julia> SAM.MetaInfo("CO", "some comment")
BioAlignments.SAM.MetaInfo:
    tag: CO
  value: some comment

julia> string(ans)
"@CO	some comment"

julia> SAM.MetaInfo("SQ", ["SN" => "chr1", "LN" => 12345])
BioAlignments.SAM.MetaInfo:
    tag: SQ
  value: SN=chr1 LN=12345

julia> string(ans)
"@SQ	SN:chr1	LN:12345"

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XAM.SAM.MetaInfo — Method.

MetaInfo(str::AbstractString)

Create a SAM metainfo from str.

Examples

julia> SAM.MetaInfo("@CO	some comment")
BioAlignments.SAM.MetaInfo:
    tag: CO
  value: some comment

julia> SAM.MetaInfo("@SQ	SN:chr1	LN:12345")
BioAlignments.SAM.MetaInfo:
    tag: SQ
  value: SN=chr1 LN=12345

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XAM.SAM.Reader — Method.

SAM.Reader(input::IO)

Create a data reader of the SAM file format.

Arguments

input: data source

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XAM.SAM.Record — Method.

SAM.Record(str::AbstractString)

Create a SAM record from str. This function verifies the format and indexes fields for accessors.

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XAM.SAM.Record — Method.

SAM.Record(data::Vector{UInt8})

Create a SAM record from data. This function verifies the format and indexes fields for accessors. Note that the ownership of data is transferred to a new record object.

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XAM.SAM.Record — Method.

SAM.Record()

Create an unfilled SAM record.

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XAM.SAM.Writer — Type.

Writer(output::IO, header::Header=Header())

Create a data writer of the SAM file format.

Arguments

output: data sink
header=Header(): SAM header object

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Base.findall — Method.

find(header::Header, key::AbstractString)::Vector{MetaInfo}

Find metainfo objects satisfying SAM.tag(metainfo) == key.

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BioGenerics.header — Method.

header(reader::Reader)::Header

Get the header of reader.

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XAM.SAM.alignlength — Method.

alignlength(record::Record)::Int

Get the alignment length of record.

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XAM.SAM.alignment — Method.

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

Get the alignment of record.

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XAM.SAM.auxdata — Method.

auxdata(record::Record)::Dict{String,Any}

Get the auxiliary data (optional fields) of record.

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XAM.SAM.cigar — Method.

cigar(record::Record)::String

Get the CIGAR string of record.

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XAM.SAM.flag — Method.

flag(record::Record)::UInt16

Get the bitwise flag of record.

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XAM.SAM.iscomment — Method.

iscomment(metainfo::MetaInfo)::Bool

Test if metainfo is a comment (i.e. its tag is "CO").

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XAM.SAM.ismapped — Method.

ismapped(record::Record)::Bool

Test if record is mapped.

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XAM.SAM.isnextmapped — Method.

isnextmapped(record::Record)::Bool

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

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XAM.SAM.isprimary — Method.

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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XAM.SAM.keyvalues — Method.

keyvalues(metainfo::MetaInfo)::Vector{Pair{String,String}}

Get the values of metainfo as string pairs.

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XAM.SAM.mappingquality — Method.

mappingquality(record::Record)::UInt8

Get the mapping quality of record.

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XAM.SAM.nextposition — Method.

nextposition(record::Record)::Int

Get the position of the mate/next read of record.

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XAM.SAM.nextrefname — Method.

nextrefname(record::Record)::String

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

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XAM.SAM.position — Method.

position(record::Record)::Int

Get the 1-based leftmost mapping position of record.

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XAM.SAM.quality — Method.

quality(::Type{String}, record::Record)::String

Get the ASCII-encoded base quality of record.

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XAM.SAM.quality — Method.

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

Get the Phred-scaled base quality of record.

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XAM.SAM.refname — Method.

refname(record::Record)::String

Get the reference sequence name of record.

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XAM.SAM.rightposition — Method.

rightposition(record::Record)::Int

Get the 1-based rightmost mapping position of record.

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XAM.SAM.seqlength — Method.

seqlength(record::Record)::Int

Get the sequence length of record.

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XAM.SAM.sequence — Method.

sequence(::Type{String}, record::Record)::String

Get the segment sequence of record as String.

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XAM.SAM.sequence — Method.

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

Get the segment sequence of record.

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XAM.SAM.tag — Method.

tag(metainfo::MetaInfo)::String

Get the tag of metainfo.

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XAM.SAM.templength — Method.

templength(record::Record)::Int

Get the template length of record.

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XAM.SAM.tempname — Method.

tempname(record::Record)::String

Get the query template name of record.

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XAM.SAM.value — Method.

value(metainfo::MetaInfo)::String

Get the value of metainfo as a string.

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Note that in the BAM specification, the field called cigar typically stores the cigar string of the record. However, this is not always true, sometimes the true cigar is very long, and due to some constraints of the BAM format, the actual cigar string is stored in an extra tag: CG:B,I, and the cigar field stores a pseudo-cigar string.

Calling this method with checkCG set to true (default) this method will always yield the true cigar string, because this is probably what you want the vast majority of the time.

If you have a record that stores the true cigar in a CG:B,I tag, but you still want to access the pseudo-cigar that is stored in the cigar field of the BAM record, then you can set checkCG to false.

Public API Reference

Contents

SAM API

BAM API