From 8c1e2c14da4735ca43b7b2c24679f3f524762181 Mon Sep 17 00:00:00 2001 From: zeptodoctor <44736852+zeptodoctor@users.noreply.github.com> Date: Sun, 19 Jan 2020 12:10:08 +0000 Subject: [PATCH] build based on 6f5f1db --- dev/api/api/index.html | 6 +++--- dev/hts-files/index.html | 4 ++-- dev/index.html | 2 +- dev/search/index.html | 2 +- 4 files changed, 7 insertions(+), 7 deletions(-) diff --git a/dev/api/api/index.html b/dev/api/api/index.html index a4d9328..218941a 100644 --- a/dev/api/api/index.html +++ b/dev/api/api/index.html @@ -1,5 +1,5 @@ -API Reference · XAM.jl
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Public API Reference

Contents

Index

SAM API

The following methods and types are provided by the SAM submodule for public use.

XAM.SAM.MetaInfo — Method
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")
+API Reference · XAM.jl
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Public API Reference
Contents
Index
SAM API
The following methods and types are provided by the SAM submodule for public use.
XAM.SAM.MetaInfo — Method
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
@@ -13,7 +13,7 @@ BioAlignments.SAM.MetaInfo:
   value: SN=chr1 LN=12345
 
 julia> string(ans)
-"@SQ	SN:chr1	LN:12345"
source
XAM.SAM.MetaInfo — Method
MetaInfo(str::AbstractString)
Create a SAM metainfo from str.
Examples
julia> SAM.MetaInfo("@CO	some comment")
+"@SQ	SN:chr1	LN:12345"
source
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
@@ -21,4 +21,4 @@ BioAlignments.SAM.MetaInfo:
 julia> SAM.MetaInfo("@SQ	SN:chr1	LN:12345")
 BioAlignments.SAM.MetaInfo:
     tag: SQ
-  value: SN=chr1 LN=12345
source
XAM.SAM.Reader — Method
SAM.Reader(input::IO)
Create a data reader of the SAM file format.
Arguments
  • input: data source
source
XAM.SAM.Record — Method
SAM.Record(str::AbstractString)
Create a SAM record from str. This function verifies the format and indexes fields for accessors.
source
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.
source
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
source
Base.findall — Method
find(header::Header, key::AbstractString)::Vector{MetaInfo}
Find metainfo objects satisfying SAM.tag(metainfo) == key.
source
XAM.SAM.auxdata — Method
auxdata(record::Record)::Dict{String,Any}
Get the auxiliary data (optional fields) of record.
source
XAM.SAM.iscomment — Method
iscomment(metainfo::MetaInfo)::Bool
Test if metainfo is a comment (i.e. its tag is "CO").
source
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.
source
XAM.SAM.keyvalues — Method
keyvalues(metainfo::MetaInfo)::Vector{Pair{String,String}}
Get the values of metainfo as string pairs.
source
XAM.SAM.nextrefname — Method
nextrefname(record::Record)::String
Get the reference name of the mate/next read of record.
source
XAM.SAM.position — Method
position(record::Record)::Int
Get the 1-based leftmost mapping position of record.
source
XAM.SAM.quality — Method
quality(::Type{String}, record::Record)::String
Get the ASCII-encoded base quality of record.
source
XAM.SAM.quality — Method
quality(record::Record)::Vector{UInt8}
Get the Phred-scaled base quality of record.
source
XAM.SAM.refname — Method
refname(record::Record)::String
Get the reference sequence name of record.
source
XAM.SAM.sequence — Method
sequence(::Type{String}, record::Record)::String
Get the segment sequence of record as String.
source
XAM.SAM.sequence — Method
sequence(record::Record)::BioSequences.DNASequence
Get the segment sequence of record.
source
XAM.SAM.value — Method
value(metainfo::MetaInfo)::String
Get the value of metainfo as a string.
source
BAM API
The following methods and types are provided by the BAM submodule for public use.
XAM.BAM.BAI — Method
BAI(filename::AbstractString)
Load a BAI index from filename.
source
XAM.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)
source
XAM.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
source
BioGenerics.header — Method
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.
source
XAM.BAM.cigar — Function
cigar(record::Record)::String
Get the CIGAR string of record.
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.
See also BAM.cigar_rle.
source
XAM.BAM.cigar_rle — Function
cigar_rle(record::Record, checkCG::Bool = true)::Tuple{Vector{BioAlignments.Operation},Vector{Int}}
Get a run-length encoded tuple (ops, lens) of the CIGAR string in record.
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.
See also BAM.cigar.
source
XAM.BAM.ispositivestrand — Method
ispositivestrand(record::Record)::Bool
Test if record is aligned to the positive strand.
This is equivalent to flag(record) & 0x10 == 0.
source
XAM.BAM.isprimary — Method
isprimary(record::Record)::Bool
Test if record is a primary line of the read.
This is equivalent to flag(record) & 0x900 == 0.
source
XAM.BAM.n_cigar_op — Function
n_cigar_op(record::Record, checkCG::Bool = true)
Return the number of operations in the CIGAR string of record.
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 number of operations in 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 get the number of operations in the cigar field of the BAM record, then set checkCG to false.
source
XAM.BAM.nextposition — Method
nextposition(record::Record)::Int
Get the 1-based leftmost mapping position of the next/mate read of record.
source
XAM.BAM.nextrefname — Method
nextrefname(record::Record)::String
Get the reference name of the mate/next read of record.
source
XAM.BAM.position — Method
position(record::Record)::Int
Get the 1-based leftmost mapping position of record.
source
XAM.BAM.refid — Method
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.rname
source
XAM.BAM.reflen — Method
reflen(record::Record)::Int
Get the length of the reference sequence this record applies to.
source
XAM.BAM.refname — Method
refname(record::Record)::String
Get the reference sequence name of record.
See also: BAM.refid
source
XAM.BAM.sequence — Method
sequence(record::Record)::BioSequences.DNASequence
Get the segment sequence of record.
source

+  value: SN=chr1 LN=12345
source
XAM.SAM.Reader — Method
SAM.Reader(input::IO)

Create a data reader of the SAM file format.

Arguments

  • input: data source
source
XAM.SAM.Record — Method
SAM.Record(str::AbstractString)

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

source
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.

source
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
source
Base.findall — Method
find(header::Header, key::AbstractString)::Vector{MetaInfo}

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

source
XAM.SAM.auxdata — Method
auxdata(record::Record)::Dict{String,Any}

Get the auxiliary data (optional fields) of record.

source
XAM.SAM.iscomment — Method
iscomment(metainfo::MetaInfo)::Bool

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

source
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.

source
XAM.SAM.keyvalues — Method
keyvalues(metainfo::MetaInfo)::Vector{Pair{String,String}}

Get the values of metainfo as string pairs.

source
XAM.SAM.nextrefname — Method
nextrefname(record::Record)::String

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

source
XAM.SAM.position — Method
position(record::Record)::Int

Get the 1-based leftmost mapping position of record.

source
XAM.SAM.quality — Method
quality(::Type{String}, record::Record)::String

Get the ASCII-encoded base quality of record.

source
XAM.SAM.quality — Method
quality(record::Record)::Vector{UInt8}

Get the Phred-scaled base quality of record.

source
XAM.SAM.refname — Method
refname(record::Record)::String

Get the reference sequence name of record.

source
XAM.SAM.sequence — Method
sequence(::Type{String}, record::Record)::String

Get the segment sequence of record as String.

source
XAM.SAM.sequence — Method
sequence(record::Record)::BioSequences.DNASequence

Get the segment sequence of record.

source
XAM.SAM.value — Method
value(metainfo::MetaInfo)::String

Get the value of metainfo as a string.

source

BAM API

The following methods and types are provided by the BAM submodule for public use.

XAM.BAM.BAI — Method
BAI(filename::AbstractString)

Load a BAI index from filename.

source
XAM.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)
source
XAM.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
source
BioGenerics.header — Method
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.

source
XAM.BAM.cigar — Function
cigar(record::Record)::String

Get the CIGAR string of record.

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.

See also BAM.cigar_rle.

source
XAM.BAM.cigar_rle — Function
cigar_rle(record::Record, checkCG::Bool = true)::Tuple{Vector{BioAlignments.Operation},Vector{Int}}

Get a run-length encoded tuple (ops, lens) of the CIGAR string in record.

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.

See also BAM.cigar.

source
XAM.BAM.ispositivestrand — Method
ispositivestrand(record::Record)::Bool

Test if record is aligned to the positive strand.

This is equivalent to flag(record) & 0x10 == 0.

source
XAM.BAM.isprimary — Method
isprimary(record::Record)::Bool

Test if record is a primary line of the read.

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

source
XAM.BAM.n_cigar_op — Function
n_cigar_op(record::Record, checkCG::Bool = true)

Return the number of operations in the CIGAR string of record.

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 number of operations in 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 get the number of operations in the cigar field of the BAM record, then set checkCG to false.

source
XAM.BAM.nextposition — Method
nextposition(record::Record)::Int

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

source
XAM.BAM.nextrefname — Method
nextrefname(record::Record)::String

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

source
XAM.BAM.position — Method
position(record::Record)::Int

Get the 1-based leftmost mapping position of record.

source
XAM.BAM.refid — Method
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.rname

source
XAM.BAM.reflen — Method
reflen(record::Record)::Int

Get the length of the reference sequence this record applies to.

source
XAM.BAM.refname — Method
refname(record::Record)::String

Get the reference sequence name of record.

See also: BAM.refid

source
XAM.BAM.sequence — Method
sequence(record::Record)::BioSequences.DNASequence

Get the segment sequence of record.

source
diff --git a/dev/hts-files/index.html b/dev/hts-files/index.html index e922a38..13984e4 100644 --- a/dev/hts-files/index.html +++ b/dev/hts-files/index.html @@ -51,7 +51,7 @@ julia> find(header(reader), "SQ") Bio.Align.SAM.MetaInfo: tag: SQ value: SN=mitochondria LN=366924 -

In the above we can see there were 7 sequences in the reference: 5 chromosomes, one chloroplast sequence, and one mitochondrial sequence.

SAM and BAM Records

BioAlignments supports the following accessors for SAM.Record types.

XAM.SAM.flag — Function
flag(record::Record)::UInt16

Get the bitwise flag of record.

source
XAM.SAM.ismapped — Function
ismapped(record::Record)::Bool

Test if record is mapped.

source
XAM.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.

source
XAM.SAM.refname — Function
refname(record::Record)::String

Get the reference sequence name of record.

source
XAM.SAM.position — Function
position(record::Record)::Int

Get the 1-based leftmost mapping position of record.

source
XAM.SAM.rightposition — Function
rightposition(record::Record)::Int

Get the 1-based rightmost mapping position of record.

source
XAM.SAM.isnextmapped — Function
isnextmapped(record::Record)::Bool

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

source
XAM.SAM.nextrefname — Function
nextrefname(record::Record)::String

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

source
XAM.SAM.nextposition — Function
nextposition(record::Record)::Int

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

source
XAM.SAM.mappingquality — Function
mappingquality(record::Record)::UInt8

Get the mapping quality of record.

source
XAM.SAM.cigar — Function
cigar(record::Record)::String

Get the CIGAR string of record.

source
XAM.SAM.alignment — Function
alignment(record::Record)::BioAlignments.Alignment

Get the alignment of record.

source
XAM.SAM.alignlength — Function
alignlength(record::Record)::Int

Get the alignment length of record.

source
XAM.SAM.tempname — Function
tempname(record::Record)::String

Get the query template name of record.

source
XAM.SAM.templength — Function
templength(record::Record)::Int

Get the template length of record.

source
XAM.SAM.sequence — Function
sequence(record::Record)::BioSequences.DNASequence

Get the segment sequence of record.

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

Get the segment sequence of record as String.

source
XAM.SAM.seqlength — Function
seqlength(record::Record)::Int

Get the sequence length of record.

source
XAM.SAM.quality — Function
quality(record::Record)::Vector{UInt8}

Get the Phred-scaled base quality of record.

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

Get the ASCII-encoded base quality of record.

source
XAM.SAM.auxdata — Function
auxdata(record::Record)::Dict{String,Any}

Get the auxiliary data (optional fields) of record.

source

BioAlignments supports the following accessors for BAM.Record types.

XAM.BAM.flag — Function
flag(record::Record)::UInt16

Get the bitwise flag of record.

source
XAM.BAM.ismapped — Function
ismapped(record::Record)::Bool

Test if record is mapped.

source
XAM.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.

source
XAM.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.rname

source
XAM.BAM.refname — Function
refname(record::Record)::String

Get the reference sequence name of record.

See also: BAM.refid

source
XAM.BAM.reflen — Function
reflen(record::Record)::Int

Get the length of the reference sequence this record applies to.

source
XAM.BAM.position — Function
position(record::Record)::Int

Get the 1-based leftmost mapping position of record.

source
XAM.BAM.rightposition — Function
rightposition(record::Record)::Int

Get the 1-based rightmost mapping position of record.

source
XAM.BAM.isnextmapped — Function
isnextmapped(record::Record)::Bool

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

source
XAM.BAM.nextrefid — Function
nextrefid(record::Record)::Int

Get the next/mate reference sequence ID of record.

source
XAM.BAM.nextrefname — Function
nextrefname(record::Record)::String

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

source
XAM.BAM.nextposition — Function
nextposition(record::Record)::Int

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

source
XAM.BAM.mappingquality — Function
mappingquality(record::Record)::UInt8

Get the mapping quality of record.

source
XAM.BAM.cigar — Function
cigar(record::Record)::String

Get the CIGAR string of record.

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.

See also BAM.cigar_rle.

source
XAM.BAM.alignment — Function
alignment(record::Record)::BioAlignments.Alignment

Get the alignment of record.

source
XAM.BAM.alignlength — Function
alignlength(record::Record)::Int

Get the alignment length of record.

source
XAM.BAM.tempname — Function
tempname(record::Record)::String

Get the query template name of record.

source
XAM.BAM.templength — Function
templength(record::Record)::Int

Get the template length of record.

source
XAM.BAM.sequence — Function
sequence(record::Record)::BioSequences.DNASequence

Get the segment sequence of record.

source
XAM.BAM.seqlength — Function
seqlength(record::Record)::Int

Get the sequence length of record.

source
XAM.BAM.quality — Function
quality(record::Record)::Vector{UInt8}

Get the base quality of record.

source
XAM.BAM.auxdata — Function
auxdata(record::Record)::BAM.AuxData

Get the auxiliary data of record.

source

Accessing auxiliary data

SAM and BAM records support the storing of optional data fields associated with tags.

Tagged auxiliary data follows a format of TAG:TYPE:VALUE. TAG is a two-letter string, and each tag can only appear once per record. TYPE is a single case-sensetive letter which defined the format of VALUE.

TypeDescription
'A'Printable character
'i'Signed integer
'f'Single-precision floating number
'Z'Printable string, including space
'H'Byte array in Hex format
'B'Integer of numeric array

For more information about these tags and their types we refer you to the [SAM/BAM specification][samtools-spec] and the additional [optional fields specification][samtags] document.

There are some tags that are reserved, predefined standard tags, for specific uses.

To access optional fields stored in tags, you use getindex indexing syntax on the record object. Note that accessing optional tag fields will result in type instability in Julia. This is because the type of the optional data is not known until run-time, as the tag is being read. This can have a significant impact on performance. To limit this, if the user knows the type of a value in advance, specifying it as a type annotation will alleviate the problem:

Below is an example of looping over records in a bam file and using indexing syntax to get the data stored in the "NM" tag. Note the UInt8 type assertion to alleviate type instability.

for record in open(BAM.Reader, "data.bam")
+

In the above we can see there were 7 sequences in the reference: 5 chromosomes, one chloroplast sequence, and one mitochondrial sequence.

SAM and BAM Records

BioAlignments supports the following accessors for SAM.Record types.

XAM.SAM.flag — Function
flag(record::Record)::UInt16

Get the bitwise flag of record.

source
XAM.SAM.ismapped — Function
ismapped(record::Record)::Bool

Test if record is mapped.

source
XAM.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.

source
XAM.SAM.refname — Function
refname(record::Record)::String

Get the reference sequence name of record.

source
XAM.SAM.position — Function
position(record::Record)::Int

Get the 1-based leftmost mapping position of record.

source
XAM.SAM.rightposition — Function
rightposition(record::Record)::Int

Get the 1-based rightmost mapping position of record.

source
XAM.SAM.isnextmapped — Function
isnextmapped(record::Record)::Bool

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

source
XAM.SAM.nextrefname — Function
nextrefname(record::Record)::String

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

source
XAM.SAM.nextposition — Function
nextposition(record::Record)::Int

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

source
XAM.SAM.mappingquality — Function
mappingquality(record::Record)::UInt8

Get the mapping quality of record.

source
XAM.SAM.cigar — Function
cigar(record::Record)::String

Get the CIGAR string of record.

source
XAM.SAM.alignment — Function
alignment(record::Record)::BioAlignments.Alignment

Get the alignment of record.

source
XAM.SAM.alignlength — Function
alignlength(record::Record)::Int

Get the alignment length of record.

source
XAM.SAM.tempname — Function
tempname(record::Record)::String

Get the query template name of record.

source
XAM.SAM.templength — Function
templength(record::Record)::Int

Get the template length of record.

source
XAM.SAM.sequence — Function
sequence(record::Record)::BioSequences.DNASequence

Get the segment sequence of record.

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

Get the segment sequence of record as String.

source
XAM.SAM.seqlength — Function
seqlength(record::Record)::Int

Get the sequence length of record.

source
XAM.SAM.quality — Function
quality(record::Record)::Vector{UInt8}

Get the Phred-scaled base quality of record.

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

Get the ASCII-encoded base quality of record.

source
XAM.SAM.auxdata — Function
auxdata(record::Record)::Dict{String,Any}

Get the auxiliary data (optional fields) of record.

source

BioAlignments supports the following accessors for BAM.Record types.

XAM.BAM.flag — Function
flag(record::Record)::UInt16

Get the bitwise flag of record.

source
XAM.BAM.ismapped — Function
ismapped(record::Record)::Bool

Test if record is mapped.

source
XAM.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.

source
XAM.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.rname

source
XAM.BAM.refname — Function
refname(record::Record)::String

Get the reference sequence name of record.

See also: BAM.refid

source
XAM.BAM.reflen — Function
reflen(record::Record)::Int

Get the length of the reference sequence this record applies to.

source
XAM.BAM.position — Function
position(record::Record)::Int

Get the 1-based leftmost mapping position of record.

source
XAM.BAM.rightposition — Function
rightposition(record::Record)::Int

Get the 1-based rightmost mapping position of record.

source
XAM.BAM.isnextmapped — Function
isnextmapped(record::Record)::Bool

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

source
XAM.BAM.nextrefid — Function
nextrefid(record::Record)::Int

Get the next/mate reference sequence ID of record.

source
XAM.BAM.nextrefname — Function
nextrefname(record::Record)::String

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

source
XAM.BAM.nextposition — Function
nextposition(record::Record)::Int

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

source
XAM.BAM.mappingquality — Function
mappingquality(record::Record)::UInt8

Get the mapping quality of record.

source
XAM.BAM.cigar — Function
cigar(record::Record)::String

Get the CIGAR string of record.

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.

See also BAM.cigar_rle.

source
XAM.BAM.alignment — Function
alignment(record::Record)::BioAlignments.Alignment

Get the alignment of record.

source
XAM.BAM.alignlength — Function
alignlength(record::Record)::Int

Get the alignment length of record.

source
XAM.BAM.tempname — Function
tempname(record::Record)::String

Get the query template name of record.

source
XAM.BAM.templength — Function
templength(record::Record)::Int

Get the template length of record.

source
XAM.BAM.sequence — Function
sequence(record::Record)::BioSequences.DNASequence

Get the segment sequence of record.

source
XAM.BAM.seqlength — Function
seqlength(record::Record)::Int

Get the sequence length of record.

source
XAM.BAM.quality — Function
quality(record::Record)::Vector{UInt8}

Get the base quality of record.

source
XAM.BAM.auxdata — Function
auxdata(record::Record)::BAM.AuxData

Get the auxiliary data of record.

source

Accessing auxiliary data

SAM and BAM records support the storing of optional data fields associated with tags.

Tagged auxiliary data follows a format of TAG:TYPE:VALUE. TAG is a two-letter string, and each tag can only appear once per record. TYPE is a single case-sensetive letter which defined the format of VALUE.

TypeDescription
'A'Printable character
'i'Signed integer
'f'Single-precision floating number
'Z'Printable string, including space
'H'Byte array in Hex format
'B'Integer of numeric array

For more information about these tags and their types we refer you to the [SAM/BAM specification][samtools-spec] and the additional [optional fields specification][samtags] document.

There are some tags that are reserved, predefined standard tags, for specific uses.

To access optional fields stored in tags, you use getindex indexing syntax on the record object. Note that accessing optional tag fields will result in type instability in Julia. This is because the type of the optional data is not known until run-time, as the tag is being read. This can have a significant impact on performance. To limit this, if the user knows the type of a value in advance, specifying it as a type annotation will alleviate the problem:

Below is an example of looping over records in a bam file and using indexing syntax to get the data stored in the "NM" tag. Note the UInt8 type assertion to alleviate type instability.

for record in open(BAM.Reader, "data.bam")
     nm = record["NM"]::UInt8
     # do something
 end

Getting records in a range

BioAlignments supports the BAI index to fetch records in a specific range from a BAM file. from a BAM file. [Samtools][samtools] provides index subcommand to create an index file (.bai) from a sorted BAM file.

$ samtools index -b SRR1238088.sort.bam
@@ -103,4 +103,4 @@ SAM.Writer(IOStream(<file my-data.sam>))
 julia> bamw = BAM.Writer(BGZFStream(open("my-data.bam", "w"), "w"))
 BAM.Writer(BGZFStreams.BGZFStream{IOStream}(<mode=write>))

Once you have a BAM or SAM writer, you can use the write method to write BAM.Records or SAM.Records to file:

julia> write(bamw, rec) # Here rec is a `BAM.Record`
-330780

[samtools]: https://samtools.github.io/ [samtools-spec]: https://samtools.github.io/hts-specs/SAMv1.pdf [samtags]: https://samtools.github.io/hts-specs/SAMtags.pdf [bgzfstreams]: https://github.com/BioJulia/BGZFStreams.jl [genomicfeatures]: https://github.com/BioJulia/GenomicFeatures.jl

+330780

[samtools]: https://samtools.github.io/ [samtools-spec]: https://samtools.github.io/hts-specs/SAMv1.pdf [samtags]: https://samtools.github.io/hts-specs/SAMtags.pdf [bgzfstreams]: https://github.com/BioJulia/BGZFStreams.jl [genomicfeatures]: https://github.com/BioJulia/GenomicFeatures.jl

diff --git a/dev/index.html b/dev/index.html index 04b7835..d17fef0 100644 --- a/dev/index.html +++ b/dev/index.html @@ -1,2 +1,2 @@ -Home · XAM.jl
Edit on GitHub

XAM.jl

Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public. Latest Release MIT license Join the chat at https://gitter.im/BioJulia/XAM.jl

Description

XAM provides I/O and utilities for manipulating SAM and BAM formatted alignment map files.

Installation

XAM is made available to install through BioJulia's package registry. Julia's package manager only uses the "General" package registry by default. Your Julia configuration needs to include the BioJulia registry to be able to install the latest version of XAM.

To add the BioJulia registry from the Julia REPL, press ] to enter pkg mode, then enter the following command:

registry add https://github.com/BioJulia/BioJuliaRegistry.git

Once the registry is added, you can install XAM while in pkg mode with the following command:

add XAM

If you are interested in the cutting edge of the development, please check out the develop branch to try new features before release.

+Home · XAM.jl
Edit on GitHub

XAM.jl

Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public. Latest Release MIT license Join the chat at https://gitter.im/BioJulia/XAM.jl

Description

XAM provides I/O and utilities for manipulating SAM and BAM formatted alignment map files.

Installation

XAM is made available to install through BioJulia's package registry. Julia's package manager only uses the "General" package registry by default. Your Julia configuration needs to include the BioJulia registry to be able to install the latest version of XAM.

To add the BioJulia registry from the Julia REPL, press ] to enter pkg mode, then enter the following command:

registry add https://github.com/BioJulia/BioJuliaRegistry.git

Once the registry is added, you can install XAM while in pkg mode with the following command:

add XAM

If you are interested in the cutting edge of the development, please check out the develop branch to try new features before release.

diff --git a/dev/search/index.html b/dev/search/index.html index 43a32bd..319f86e 100644 --- a/dev/search/index.html +++ b/dev/search/index.html @@ -1,2 +1,2 @@ -Search · XAM.jl

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