A mapped read.
Details of the mate read alignment
Details of the mate read alignment
Contig/chromosome of the mate read
0-based start position of the mate read
Insert size between the reads if defined
Whether the mate is on the positive strand
PairedRead is a MappedRead or UnmappedRead with the additional mate information
PairedRead is a MappedRead or UnmappedRead with the additional mate information
UnmappedRead or MappedRead
Unmapped or MappedRead base read
Whether the read is earlier that the the mate read
Alignment location of the mate if it the mate is aligned
The fields in the Read trait are common to any read, whether mapped (aligned) or not.
An unmapped read.
An unmapped read. See the Read trait for field descriptions.
A mapped read. See the Read trait for some of the field descriptions.
the contig name (e.g. "chr12") that this read was mapped to.
the mapping quality, phred scaled.
the (0-based) reference locus that the first base in this read aligns to.
parsed samtools CIGAR object.