int)returns the index of the mate sequence in the list (if any) and
getMateExpectedDistance(int)returns the expected distance of the mate.
getImmutablePairedReadManager()returns an immutable view of the paired properties and also provides additional functionality. See
PairedReadManagerThe sequence viewer plugin displays paired reads with a little paired-read icon to the left of their name. For paired reads in an alignment, the sequence viewer also links them together on the same line as long as the 'Link Paired Reads' setting (under 'Advanced') is on. The sequence viewer also has a color scheme to color paired reads based on how close they are to their expected distance.
|Modifier and Type||Method and Description|
An immutable view of the paired reads managed by this list or alignment.
Gets the expected mate distance (also known as predicted median insert size) of this nucleotide sequence from its mate.
Gets the index of the mate (if any) of the nucleotide sequence at this index.
int getMateExpectedDistance(int sequenceIndex)
sequenceIndex- the index of the nucleotide sequence for which to get the mate index of.
getMateIndex(int)will be -1.
int getMateIndex(int sequenceIndex)
sequenceIndex- the index of the nucleotide sequence to get the mate index of