bx.align.sitemask.quality module

Support for masking out sites in alignments based on sequence quality. Both simple masking of regions below some threshold and masking using the neighborhood quality standard (NQS) are supported. Uses sequence quality values stored in a bx.binned_array.FileBinnedArray.

class bx.align.sitemask.quality.NQS(qualfiles=None, qualspecies=None, minqual=None, mask='?', cache=100)

Bases: Masker

class bx.align.sitemask.quality.Simple(qualfiles=None, qualspecies=None, minqual=None, mask='?', cache=100)

Bases: Masker