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.
the mapping quality, phred scaled.
The base qualities, phred scaled.
The base qualities, phred scaled. These are numbers, and are NOT character encoded.
parsed samtools CIGAR object.
Individual components of the CIGAR string (e.
Individual components of the CIGAR string (e.g. "10M"), parsed, and as a Scala buffer.
the contig name (e.
the contig name (e.g. "chr12") that this read was mapped to.
The end of the alignment, exclusive.
The end of the alignment, exclusive. This is the first reference locus AFTER the locus corresponding to the last base in this read.
Whether the read failed predefined vendor checks for quality
Whether the read failed predefined vendor checks for quality
Is this read a duplicate of another?
Is this read a duplicate of another?
Is this read mapped?
Is this read mapped?
Whether read is from a paired-end library
Whether read is from a paired-end library
The nucleotide sequence.
The nucleotide sequence.
the (0-based) reference locus that the first base in this read aligns to.
the (0-based) reference locus that the first base in this read aligns to.
The end of the read's alignment, including any final clipped bases, exclusive.
A read can be "clipped", meaning that some prefix or suffix of it did not align.
A read can be "clipped", meaning that some prefix or suffix of it did not align. This is the start of the whole read's alignment, including any initial clipped bases.
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.