bio.std.hts.bam.validation.alignment

Public Imports

bio.std.hts.bam.read

public import bio.std.hts.bam.read;

bio.std.hts.bam.tagvalue

public import bio.std.hts.bam.tagvalue;

Members

Aliases

PredefinedTags

alias PredefinedTags = TypeTuple!(TagType!("AM", int), TagType!("AS", int), TagType!("BC", string), TagType!("BQ", string), TagType!("CC", string), TagType!("CM", int), TagType!("CP", int), TagType!("CQ", string), TagType!("CS", string), TagType!("E2", string), TagType!("FI", int), TagType!("FS", string), TagType!("FZ", ushort[]), TagType!("LB", string), TagType!("H0", int), TagType!("H1", int), TagType!("H2", int), TagType!("HI", int), TagType!("IH", int), TagType!("MD", string), TagType!("MQ", int), TagType!("NH", int), TagType!("NM", int), TagType!("OQ", string), TagType!("OP", int), TagType!("OC", string), TagType!("PG", string), TagType!("PQ", int), TagType!("PU", string), TagType!("Q2", string), TagType!("R2", string), TagType!("RG", string), TagType!("SM", int), TagType!("TC", int), TagType!("U2", string), TagType!("UQ", int))

Compile-time available information about predefined tags

Classes

AbstractAlignmentValidator

class AbstractAlignmentValidator

Abstract class encapsulating visitation of SAM header elements.

Enums

AlignmentError

enum AlignmentError

Alignment validation error types.

CigarError

enum CigarError

CIGAR string validation error types.

TagError

enum TagError

Auxiliary data validation error types.

Functions

isValid

bool isValid(BamRead alignment)

Check if alignment is valid

Structs

TagType

struct TagType(string key, T)

Designates pair of predefined key from SAM/BAM specification and expected type of tags with that key.

Templates

PredefinedTagType

template PredefinedTagType(string s)

Get predefined tag type by its key, in compile-time.

• alignment
• samheader