const module

class ValidNucleotides(*values)

Bases: Enum

VCF nucleotides, which hairpin2 is able to process.

ALL = {'*', 'A', 'C', 'G', 'N', 'T'}

class Strand(*values)

Bases: StrEnum

Enum used to indicate strandedness

BOTH = 'BOTH'

F = 'F'

R = 'R'

class MutTypes(*values)

Bases: StrEnum

VCF Variant types which hairpin2 is able to process.

SUB = 'SUB'

DEL = 'DEL'

INS = 'INS'

class Tags(*values)

Bases: StrEnum

Tags applied by additive read processors.

SUPPORT_TAG = 'SUPPORTS-VAR'

OVERLAP_TAG = 'IS-OVERLAPPING-READ2'

LOW_QUAL_TAG = 'LOW-QUAL'

STUTTER_DUP_TAG = 'IS-STUTTER-DUP'

class TaggerNamespaces(*values)

Bases: StrEnum

Process names for additive read processors (functions which add tag data to reads during execution).

MARK_SUPPORT = 'mark-support'

MARK_OVERLAP = 'mark-overlap'

MARK_LOW_QUAL = 'mark-low-qual'

MARK_STUTTER_DUP = 'mark-duplicates'

class FlaggerNamespaces(*values)

Bases: StrEnum

Process/Flag names for variant flaggers, which flag variants in the output VCF.

LOW_QUAL = 'LQF'

DUPLICATION = 'DVF'

POOR_ALIGNMENT_SCORE = 'ALF'

ANOMALOUS_DISTRIBUTION = 'ADF'