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SAM

Description

SAM is a text-based file format for representing sequence alignments.

Reader type: SAM.Reader
Writer type: SAM.Writer
Element type: SAM.Record

This module provides 16-bit flags defined in the SAM specs:

Flag	Bit	Description
`SAM.FLAG_PAIRED`	`0x0001`	template having multiple segments in sequencing
`SAM.FLAG_PROPER_PAIR`	`0x0002`	each segment properly aligned according to the aligner
`SAM.FLAG_UNMAP`	`0x0004`	segment unmapped
`SAM.FLAG_MUNMAP`	`0x0008`	next segment in the template unmapped
`SAM.FLAG_REVERSE`	`0x0010`	SEQ being reverse complemented
`SAM.FLAG_MREVERSE`	`0x0020`	SEQ of the next segment in the template being reverse complemented
`SAM.FLAG_READ1`	`0x0040`	the first segment in the template
`SAM.FLAG_READ2`	`0x0080`	the last segment in the template
`SAM.FLAG_SECONDARY`	`0x0100`	secondary alignment
`SAM.FLAG_QCFAIL`	`0x0200`	not passing filters, such as platform/vendor quality controls
`SAM.FLAG_DUP`	`0x0400`	PCR or optical duplicate
`SAM.FLAG_SUPPLEMENTARY`	`0x0800`	supplementary alignment

Examples

TODO

Accessors

# BioAlignments.SAM.Reader — Type.

SAM.Reader(input::IO)

Create a data reader of the SAM file format.

Arguments

input: data source

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# BioAlignments.SAM.header — Function.

header(reader::Reader)::Header

Get the header of reader.

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# BioAlignments.SAM.Header — Type.

SAM.Header()

Create an empty header.

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# Base.find — Method.

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

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

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# BioAlignments.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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# BioAlignments.SAM.MetaInfo — Type.

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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MetaInfo(tag::AbstractString, value)

Create a SAM metainfo with tag and value.

tag is a two-byte ASCII string. If tag is "CO", value must be a string; otherwise, value is an iterable object with key and value pairs.

Examples

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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# BioAlignments.SAM.iscomment — Function.

iscomment(metainfo::MetaInfo)::Bool

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

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# BioAlignments.SAM.tag — Function.

tag(metainfo::MetaInfo)::String

Get the tag of metainfo.

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# BioAlignments.SAM.value — Function.

value(metainfo::MetaInfo)::String

Get the value of metainfo as a string.

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# BioAlignments.SAM.keyvalues — Function.

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

Get the values of metainfo as string pairs.

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# BioAlignments.SAM.Record — Type.

SAM.Record()

Create an unfilled SAM record.

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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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SAM.Record(str::AbstractString)

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

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# BioAlignments.SAM.flag — Function.

flag(record::Record)::UInt16

Get the bitwise flag of record.

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# BioAlignments.SAM.ismapped — Function.

ismapped(record::Record)::Bool

Test if record is mapped.

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# BioAlignments.SAM.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.SAM.refname — Function.

refname(record::Record)::String

Get the reference sequence name of record.

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# BioAlignments.SAM.position — Function.

position(record::Record)::Int

Get the 1-based leftmost mapping position of record.

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# BioAlignments.SAM.rightposition — Function.

rightposition(record::Record)::Int

Get the 1-based rightmost mapping position of record.

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# BioAlignments.SAM.isnextmapped — Function.

isnextmapped(record::Record)::Bool

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

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# BioAlignments.SAM.nextrefname — Function.

nextrefname(record::Record)::String

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

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# BioAlignments.SAM.nextposition — Function.

nextposition(record::Record)::Int

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

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# BioAlignments.SAM.mappingquality — Function.

mappingquality(record::Record)::UInt8

Get the mapping quality of record.

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# BioAlignments.SAM.cigar — Function.

cigar(record::Record)::String

Get the CIGAR string of record.

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# BioAlignments.SAM.alignment — Function.

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

Get the alignment of record.

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# BioAlignments.SAM.alignlength — Function.

alignlength(record::Record)::Int

Get the alignment length of record.

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# BioAlignments.SAM.tempname — Function.

tempname(record::Record)::String

Get the query template name of record.

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# BioAlignments.SAM.templength — Function.

templength(record::Record)::Int

Get the template length of record.

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# BioAlignments.SAM.sequence — Function.

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

Get the segment sequence of record.

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

Get the segment sequence of record as String.

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# BioAlignments.SAM.seqlength — Function.

seqlength(record::Record)::Int

Get the sequence length of record.

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# BioAlignments.SAM.quality — Function.

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

Get the Phred-scaled base quality of record.

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

Get the ASCII-encoded base quality of record.

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# BioAlignments.SAM.auxdata — Function.

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

Get the auxiliary data (optional fields) of record.

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