ValidAlignmentEndReadFilter

Description

Keep only reads where the read end corresponds to a proper alignment – that is, the read ends after the start (non-negative number of bases in the reference).

This is calculated as:

end - start + 1 ≥ 0
where
start = 1-based inclusive leftmost position of the clipped sequence (0 if no position)
end = 1-based inclusive rightmost position of the clipped sequence (0 if unmapped)


Note: keep also unmapped reads (align to zero bases in the reference). See MappedReadFilter for criteria defining an unmapped read.

See additional information in the following pages:

• MappedReadFilter