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(readname, chrom, lpos, rpos, strand, binaryseq, binaryqual, cigar, MD)

Bases: object

MD: bytes

QUAL: bytes

SEQ: bytes

binaryqual: bytes

binaryseq: bytes

chrom: bytes

cigar: tuple

get_FASTQ()

Get FASTQ format text.

Return type:: bytes

get_REFSEQ()

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

Return type:: bytearray

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.

Return type:: tuple

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_n_edits()

The number is from self.cigar and self.MD.

Return type:: typedef

get_variant_bq_by_ref_pos(ref_pos)

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

variants will be

=, if identical
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.

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

Base quality is the raw Phred-scaled base quality.

Return type:: tuple

l: typedef

lpos: typedef

n_edits: typedef

readname: bytes

relative_ref_pos_to_relative_query_pos(relative_ref_pos)

Convert relative pos on ref to pos on query.

Return type:: typedef

rpos: typedef

strand: typedef

MACS3.Signal.ReadAlignment.bool(*args, **kwargs)