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BAM

Description

BAM is a binary counterpart of the SAM file format.

Reader type: BAM.Reader
Writer type: BAM.Writer
Element type: BAM.Record

When writing data in the BAM file format, the underlying output stream needs to be wrapped with a BGZFStream object provided from BGZFStreams.jl.

Examples

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Accessors

# BioAlignments.BAM.Reader — Type.

BAM.Reader(input::IO; index=nothing)

Create a data reader of the BAM file format.

Arguments

input: data source
index=nothing: filepath to a random access index (currently bai is Supported)

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# BioAlignments.BAM.header — Function.

header(reader::Reader; fillSQ::Bool=false)::SAM.Header

Get the header of reader.

If fillSQ is true, this function fills missing "SQ" metainfo in the header.

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# BioAlignments.BAM.Writer — Type.

BAM.Writer(output::BGZFStream, header::SAM.Header)

Create a data writer of the BAM file format.

Arguments

output: data sink
header: SAM header object

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# BioAlignments.BAM.Record — Type.

BAM.Record()

Create an unfilled BAM record.

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# BioAlignments.BAM.flag — Function.

flag(record::Record)::UInt16

Get the bitwise flag of record.

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# BioAlignments.BAM.ismapped — Function.

ismapped(record::Record)::Bool

Test if record is mapped.

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# BioAlignments.BAM.isprimary — Function.

isprimary(record::Record)::Bool

Test if record is a primary line of the read.

This is equivalent to flag(record) & 0x900 == 0.

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# BioAlignments.BAM.refid — Function.

refid(record::Record)::Int

Get the reference sequence ID of record.

The ID is 1-based (i.e. the first sequence is 1) and is 0 for a record without a mapping position.

See also: BAM.refid

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# BioAlignments.BAM.position — Function.

position(record::Record)::Int

Get the 1-based leftmost mapping position of record.

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# BioAlignments.BAM.rightposition — Function.

rightposition(record::Record)::Int

Get the 1-based rightmost mapping position of record.

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# BioAlignments.BAM.isnextmapped — Function.

isnextmapped(record::Record)::Bool

Test if the mate/next read of record is mapped.

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# BioAlignments.BAM.nextrefid — Function.

nextrefid(record::Record)::Int

Get the next/mate reference sequence ID of record.

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# BioAlignments.BAM.nextrefname — Function.

nextrefname(record::Record)::String

Get the reference name of the mate/next read of record.

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# BioAlignments.BAM.nextposition — Function.

nextposition(record::Record)::Int

Get the 1-based leftmost mapping position of the next/mate read of record.

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# BioAlignments.BAM.mappingquality — Function.

mappingquality(record::Record)::UInt8

Get the mapping quality of record.

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# BioAlignments.BAM.cigar — Function.

cigar(record::Record)::String

Get the CIGAR string of record.

See also BAM.cigar.

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# BioAlignments.BAM.alignment — Function.

alignment(record::Record)::BioAlignments.Alignment

Get the alignment of record.

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# BioAlignments.BAM.alignlength — Function.

alignlength(record::Record)::Int

Get the alignment length of record.

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# BioAlignments.BAM.tempname — Function.

tempname(record::Record)::String

Get the query template name of record.

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# BioAlignments.BAM.templength — Function.

templength(record::Record)::Int

Get the template length of record.

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# BioAlignments.BAM.sequence — Function.

sequence(record::Record)::BioSequences.DNASequence

Get the segment sequence of record.

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# BioAlignments.BAM.seqlength — Function.

seqlength(record::Record)::Int

Get the sequence length of record.

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# BioAlignments.BAM.quality — Function.

quality(record::Record)::Vector{UInt8}

Get the base quality of record.

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# BioAlignments.BAM.auxdata — Function.

auxdata(record::Record)::BAM.AuxData

Get the auxiliary data of record.

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