MACS3.Signal.ReadAlignment module

Module for SAPPER ReadAlignment class

This code is free software; you can redistribute it and/or modify it under the terms of the BSD License (see the file COPYING included with the distribution).

class MACS3.Signal.ReadAlignment.ReadAlignment

Bases: object

get_FASTQ()

Get FASTQ format text.

get_REFSEQ()

Fetch reference sequence, using self.MD and self.cigar

get_base_bq_by_ref_pos(ref_pos)

Get base and base quality by ref position. Base quality is in Phred scale.

Returned bq is the raw Phred-scaled base quality.

get_base_by_ref_pos(ref_pos)

Get base by ref position.

get_bq_by_ref_pos(ref_pos)

Get base quality by ref position. Base quality is in Phred scale.

Returned value is the raw Phred-scaled base quality.

get_variant_bq_by_ref_pos(ref_pos)

Get any variants (different with reference) and base quality by ref position.

variants will be

  1. =, if identical

  2. A/T/C/G, if SNV

3) -, if the reference base is deleted, in this case, bq will be the highest possible bq, which is 93.

  1. ^<A/T/C/G>+, if there is an insertion at the location

Base quality is the raw Phred-scaled base quality.