2.1.5 OrderFilter: check and eventually discard unordered or overlapping blocks

The OrderFilter filter check if blocks are sorted according to previous block.

Synopsis:

maf.filter=                                 \
    [...],
    OrderFilter(                            \
        reference=ref_genome,               \
        do_unsorted=discard,                \
        do_overlapping=discard),            \
    [...]

Arguments:

reference={string}

The sequence for which coordinates should be checked. Block where the reference sequence is absent will be considered as ordered.

Important note: the alignment is supposed to be projected according to the reference sequence. Using the filter on another species might lead to unexpected behavior, in particular as the the reference species is supposed to be mapped on the + strand only.

do_unsorted={none|discard|error}

Action to perform in case an unsorted block is found (that is, when the right coordinate of the current block is before the left coordinate of the previous one). If ’discard’, the block will be removed. If ’error’, the maffilter with stop with an error.

do_overlapping={none|discard|error}

Action to perform in case an ovelrapping block is found (that is, when the left coordinate of the current block is before the right coordinate of the previous one, and the right coordinate of the current block is not before the left coordinate of the previous one). If ’discard’, the block will be removed. If ’error’, the maffilter with stop with an error.