2.1.8 Split alignment blocks into smaller parts

The WindowSplit filter subdivides blocks into smaller ones of a regular size, typically for window-based analyses. It is possible to generate overlapping windows.

Synopsis:

maf.filter=                                 \
    [...],
    WindowSplit(                            \
        preferred_size=1000,                \
        align=center,                       \
        keep_small_blocks=no),              \
    [...]

Arguments:

preferred_size={int>0}

The preferred size for the output windows.

align={ragged_left|ragged_right|center|adjust}

Specifies how to align windows on the block:

keep_small_blocks = {boolean}

Tell if blocks with an original size smaller that the window size should be kept (and untouched). This option only works if the align option is set to adjust. The combination of "align=adjust" and "keep_small_blocks=yes" allows to ensure that blocks do not exceed a given size, without losing any data.

ragged_left

Block   |----------------------------|
Windows |----|----|----|----|----|XXXX

ragged_right

Block   |----------------------------|
Windows XXXX|----|----|----|----|----|

center

Block   |----------------------------|
Windows XX|----|----|----|----|----|XX

adjust

Block   |----------------------------|
Windows |-----|-----|-----|-----|----|

In the first three case, some parts of the original block (shown with X) will be discarded. In the last case, the windows will have at least the specified size, but might be larger.