Methods¶

$alignment = $pileup->alignment

Return the Bio::DB::Bam::Alignment or Bio::DB::Bam::AlignWrapper object representing the aligned read.

$alignment = $pileup->b

This method is an alias for alignment(). It is available for compatibility with the C API.

$qpos = $pileup->qpos

Return the position of this aligned column in read coordinates, using zero-based coordinates.

$pos = $pileup->pos

Return the position of this aligned column in read coordinates, using 1-based coordinates.

$indel = $pileup->indel

If this column is an indel, return a positive integer for an insertion relative to the reference, a negative integer for a deletion relative to the reference, or 0 for no indel at this column.

$is_del = $pileup->is_del

True if the base on the padded read is a deletion.

$level = $pileup->level

If pileup() or fast_pileup() was invoked with the "keep_level" flag, then this method will return a positive integer indicating the level of the read in a printed multiple alignment.

$pileup->is_head

$pileup->is_tail

These fields are defined in bam.h but their interpretation is obscure.