diff --git a/dev/api/public/index.html b/dev/api/public/index.html new file mode 100644 index 0000000..8eb1d7b --- /dev/null +++ b/dev/api/public/index.html @@ -0,0 +1,24 @@ + +Public · XAM.jl
Public

Public API Reference

Contents

SAM API

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

XAM.SAM.FLAG_DUP — Constant.

0x0400: optical or PCR duplicate

source
XAM.SAM.FLAG_MREVERSE — Constant.

0x0020: the mate is mapped to the reverse strand

source
XAM.SAM.FLAG_MUNMAP — Constant.

0x0008: the mate is unmapped

source
XAM.SAM.FLAG_PAIRED — Constant.

0x0001: the read is paired in sequencing, no matter whether it is mapped in a pair

source
XAM.SAM.FLAG_PROPER_PAIR — Constant.

0x0002: the read is mapped in a proper pair

source
XAM.SAM.FLAG_QCFAIL — Constant.

0x0200: QC failure

source
XAM.SAM.FLAG_READ1 — Constant.

0x0040: this is read1

source
XAM.SAM.FLAG_READ2 — Constant.

0x0080: this is read2

source
XAM.SAM.FLAG_REVERSE — Constant.

0x0010: the read is mapped to the reverse strand

source
XAM.SAM.FLAG_SECONDARY — Constant.

0x0100: not primary alignment

source
XAM.SAM.FLAG_SUPPLEMENTARY — Constant.

0x0800: supplementary alignment

source
XAM.SAM.FLAG_UNMAP — Constant.

0x0004: the read itself is unmapped; conflictive with SAM.FLAGPROPERPAIR

source
XAM.SAM.Header — Method.
SAM.Header()

Create an empty header.

source
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
+
+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"
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
+
+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.Record — Method.
SAM.Record()

Create an unfilled SAM record.

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
BioCore.header — Method.
header(reader::Reader)::Header

Get the header of reader.

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

Get the alignment length of record.

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

Get the alignment of record.

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

Get the auxiliary data (optional fields) of record.

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

Get the CIGAR string of record.

source
XAM.SAM.flag — Method.
flag(record::Record)::UInt16

Get the bitwise flag 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.ismapped — Method.
ismapped(record::Record)::Bool

Test if record is mapped.

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

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

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.mappingquality — Method.
mappingquality(record::Record)::UInt8

Get the mapping quality of record.

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

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

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.rightposition — Method.
rightposition(record::Record)::Int

Get the 1-based rightmost mapping position of record.

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

Get the sequence length 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.tag — Method.
tag(metainfo::MetaInfo)::String

Get the tag of metainfo.

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

Get the template length of record.

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

Get the query template name 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.BAI — Method.
BAI(input::IO)

Load a BAI index from input.

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.Record — Type.
BAM.Record()

Create an unfilled BAM record.

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
BioCore.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.alignlength — Method.
alignlength(record::Record)::Int

Get the alignment length of record.

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

Get the alignment of record.

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

Get the auxiliary data 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.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.flag — Method.
flag(record::Record)::UInt16

Get the bitwise flag of record.

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

Test if record is mapped.

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

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

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.mappingquality — Method.
mappingquality(record::Record)::UInt8

Get the mapping quality of record.

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.nextrefid — Method.
nextrefid(record::Record)::Int

Get the next/mate reference sequence ID 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.quality — Method.
quality(record::Record)::Vector{UInt8}

Get the base quality 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.rightposition — Method.
rightposition(record::Record)::Int

Get the 1-based rightmost mapping position of record.

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

Get the sequence length of record.

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

Get the segment sequence of record.

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

Get the template length of record.

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

Get the query template name of record.

source
diff --git a/dev/assets/arrow.svg b/dev/assets/arrow.svg new file mode 100644 index 0000000..ee2798d --- /dev/null +++ b/dev/assets/arrow.svg @@ -0,0 +1,63 @@ + + + + + + + + + + image/svg+xml + + + + + + + + + diff --git a/dev/assets/documenter.css b/dev/assets/documenter.css new file mode 100644 index 0000000..7cd2662 --- /dev/null +++ b/dev/assets/documenter.css @@ -0,0 +1,601 @@ +/* + * The default CSS style for Documenter.jl generated sites + * + * Heavily inspired by the Julia Sphinx theme + * https://github.com/JuliaLang/JuliaDoc + * which extends the sphinx_rtd_theme + * https://github.com/snide/sphinx_rtd_theme + * + * Part of Documenter.jl + * https://github.com/JuliaDocs/Documenter.jl + * + * License: MIT + */ + +/* fonts */ +body, input { + font-family: 'Lato', 'Helvetica Neue', Arial, sans-serif; + font-size: 16px; + color: #222; + text-rendering: optimizeLegibility; +} + +pre, code, kbd { + font-family: 'Roboto Mono', Monaco, courier, monospace; + font-size: 0.90em; +} + +pre code { + font-size: 1em; +} + +a { + color: #2980b9; + text-decoration: none; +} + +a:hover { + color: #3091d1; +} + +a:visited { + color: #9b59b6; +} + +body { + line-height: 1.5; +} + +h1 { + font-size: 1.75em; +} + +/* Unless the

the is very first thing on the page (i.e. the second element + * in the
, * after the
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This way we get a reasonable fallback if CSS3 + * selectors are not supported in the browser. + */ +article > h1:not(:nth-child(2)) { + margin: 2.5em 0 0; + padding-bottom: 0.30em; + border-bottom: 1px solid #e5e5e5; +} +h2 { + font-size: 1.50em; + margin: 2.3em 0 0; + padding-bottom: 0.25em; + border-bottom: 1px solid #e5e5e5; +} +h3 { + font-size: 1.25em; + margin: 2.0em 0 0; +} +h4 { font-size: 1.15em; } +h5 { font-size: 1.10em; } +h6 { font-size: 1em; } + +h4, h5, h6 { + margin-top: 1.5em; + margin-bottom: 1em; +} + +img { + max-width: 100%; +} + +table { + border-collapse: collapse; + margin: 1em 0; +} + +th, td { + border: 1px solid #e1e4e5; + padding: 0.5em 1em; +} + +th { + border-bottom-width: 2px; +} + +tr:nth-child(even) { + background-color: #f3f6f6; +} + +hr { + border: 0; + border-top: 1px solid #e5e5e5; +} + +/* Inline code and code blocks */ + +code { + padding: 0.1em; + background-color: rgba(0,0,0,.04); + border-radius: 3px; +} + +pre { + background-color: #f5f5f5; + border: 1px solid #dddddd; 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+ * highlight.js applies the .hljs style directly to the  tag.
+ */
+.hljs {
+    background-color: transparent;
+    padding: 0;
+}
+
+@media only screen and (max-width: 768px) {
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+        width: 16em;
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+        -webkit-transition-property: left; /* Safari */
+        -webkit-transition-duration: 0.3s; /* Safari */
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+        z-index: 2;
+        box-shadow: 5px 0px 5px 0px rgb(210,210,210);
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+    article > header div#topbar {
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+        -webkit-transition-duration: 0.3s; /* Safari */
+        transition-property: top;
+        transition-duration: 0.3s;
+    }
+
+    article > header div#topbar.headroom--unpinned.headroom--not-top.headroom--not-bottom {
+        top: -4em;
+        -webkit-transition-property: top; /* Safari */
+        -webkit-transition-duration: 0.7s; /* Safari */
+        transition-property: top;
+        transition-duration: 0.7s;
+    }
+
+    article > header div#topbar span {
+        width: 80%;
+        height: 1.5em;
+        margin-top: -0.1em;
+        margin-left: 0.9em;
+        font-size: 1.2em;
+        overflow: hidden;
+    }
+
+    article > header div#topbar a.fa-bars {
+        float: right;
+        padding: 0.6em;
+        margin-top: -0.6em;
+        margin-right: 0.3em;
+        font-size: 1.5em;
+    }
+
+    article > header div#topbar a.fa-bars:visited {
+        color: #3091d1;
+    }
+
+    article table {
+        overflow-x: auto;
+        display: block;
+    }
+
+    article div.MathJax_Display {
+        overflow: scroll;
+    }
+
+    article span.MathJax {
+        overflow: hidden;
+    }
+}
+
+@media only screen and (max-width: 320px) {
+    body {
+        font-size: 15px;
+    }
+}
diff --git a/dev/assets/documenter.js b/dev/assets/documenter.js
new file mode 100644
index 0000000..761ae29
--- /dev/null
+++ b/dev/assets/documenter.js
@@ -0,0 +1,132 @@
+/*
+ * Part of Documenter.jl
+ *     https://github.com/JuliaDocs/Documenter.jl
+ *
+ * License: MIT
+ */
+
+requirejs.config({
+    paths: {
+        'jquery': 'https://cdnjs.cloudflare.com/ajax/libs/jquery/3.1.1/jquery.min',
+        'jqueryui': 'https://cdnjs.cloudflare.com/ajax/libs/jqueryui/1.12.0/jquery-ui.min',
+        'headroom': 'https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.3/headroom.min',
+        'mathjax': 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS_HTML',
+        'highlight': 'https://cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/highlight.min',
+        'highlight-julia': 'https://cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/languages/julia.min',
+        'highlight-julia-repl': 'https://cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/languages/julia-repl.min',
+    },
+    shim: {
+        'mathjax' : {
+            exports: "MathJax"
+        },
+        'highlight-julia': ['highlight'],
+        'highlight-julia-repl': ['highlight'],
+    }
+});
+
+// Load MathJax
+require(['mathjax'], function(MathJax) {
+    MathJax.Hub.Config({
+      "tex2jax": {
+        inlineMath: [['$','$'], ['\\(','\\)']],
+        processEscapes: true
+      }
+    });
+    MathJax.Hub.Config({
+      config: ["MMLorHTML.js"],
+      jax: [
+        "input/TeX",
+        "output/HTML-CSS",
+        "output/NativeMML"
+      ],
+      extensions: [
+        "MathMenu.js",
+        "MathZoom.js",
+        "TeX/AMSmath.js",
+        "TeX/AMSsymbols.js",
+        "TeX/autobold.js",
+        "TeX/autoload-all.js"
+      ]
+    });
+    MathJax.Hub.Config({
+      TeX: { equationNumbers: { autoNumber: "AMS" } }
+    });
+})
+
+require(['jquery', 'highlight', 'highlight-julia', 'highlight-julia-repl'], function($, hljs) {
+    $(document).ready(function() {
+        hljs.initHighlighting();
+    })
+
+})
+
+// update the version selector with info from the siteinfo.js and ../versions.js files
+require(['jquery'], function($) {
+    $(document).ready(function() {
+        var version_selector = $("#version-selector");
+
+        // add the current version to the selector based on siteinfo.js, but only if the selector is empty
+        if (typeof DOCUMENTER_CURRENT_VERSION !== 'undefined' && $('#version-selector > option').length == 0) {
+            var option = $("");
+            version_selector.append(option);
+        }
+
+        if (typeof DOC_VERSIONS !== 'undefined') {
+            var existing_versions = $('#version-selector > option');
+            var existing_versions_texts = existing_versions.map(function(i,x){return x.text});
+            DOC_VERSIONS.forEach(function(each) {
+                var version_url = documenterBaseURL + "/../" + each;
+                var existing_id = $.inArray(each, existing_versions_texts);
+                // if not already in the version selector, add it as a new option,
+                // otherwise update the old option with the URL and enable it
+                if (existing_id == -1) {
+                    var option = $("");
+                    version_selector.append(option);
+                } else {
+                    var option = existing_versions[existing_id];
+                    option.value = version_url;
+                    option.disabled = false;
+                }
+            });
+        }
+
+        // only show the version selector if the selector has been populated
+        if ($('#version-selector > option').length > 0) {
+            version_selector.css("visibility", "visible");
+        }
+
+        // Scroll the navigation bar to the currently selected menu item
+        $("nav.toc > ul").get(0).scrollTop = $(".current").get(0).offsetTop - $("nav.toc > ul").get(0).offsetTop;
+    })
+
+})
+
+// mobile
+require(['jquery', 'headroom'], function($, Headroom) {
+    $(document).ready(function() {
+        var navtoc = $("nav.toc");
+        $("nav.toc li.current a.toctext").click(function() {
+            navtoc.toggleClass('show');
+        });
+        $("article > header div#topbar a.fa-bars").click(function(ev) {
+            ev.preventDefault();
+            navtoc.toggleClass('show');
+            if (navtoc.hasClass('show')) {
+                var title = $("article > header div#topbar span").text();
+                $("nav.toc ul li a:contains('" + title + "')").focus();
+            }
+        });
+        $("article#docs").bind('click', function(ev) {
+            if ($(ev.target).is('div#topbar a.fa-bars')) {
+                return;
+            }
+            if (navtoc.hasClass('show')) {
+                navtoc.removeClass('show');
+            }
+        });
+        if ($("article > header div#topbar").css('display') == 'block') {
+            var headroom = new Headroom(document.querySelector("article > header div#topbar"), {"tolerance": {"up": 10, "down": 10}});
+            headroom.init();
+        }
+    })
+})
diff --git a/dev/assets/search.js b/dev/assets/search.js
new file mode 100644
index 0000000..5d32c3a
--- /dev/null
+++ b/dev/assets/search.js
@@ -0,0 +1,250 @@
+/*
+ * Part of Documenter.jl
+ *     https://github.com/JuliaDocs/Documenter.jl
+ *
+ * License: MIT
+ */
+
+// parseUri 1.2.2
+// (c) Steven Levithan 
+// MIT License
+function parseUri (str) {
+	var	o   = parseUri.options,
+		m   = o.parser[o.strictMode ? "strict" : "loose"].exec(str),
+		uri = {},
+		i   = 14;
+
+	while (i--) uri[o.key[i]] = m[i] || "";
+
+	uri[o.q.name] = {};
+	uri[o.key[12]].replace(o.q.parser, function ($0, $1, $2) {
+		if ($1) uri[o.q.name][$1] = $2;
+	});
+
+	return uri;
+};
+parseUri.options = {
+	strictMode: false,
+	key: ["source","protocol","authority","userInfo","user","password","host","port","relative","path","directory","file","query","anchor"],
+	q:   {
+		name:   "queryKey",
+		parser: /(?:^|&)([^&=]*)=?([^&]*)/g
+	},
+	parser: {
+		strict: /^(?:([^:\/?#]+):)?(?:\/\/((?:(([^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?))?((((?:[^?#\/]*\/)*)([^?#]*))(?:\?([^#]*))?(?:#(.*))?)/,
+		loose:  /^(?:(?![^:@]+:[^:@\/]*@)([^:\/?#.]+):)?(?:\/\/)?((?:(([^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?)(((\/(?:[^?#](?![^?#\/]*\.[^?#\/.]+(?:[?#]|$)))*\/?)?([^?#\/]*))(?:\?([^#]*))?(?:#(.*))?)/
+	}
+};
+
+requirejs.config({
+    paths: {
+        'jquery': 'https://cdnjs.cloudflare.com/ajax/libs/jquery/3.1.1/jquery.min',
+        'lunr': 'https://cdnjs.cloudflare.com/ajax/libs/lunr.js/2.3.5/lunr.min',
+        'lodash': 'https://cdnjs.cloudflare.com/ajax/libs/lodash.js/4.17.11/lodash.min',
+    }
+});
+
+var currentScript = document.currentScript;
+
+require(["jquery", "lunr", "lodash"], function($, lunr, _) {
+    $("#search-form").submit(function(e) {
+        e.preventDefault()
+    })
+
+    // list below is the lunr 2.1.3 list minus the intersect with names(Base)
+    // (all, any, get, in, is, which) and (do, else, for, let, where, while, with)
+    // ideally we'd just filter the original list but it's not available as a variable
+    lunr.stopWordFilter = lunr.generateStopWordFilter([
+        'a',
+        'able',
+        'about',
+        'across',
+        'after',
+        'almost',
+        'also',
+        'am',
+        'among',
+        'an',
+        'and',
+        'are',
+        'as',
+        'at',
+        'be',
+        'because',
+        'been',
+        'but',
+        'by',
+        'can',
+        'cannot',
+        'could',
+        'dear',
+        'did',
+        'does',
+        'either',
+        'ever',
+        'every',
+        'from',
+        'got',
+        'had',
+        'has',
+        'have',
+        'he',
+        'her',
+        'hers',
+        'him',
+        'his',
+        'how',
+        'however',
+        'i',
+        'if',
+        'into',
+        'it',
+        'its',
+        'just',
+        'least',
+        'like',
+        'likely',
+        'may',
+        'me',
+        'might',
+        'most',
+        'must',
+        'my',
+        'neither',
+        'no',
+        'nor',
+        'not',
+        'of',
+        'off',
+        'often',
+        'on',
+        'only',
+        'or',
+        'other',
+        'our',
+        'own',
+        'rather',
+        'said',
+        'say',
+        'says',
+        'she',
+        'should',
+        'since',
+        'so',
+        'some',
+        'than',
+        'that',
+        'the',
+        'their',
+        'them',
+        'then',
+        'there',
+        'these',
+        'they',
+        'this',
+        'tis',
+        'to',
+        'too',
+        'twas',
+        'us',
+        'wants',
+        'was',
+        'we',
+        'were',
+        'what',
+        'when',
+        'who',
+        'whom',
+        'why',
+        'will',
+        'would',
+        'yet',
+        'you',
+        'your'
+        ])
+
+    // add . as a separator, because otherwise "title": "Documenter.Anchors.add!"
+    // would not find anything if searching for "add!", only for the entire qualification
+    lunr.tokenizer.separator = /[\s\-\.]+/
+
+    // custom trimmer that doesn't strip @ and !, which are used in julia macro and function names
+    lunr.trimmer = function (token) {
+        return token.update(function (s) {
+            return s.replace(/^[^a-zA-Z0-9@!]+/, '').replace(/[^a-zA-Z0-9@!]+$/, '')
+        })
+    }
+
+    lunr.Pipeline.registerFunction(lunr.stopWordFilter, 'juliaStopWordFilter')
+    lunr.Pipeline.registerFunction(lunr.trimmer, 'juliaTrimmer')
+
+    var index = lunr(function () {
+        this.ref('location')
+        this.field('title')
+        this.field('text')
+        documenterSearchIndex['docs'].forEach(function(e) {
+            this.add(e)
+        }, this)
+    })
+    var store = {}
+
+    documenterSearchIndex['docs'].forEach(function(e) {
+        store[e.location] = {title: e.title, category: e.category}
+    })
+
+    $(function(){
+        function update_search(querystring) {
+            tokens = lunr.tokenizer(querystring)
+            results = index.query(function (q) {
+                tokens.forEach(function (t) {
+                    q.term(t.toString(), {
+                        fields: ["title"],
+                        boost: 100,
+                        usePipeline: false,
+                        editDistance: 0,
+                        wildcard: lunr.Query.wildcard.NONE
+                    })
+                    q.term(t.toString(), {
+                        fields: ["title"],
+                        boost: 10,
+                        usePipeline: false,
+                        editDistance: 2,
+                        wildcard: lunr.Query.wildcard.NONE
+                    })
+                    q.term(t.toString(), {
+                        fields: ["text"],
+                        boost: 1,
+                        usePipeline: true,
+                        editDistance: 0,
+                        wildcard: lunr.Query.wildcard.NONE
+                    })
+                })
+            })
+            $('#search-info').text("Number of results: " + results.length)
+            $('#search-results').empty()
+            results.forEach(function(result) {
+                data = store[result.ref]
+                link = $('')
+                link.text(data.title)
+                link.attr('href', documenterBaseURL+'/'+result.ref)
+                cat = $('('+data.category+')')
+                li = $('
  • ').append(link).append(" ").append(cat)
+                $('#search-results').append(li)
+            })
+        }
+
+        function update_search_box() {
+            querystring = $('#search-query').val()
+            update_search(querystring)
+        }
+
+        $('#search-query').keyup(_.debounce(update_search_box, 250))
+        $('#search-query').change(update_search_box)
+
+        search_query_uri = parseUri(window.location).queryKey["q"]
+        if(search_query_uri !== undefined) {
+            search_query = decodeURIComponent(search_query_uri.replace(/\+/g, '%20'))
+            $("#search-query").val(search_query)
+        }
+        update_search_box();
+    })
+})
diff --git a/dev/hts-files/index.html b/dev/hts-files/index.html
new file mode 100644
index 0000000..f643e72
--- /dev/null
+++ b/dev/hts-files/index.html
@@ -0,0 +1,106 @@
+
+SAM and BAM · XAM.jl
    SAM and BAM
    SAM and BAM
    Introduction
    High-throughput sequencing (HTS) technologies generate a large amount of data in the form of a large number of nucleotide sequencing reads. One of the most common tasks in bioinformatics is to align these reads against known reference genomes, chromosomes, or contigs. BioAlignments provides several data formats commonly used for this kind of task.
    BioAlignments offers high-performance tools for SAM and BAM file formats, which are the most popular file formats.
    If you have questions about the SAM and BAM formats or any of the terminology used when discussing these formats, see the published [specification][samtools-spec], which is maintained by the [samtools group][samtools].
    A very very simple SAM file looks like the following:
    @HD VN:1.6 SO:coordinate
+@SQ SN:ref LN:45
+r001   99 ref  7 30 8M2I4M1D3M = 37  39 TTAGATAAAGGATACTG *
+r002    0 ref  9 30 3S6M1P1I4M *  0   0 AAAAGATAAGGATA    *
+r003    0 ref  9 30 5S6M       *  0   0 GCCTAAGCTAA       * SA:Z:ref,29,-,6H5M,17,0;
+r004    0 ref 16 30 6M14N5M    *  0   0 ATAGCTTCAGC       *
+r003 2064 ref 29 17 6H5M       *  0   0 TAGGC             * SA:Z:ref,9,+,5S6M,30,1;
+r001  147 ref 37 30 9M         =  7 -39 CAGCGGCAT         * NM:i:1
    Where the first two lines are part of the "header", and the following lines are "records". Each record describes how a read aligns to some reference sequence. Sometimes one record describes one read, but there are other cases like chimeric reads and split alignments, where multiple records apply to one read. In the example above, r003 is a chimeric read, and r004 is a split alignment, and r001 are mate pair reads. Again, we refer you to the official [specification][samtools-spec] for more details.
    A BAM file stores this same information but in a binary and compressible format that does not make for pretty printing here!
    Reading SAM and BAM files
    A typical script iterating over all records in a file looks like below:
    using BioAlignments
+
+# Open a BAM file.
+reader = open(BAM.Reader, "data.bam")
+
+# Iterate over BAM records.
+for record in reader
+    # `record` is a BAM.Record object.
+    if BAM.ismapped(record)
+        # Print the mapped position.
+        println(BAM.refname(record), ':', BAM.position(record))
+    end
+end
+
+# Close the BAM file.
+close(reader)
    The size of a BAM file is often extremely large. The iterator interface demonstrated above allocates an object for each record and that may be a bottleneck of reading data from a BAM file. In-place reading reuses a pre-allocated object for every record and less memory allocation happens in reading:
    reader = open(BAM.Reader, "data.bam")
+record = BAM.Record()
+while !eof(reader)
+    read!(reader, record)
+    # do something
+end
    SAM and BAM Headers
    Both SAM.Reader and BAM.Reader implement the header function, which returns a SAM.Header object. To extract certain information out of the headers, you can use the find method on the header to extract information according to SAM/BAM tag. Again we refer you to the [specification][samtools-spec] for full details of all the different tags that can occur in headers, and what they mean.
    Below is an example of extracting all the info about the reference sequences from the BAM header. In SAM/BAM, any description of a reference sequence is stored in the header, under a tag denoted SQ (think reference SeQuence!).
    julia> reader = open(SAM.Reader, "data.sam");
+
+julia> find(header(reader), "SQ")
+7-element Array{Bio.Align.SAM.MetaInfo,1}:
+ Bio.Align.SAM.MetaInfo:
+    tag: SQ
+  value: SN=Chr1 LN=30427671
+ Bio.Align.SAM.MetaInfo:
+    tag: SQ
+  value: SN=Chr2 LN=19698289
+ Bio.Align.SAM.MetaInfo:
+    tag: SQ
+  value: SN=Chr3 LN=23459830
+ Bio.Align.SAM.MetaInfo:
+    tag: SQ
+  value: SN=Chr4 LN=18585056
+ Bio.Align.SAM.MetaInfo:
+    tag: SQ
+  value: SN=Chr5 LN=26975502
+ Bio.Align.SAM.MetaInfo:
+    tag: SQ
+  value: SN=chloroplast LN=154478
+ 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")
+    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.  [Samtools][samtools] provides index subcommand to create an index file (.bai) from a sorted BAM file.
    $ samtools index -b SRR1238088.sort.bam
+$ ls SRR1238088.sort.bam*
+SRR1238088.sort.bam     SRR1238088.sort.bam.bai
    eachoverlap(reader, chrom, range) returns an iterator of BAM records overlapping the query interval:
    reader = open(BAM.Reader, "SRR1238088.sort.bam", index="SRR1238088.sort.bam.bai")
+for record in eachoverlap(reader, "Chr2", 10000:11000)
+    # `record` is a BAM.Record object
+    # ...
+end
+close(reader)
    Getting records overlapping genomic features
    eachoverlap also accepts the Interval type defined in GenomicFeatures.jl.
    This allows you to do things like first read in the genomic features from a GFF3 file, and then for each feature, iterate over all the BAM records that overlap with that feature.
    # Load GFF3 module.
+using GenomicFeatures
+using BioAlignments
+
+# Load genomic features from a GFF3 file.
+features = open(collect, GFF3.Reader, "TAIR10_GFF3_genes.gff")
+
+# Keep mRNA features.
+filter!(x -> GFF3.featuretype(x) == "mRNA", features)
+
+# Open a BAM file and iterate over records overlapping mRNA transcripts.
+reader = open(BAM.Reader, "SRR1238088.sort.bam", index = "SRR1238088.sort.bam.bai")
+for feature in features
+    for record in eachoverlap(reader, feature)
+        # `record` overlaps `feature`.
+        # ...
+    end
+end
+close(reader)
    Writing files
    In order to write a BAM or SAM file, you must first create a SAM.Header.
    A SAM.Header is constructed from a vector of SAM.MetaInfo objects.
    For example, to create the following simple header:
    @HD VN:1.6 SO:coordinate
+@SQ SN:ref LN:45
    julia> a = SAM.MetaInfo("HD", ["VN" => 1.6, "SO" => "coordinate"])
+SAM.MetaInfo:
+    tag: HD
+  value: VN=1.6 SO=coordinate
+
+julia> b = SAM.MetaInfo("SQ", ["SN" => "ref", "LN" => 45])
+SAM.MetaInfo:
+    tag: SQ
+  value: SN=ref LN=45
+
+julia> h = SAM.Header([a, b])
+SAM.Header(SAM.MetaInfo[SAM.MetaInfo:
+    tag: HD
+  value: VN=1.6 SO=coordinate, SAM.MetaInfo:
+    tag: SQ
+  value: SN=ref LN=45])
+
    Then to create the writer for a SAM file, construct a SAM.Writer using the header and an IO type:
    julia> samw = SAM.Writer(open("my-data.sam", "w"), h)
+SAM.Writer(IOStream(<file my-data.sam>))
+
    To make a BAM Writer is slightly different, as you need to use a specific stream type from the [BGZFStreams][bgzfstreams] package:
    julia> using BGZFStreams
+
+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
    
diff --git a/dev/index.html b/dev/index.html
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+
+Home · XAM.jl
    Home
    XAM
    Latest Release MIT license Stable documentation Latest documentation <!– Pkg Status –> Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.
    Chat
    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 by default only watches the "General" package registry, so before you start, you should add the BioJulia package registry.
    Start a julia terminal, hit the ] key to enter pkg mode (you should see the prompt change from julia> to pkg> ), then enter the following command:
    registry add https://github.com/BioJulia/BioJuliaRegistry.git
    After you've added the registry, you can install XAM from the julia REPL. Press ] to enter pkg mode again, and enter the following:
    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.
    Testing
    XAM is tested against Julia 1.X on Linux, OS X, and Windows.
    Latest build status:
     Build status 
    Contributing
    We appreciate contributions from users including reporting bugs, fixing issues, improving performance and adding new features.
    Take a look at the contributing files detailed contributor and maintainer guidelines, and code of conduct.
    Financial contributions
    We also welcome financial contributions in full transparency on our open collective. Anyone can file an expense. If the expense makes sense for the development of the community, it will be "merged" in the ledger of our open collective by the core contributors and the person who filed the expense will be reimbursed.
    Backers & Sponsors
    Thank you to all our backers and sponsors!
    Love our work and community? Become a backer.
    backers
    Does your company use BioJulia? Help keep BioJulia feature rich and healthy by sponsoring the project Your logo will show up here with a link to your website.
             
    Questions?
    If you have a question about contributing or using BioJulia software, come on over and chat to us on Gitter, or you can try the Bio category of the Julia discourse site.
    
diff --git a/dev/search/index.html b/dev/search/index.html
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+++ b/dev/search/index.html
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+
+Search · XAM.jl
    Search
    Search
    Number of results: loading...
      
diff --git a/dev/search_index.js b/dev/search_index.js
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+++ b/dev/search_index.js
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+var documenterSearchIndex = {"docs":
+[{"location":"#XAM-1","page":"Home","title":"XAM","text":"","category":"section"},{"location":"#","page":"Home","title":"Home","text":"(Image: Latest Release) (Image: MIT license) (Image: Stable documentation) (Image: Latest documentation)  (Image: Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.)","category":"page"},{"location":"#","page":"Home","title":"Home","text":"(Image: Chat)","category":"page"},{"location":"#Description-1","page":"Home","title":"Description","text":"","category":"section"},{"location":"#","page":"Home","title":"Home","text":"XAM provides I/O and utilities for manipulating SAM and BAM, formatted alignment map files.","category":"page"},{"location":"#Installation-1","page":"Home","title":"Installation","text":"","category":"section"},{"location":"#","page":"Home","title":"Home","text":"XAM is made available to install through BioJulia's package registry.","category":"page"},{"location":"#","page":"Home","title":"Home","text":"Julia by default only watches the \"General\" package registry, so before you start, you should add the BioJulia package registry.","category":"page"},{"location":"#","page":"Home","title":"Home","text":"Start a julia terminal, hit the ] key to enter pkg mode (you should see the prompt change from julia> to pkg> ), then enter the following command:","category":"page"},{"location":"#","page":"Home","title":"Home","text":"registry add https://github.com/BioJulia/BioJuliaRegistry.git","category":"page"},{"location":"#","page":"Home","title":"Home","text":"After you've added the registry, you can install XAM from the julia REPL. Press ] to enter pkg mode again, and enter the following:","category":"page"},{"location":"#","page":"Home","title":"Home","text":"add XAM","category":"page"},{"location":"#","page":"Home","title":"Home","text":"If you are interested in the cutting edge of the development, please check out the develop branch to try new features before release.","category":"page"},{"location":"#Testing-1","page":"Home","title":"Testing","text":"","category":"section"},{"location":"#","page":"Home","title":"Home","text":"XAM is tested against Julia 1.X on Linux, OS X, and Windows.","category":"page"},{"location":"#","page":"Home","title":"Home","text":"Latest build status:","category":"page"},{"location":"#","page":"Home","title":"Home","text":"(Image: ) (Image: Build status) (Image: )","category":"page"},{"location":"#Contributing-1","page":"Home","title":"Contributing","text":"","category":"section"},{"location":"#","page":"Home","title":"Home","text":"We appreciate contributions from users including reporting bugs, fixing issues, improving performance and adding new features.","category":"page"},{"location":"#","page":"Home","title":"Home","text":"Take a look at the contributing files detailed contributor and maintainer guidelines, and code of conduct.","category":"page"},{"location":"#Financial-contributions-1","page":"Home","title":"Financial contributions","text":"","category":"section"},{"location":"#","page":"Home","title":"Home","text":"We also welcome financial contributions in full transparency on our open collective. Anyone can file an expense. If the expense makes sense for the development of the community, it will be \"merged\" in the ledger of our open collective by the core contributors and the person who filed the expense will be reimbursed.","category":"page"},{"location":"#Backers-and-Sponsors-1","page":"Home","title":"Backers & Sponsors","text":"","category":"section"},{"location":"#","page":"Home","title":"Home","text":"Thank you to all our backers and sponsors!","category":"page"},{"location":"#","page":"Home","title":"Home","text":"Love our work and community? Become a backer.","category":"page"},{"location":"#","page":"Home","title":"Home","text":"(Image: backers)","category":"page"},{"location":"#","page":"Home","title":"Home","text":"Does your company use BioJulia? Help keep BioJulia feature rich and healthy by sponsoring the project Your logo will show up here with a link to your website.","category":"page"},{"location":"#","page":"Home","title":"Home","text":"(Image: ) (Image: ) (Image: ) (Image: ) (Image: ) (Image: ) (Image: ) (Image: ) (Image: ) (Image: )","category":"page"},{"location":"#Questions?-1","page":"Home","title":"Questions?","text":"","category":"section"},{"location":"#","page":"Home","title":"Home","text":"If you have a question about contributing or using BioJulia software, come on over and chat to us on Gitter, or you can try the Bio category of the Julia discourse site.","category":"page"},{"location":"hts-files/#SAM-and-BAM-1","page":"SAM and BAM","title":"SAM and BAM","text":"","category":"section"},{"location":"hts-files/#Introduction-1","page":"SAM and BAM","title":"Introduction","text":"","category":"section"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"High-throughput sequencing (HTS) technologies generate a large amount of data in the form of a large number of nucleotide sequencing reads. One of the most common tasks in bioinformatics is to align these reads against known reference genomes, chromosomes, or contigs. BioAlignments provides several data formats commonly used for this kind of task.","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"BioAlignments offers high-performance tools for SAM and BAM file formats, which are the most popular file formats.","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"If you have questions about the SAM and BAM formats or any of the terminology used when discussing these formats, see the published [specification][samtools-spec], which is maintained by the [samtools group][samtools].","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"A very very simple SAM file looks like the following:","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"@HD VN:1.6 SO:coordinate\n@SQ SN:ref LN:45\nr001   99 ref  7 30 8M2I4M1D3M = 37  39 TTAGATAAAGGATACTG *\nr002    0 ref  9 30 3S6M1P1I4M *  0   0 AAAAGATAAGGATA    *\nr003    0 ref  9 30 5S6M       *  0   0 GCCTAAGCTAA       * SA:Z:ref,29,-,6H5M,17,0;\nr004    0 ref 16 30 6M14N5M    *  0   0 ATAGCTTCAGC       *\nr003 2064 ref 29 17 6H5M       *  0   0 TAGGC             * SA:Z:ref,9,+,5S6M,30,1;\nr001  147 ref 37 30 9M         =  7 -39 CAGCGGCAT         * NM:i:1","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"Where the first two lines are part of the \"header\", and the following lines are \"records\". Each record describes how a read aligns to some reference sequence. Sometimes one record describes one read, but there are other cases like chimeric reads and split alignments, where multiple records apply to one read. In the example above, r003 is a chimeric read, and r004 is a split alignment, and r001 are mate pair reads. Again, we refer you to the official [specification][samtools-spec] for more details.","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"A BAM file stores this same information but in a binary and compressible format that does not make for pretty printing here!","category":"page"},{"location":"hts-files/#Reading-SAM-and-BAM-files-1","page":"SAM and BAM","title":"Reading SAM and BAM files","text":"","category":"section"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"A typical script iterating over all records in a file looks like below:","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"using BioAlignments\n\n# Open a BAM file.\nreader = open(BAM.Reader, \"data.bam\")\n\n# Iterate over BAM records.\nfor record in reader\n    # `record` is a BAM.Record object.\n    if BAM.ismapped(record)\n        # Print the mapped position.\n        println(BAM.refname(record), ':', BAM.position(record))\n    end\nend\n\n# Close the BAM file.\nclose(reader)","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"The size of a BAM file is often extremely large. The iterator interface demonstrated above allocates an object for each record and that may be a bottleneck of reading data from a BAM file. In-place reading reuses a pre-allocated object for every record and less memory allocation happens in reading:","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"reader = open(BAM.Reader, \"data.bam\")\nrecord = BAM.Record()\nwhile !eof(reader)\n    read!(reader, record)\n    # do something\nend","category":"page"},{"location":"hts-files/#SAM-and-BAM-Headers-1","page":"SAM and BAM","title":"SAM and BAM Headers","text":"","category":"section"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"Both SAM.Reader and BAM.Reader implement the header function, which returns a SAM.Header object. To extract certain information out of the headers, you can use the find method on the header to extract information according to SAM/BAM tag. Again we refer you to the [specification][samtools-spec] for full details of all the different tags that can occur in headers, and what they mean.","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"Below is an example of extracting all the info about the reference sequences from the BAM header. In SAM/BAM, any description of a reference sequence is stored in the header, under a tag denoted SQ (think reference SeQuence!).","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"julia> reader = open(SAM.Reader, \"data.sam\");\n\njulia> find(header(reader), \"SQ\")\n7-element Array{Bio.Align.SAM.MetaInfo,1}:\n Bio.Align.SAM.MetaInfo:\n    tag: SQ\n  value: SN=Chr1 LN=30427671\n Bio.Align.SAM.MetaInfo:\n    tag: SQ\n  value: SN=Chr2 LN=19698289\n Bio.Align.SAM.MetaInfo:\n    tag: SQ\n  value: SN=Chr3 LN=23459830\n Bio.Align.SAM.MetaInfo:\n    tag: SQ\n  value: SN=Chr4 LN=18585056\n Bio.Align.SAM.MetaInfo:\n    tag: SQ\n  value: SN=Chr5 LN=26975502\n Bio.Align.SAM.MetaInfo:\n    tag: SQ\n  value: SN=chloroplast LN=154478\n Bio.Align.SAM.MetaInfo:\n    tag: SQ\n  value: SN=mitochondria LN=366924\n","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"In the above we can see there were 7 sequences in the reference: 5 chromosomes, one chloroplast sequence, and one mitochondrial sequence.","category":"page"},{"location":"hts-files/#SAM-and-BAM-Records-1","page":"SAM and BAM","title":"SAM and BAM Records","text":"","category":"section"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"BioAlignments supports the following accessors for SAM.Record types.","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"XAM.SAM.flag\nXAM.SAM.ismapped\nXAM.SAM.isprimary\nXAM.SAM.refname\nXAM.SAM.position\nXAM.SAM.rightposition\nXAM.SAM.isnextmapped\nXAM.SAM.nextrefname\nXAM.SAM.nextposition\nXAM.SAM.mappingquality\nXAM.SAM.cigar\nXAM.SAM.alignment\nXAM.SAM.alignlength\nXAM.SAM.tempname\nXAM.SAM.templength\nXAM.SAM.sequence\nXAM.SAM.seqlength\nXAM.SAM.quality\nXAM.SAM.auxdata","category":"page"},{"location":"hts-files/#XAM.SAM.flag","page":"SAM and BAM","title":"XAM.SAM.flag","text":"flag(record::Record)::UInt16\n\nGet the bitwise flag of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.SAM.ismapped","page":"SAM and BAM","title":"XAM.SAM.ismapped","text":"ismapped(record::Record)::Bool\n\nTest if record is mapped.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.SAM.isprimary","page":"SAM and BAM","title":"XAM.SAM.isprimary","text":"isprimary(record::Record)::Bool\n\nTest if record is a primary line of the read.\n\nThis is equivalent to flag(record) & 0x900 == 0.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.SAM.refname","page":"SAM and BAM","title":"XAM.SAM.refname","text":"refname(record::Record)::String\n\nGet the reference sequence name of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.SAM.position","page":"SAM and BAM","title":"XAM.SAM.position","text":"position(record::Record)::Int\n\nGet the 1-based leftmost mapping position of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.SAM.rightposition","page":"SAM and BAM","title":"XAM.SAM.rightposition","text":"rightposition(record::Record)::Int\n\nGet the 1-based rightmost mapping position of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.SAM.isnextmapped","page":"SAM and BAM","title":"XAM.SAM.isnextmapped","text":"isnextmapped(record::Record)::Bool\n\nTest if the mate/next read of record is mapped.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.SAM.nextrefname","page":"SAM and BAM","title":"XAM.SAM.nextrefname","text":"nextrefname(record::Record)::String\n\nGet the reference name of the mate/next read of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.SAM.nextposition","page":"SAM and BAM","title":"XAM.SAM.nextposition","text":"nextposition(record::Record)::Int\n\nGet the position of the mate/next read of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.SAM.mappingquality","page":"SAM and BAM","title":"XAM.SAM.mappingquality","text":"mappingquality(record::Record)::UInt8\n\nGet the mapping quality of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.SAM.cigar","page":"SAM and BAM","title":"XAM.SAM.cigar","text":"cigar(record::Record)::String\n\nGet the CIGAR string of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.SAM.alignment","page":"SAM and BAM","title":"XAM.SAM.alignment","text":"alignment(record::Record)::BioAlignments.Alignment\n\nGet the alignment of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.SAM.alignlength","page":"SAM and BAM","title":"XAM.SAM.alignlength","text":"alignlength(record::Record)::Int\n\nGet the alignment length of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.SAM.tempname","page":"SAM and BAM","title":"XAM.SAM.tempname","text":"tempname(record::Record)::String\n\nGet the query template name of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.SAM.templength","page":"SAM and BAM","title":"XAM.SAM.templength","text":"templength(record::Record)::Int\n\nGet the template length of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.SAM.sequence","page":"SAM and BAM","title":"XAM.SAM.sequence","text":"sequence(record::Record)::BioSequences.DNASequence\n\nGet the segment sequence of record.\n\n\n\n\n\nsequence(::Type{String}, record::Record)::String\n\nGet the segment sequence of record as String.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.SAM.seqlength","page":"SAM and BAM","title":"XAM.SAM.seqlength","text":"seqlength(record::Record)::Int\n\nGet the sequence length of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.SAM.quality","page":"SAM and BAM","title":"XAM.SAM.quality","text":"quality(record::Record)::Vector{UInt8}\n\nGet the Phred-scaled base quality of record.\n\n\n\n\n\nquality(::Type{String}, record::Record)::String\n\nGet the ASCII-encoded base quality of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.SAM.auxdata","page":"SAM and BAM","title":"XAM.SAM.auxdata","text":"auxdata(record::Record)::Dict{String,Any}\n\nGet the auxiliary data (optional fields) of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"BioAlignments supports the following accessors for BAM.Record types.","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"XAM.BAM.flag\nXAM.BAM.ismapped\nXAM.BAM.isprimary\nXAM.BAM.refid\nXAM.BAM.refname\nXAM.BAM.reflen\nXAM.BAM.position\nXAM.BAM.rightposition\nXAM.BAM.isnextmapped\nXAM.BAM.nextrefid\nXAM.BAM.nextrefname\nXAM.BAM.nextposition\nXAM.BAM.mappingquality\nXAM.BAM.cigar\nXAM.BAM.alignment\nXAM.BAM.alignlength\nXAM.BAM.tempname\nXAM.BAM.templength\nXAM.BAM.sequence\nXAM.BAM.seqlength\nXAM.BAM.quality\nXAM.BAM.auxdata","category":"page"},{"location":"hts-files/#XAM.BAM.flag","page":"SAM and BAM","title":"XAM.BAM.flag","text":"flag(record::Record)::UInt16\n\nGet the bitwise flag of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.BAM.ismapped","page":"SAM and BAM","title":"XAM.BAM.ismapped","text":"ismapped(record::Record)::Bool\n\nTest if record is mapped.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.BAM.isprimary","page":"SAM and BAM","title":"XAM.BAM.isprimary","text":"isprimary(record::Record)::Bool\n\nTest if record is a primary line of the read.\n\nThis is equivalent to flag(record) & 0x900 == 0.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.BAM.refid","page":"SAM and BAM","title":"XAM.BAM.refid","text":"refid(record::Record)::Int\n\nGet the reference sequence ID of record.\n\nThe ID is 1-based (i.e. the first sequence is 1) and is 0 for a record without a mapping position.\n\nSee also: BAM.rname\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.BAM.refname","page":"SAM and BAM","title":"XAM.BAM.refname","text":"refname(record::Record)::String\n\nGet the reference sequence name of record.\n\nSee also: BAM.refid\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.BAM.reflen","page":"SAM and BAM","title":"XAM.BAM.reflen","text":"reflen(record::Record)::Int\n\nGet the length of the reference sequence this record applies to.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.BAM.position","page":"SAM and BAM","title":"XAM.BAM.position","text":"position(record::Record)::Int\n\nGet the 1-based leftmost mapping position of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.BAM.rightposition","page":"SAM and BAM","title":"XAM.BAM.rightposition","text":"rightposition(record::Record)::Int\n\nGet the 1-based rightmost mapping position of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.BAM.isnextmapped","page":"SAM and BAM","title":"XAM.BAM.isnextmapped","text":"isnextmapped(record::Record)::Bool\n\nTest if the mate/next read of record is mapped.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.BAM.nextrefid","page":"SAM and BAM","title":"XAM.BAM.nextrefid","text":"nextrefid(record::Record)::Int\n\nGet the next/mate reference sequence ID of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.BAM.nextrefname","page":"SAM and BAM","title":"XAM.BAM.nextrefname","text":"nextrefname(record::Record)::String\n\nGet the reference name of the mate/next read of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.BAM.nextposition","page":"SAM and BAM","title":"XAM.BAM.nextposition","text":"nextposition(record::Record)::Int\n\nGet the 1-based leftmost mapping position of the next/mate read of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.BAM.mappingquality","page":"SAM and BAM","title":"XAM.BAM.mappingquality","text":"mappingquality(record::Record)::UInt8\n\nGet the mapping quality of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.BAM.cigar","page":"SAM and BAM","title":"XAM.BAM.cigar","text":"cigar(record::Record)::String\n\nGet the CIGAR string of record.\n\nNote 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.\n\nCalling 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.\n\nIf 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.\n\nSee also BAM.cigar_rle.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.BAM.alignment","page":"SAM and BAM","title":"XAM.BAM.alignment","text":"alignment(record::Record)::BioAlignments.Alignment\n\nGet the alignment of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.BAM.alignlength","page":"SAM and BAM","title":"XAM.BAM.alignlength","text":"alignlength(record::Record)::Int\n\nGet the alignment length of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.BAM.tempname","page":"SAM and BAM","title":"XAM.BAM.tempname","text":"tempname(record::Record)::String\n\nGet the query template name of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.BAM.templength","page":"SAM and BAM","title":"XAM.BAM.templength","text":"templength(record::Record)::Int\n\nGet the template length of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.BAM.sequence","page":"SAM and BAM","title":"XAM.BAM.sequence","text":"sequence(record::Record)::BioSequences.DNASequence\n\nGet the segment sequence of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.BAM.seqlength","page":"SAM and BAM","title":"XAM.BAM.seqlength","text":"seqlength(record::Record)::Int\n\nGet the sequence length of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.BAM.quality","page":"SAM and BAM","title":"XAM.BAM.quality","text":"quality(record::Record)::Vector{UInt8}\n\nGet the base quality of  record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#XAM.BAM.auxdata","page":"SAM and BAM","title":"XAM.BAM.auxdata","text":"auxdata(record::Record)::BAM.AuxData\n\nGet the auxiliary data of record.\n\n\n\n\n\n","category":"function"},{"location":"hts-files/#Accessing-auxiliary-data-1","page":"SAM and BAM","title":"Accessing auxiliary data","text":"","category":"section"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"SAM and BAM records support the storing of optional data fields associated with tags.","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"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.","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"Type Description\n'A' Printable character\n'i' Signed integer\n'f' Single-precision floating number\n'Z' Printable string, including space\n'H' Byte array in Hex format\n'B' Integer of numeric array","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"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.","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"There are some tags that are reserved, predefined standard tags, for specific uses.","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"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:","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"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.","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"for record in open(BAM.Reader, \"data.bam\")\n    nm = record[\"NM\"]::UInt8\n    # do something\nend","category":"page"},{"location":"hts-files/#Getting-records-in-a-range-1","page":"SAM and BAM","title":"Getting records in a range","text":"","category":"section"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"BioAlignments supports the BAI index to fetch records in a specific range from a BAM file.  [Samtools][samtools] provides index subcommand to create an index file (.bai) from a sorted BAM file.","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"$ samtools index -b SRR1238088.sort.bam\n$ ls SRR1238088.sort.bam*\nSRR1238088.sort.bam     SRR1238088.sort.bam.bai","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"eachoverlap(reader, chrom, range) returns an iterator of BAM records overlapping the query interval:","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"reader = open(BAM.Reader, \"SRR1238088.sort.bam\", index=\"SRR1238088.sort.bam.bai\")\nfor record in eachoverlap(reader, \"Chr2\", 10000:11000)\n    # `record` is a BAM.Record object\n    # ...\nend\nclose(reader)","category":"page"},{"location":"hts-files/#Getting-records-overlapping-genomic-features-1","page":"SAM and BAM","title":"Getting records overlapping genomic features","text":"","category":"section"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"eachoverlap also accepts the Interval type defined in GenomicFeatures.jl.","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"This allows you to do things like first read in the genomic features from a GFF3 file, and then for each feature, iterate over all the BAM records that overlap with that feature.","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"# Load GFF3 module.\nusing GenomicFeatures\nusing BioAlignments\n\n# Load genomic features from a GFF3 file.\nfeatures = open(collect, GFF3.Reader, \"TAIR10_GFF3_genes.gff\")\n\n# Keep mRNA features.\nfilter!(x -> GFF3.featuretype(x) == \"mRNA\", features)\n\n# Open a BAM file and iterate over records overlapping mRNA transcripts.\nreader = open(BAM.Reader, \"SRR1238088.sort.bam\", index = \"SRR1238088.sort.bam.bai\")\nfor feature in features\n    for record in eachoverlap(reader, feature)\n        # `record` overlaps `feature`.\n        # ...\n    end\nend\nclose(reader)","category":"page"},{"location":"hts-files/#Writing-files-1","page":"SAM and BAM","title":"Writing files","text":"","category":"section"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"In order to write a BAM or SAM file, you must first create a SAM.Header.","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"A SAM.Header is constructed from a vector of SAM.MetaInfo objects.","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"For example, to create the following simple header:","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"@HD VN:1.6 SO:coordinate\n@SQ SN:ref LN:45","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"julia> a = SAM.MetaInfo(\"HD\", [\"VN\" => 1.6, \"SO\" => \"coordinate\"])\nSAM.MetaInfo:\n    tag: HD\n  value: VN=1.6 SO=coordinate\n\njulia> b = SAM.MetaInfo(\"SQ\", [\"SN\" => \"ref\", \"LN\" => 45])\nSAM.MetaInfo:\n    tag: SQ\n  value: SN=ref LN=45\n\njulia> h = SAM.Header([a, b])\nSAM.Header(SAM.MetaInfo[SAM.MetaInfo:\n    tag: HD\n  value: VN=1.6 SO=coordinate, SAM.MetaInfo:\n    tag: SQ\n  value: SN=ref LN=45])\n","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"Then to create the writer for a SAM file, construct a SAM.Writer using the header and an IO type:","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"julia> samw = SAM.Writer(open(\"my-data.sam\", \"w\"), h)\nSAM.Writer(IOStream())\n","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"To make a BAM Writer is slightly different, as you need to use a specific stream type from the [BGZFStreams][bgzfstreams] package:","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"julia> using BGZFStreams\n\njulia> bamw = BAM.Writer(BGZFStream(open(\"my-data.bam\", \"w\"), \"w\"))\nBAM.Writer(BGZFStreams.BGZFStream{IOStream}())\n","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"Once you have a BAM or SAM writer, you can use the write method to write BAM.Records or SAM.Records to file:","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"julia> write(bamw, rec) # Here rec is a `BAM.Record`\n330780","category":"page"},{"location":"hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"[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","category":"page"},{"location":"api/public/#","page":"Public","title":"Public","text":"CurrentModule = XAM\nDocTestSetup = quote\n    using XAM\nend","category":"page"},{"location":"api/public/#Public-API-Reference-1","page":"Public","title":"Public API Reference","text":"","category":"section"},{"location":"api/public/#Contents-1","page":"Public","title":"Contents","text":"","category":"section"},{"location":"api/public/#","page":"Public","title":"Public","text":"Pages = [\"public.md\"]","category":"page"},{"location":"api/public/#","page":"Public","title":"Public","text":"Pages = [\"public.md\"]","category":"page"},{"location":"api/public/#SAM-API-1","page":"Public","title":"SAM API","text":"","category":"section"},{"location":"api/public/#","page":"Public","title":"Public","text":"The following methods and types are provided by the SAM submodule for public use.","category":"page"},{"location":"api/public/#","page":"Public","title":"Public","text":"Modules = [XAM.SAM]\nprivate = false","category":"page"},{"location":"api/public/#XAM.SAM.FLAG_DUP","page":"Public","title":"XAM.SAM.FLAG_DUP","text":"0x0400: optical or PCR duplicate\n\n\n\n\n\n","category":"constant"},{"location":"api/public/#XAM.SAM.FLAG_MREVERSE","page":"Public","title":"XAM.SAM.FLAG_MREVERSE","text":"0x0020: the mate is mapped to the reverse strand\n\n\n\n\n\n","category":"constant"},{"location":"api/public/#XAM.SAM.FLAG_MUNMAP","page":"Public","title":"XAM.SAM.FLAG_MUNMAP","text":"0x0008: the mate is unmapped\n\n\n\n\n\n","category":"constant"},{"location":"api/public/#XAM.SAM.FLAG_PAIRED","page":"Public","title":"XAM.SAM.FLAG_PAIRED","text":"0x0001: the read is paired in sequencing, no matter whether it is mapped in a pair\n\n\n\n\n\n","category":"constant"},{"location":"api/public/#XAM.SAM.FLAG_PROPER_PAIR","page":"Public","title":"XAM.SAM.FLAG_PROPER_PAIR","text":"0x0002: the read is mapped in a proper pair\n\n\n\n\n\n","category":"constant"},{"location":"api/public/#XAM.SAM.FLAG_QCFAIL","page":"Public","title":"XAM.SAM.FLAG_QCFAIL","text":"0x0200: QC failure\n\n\n\n\n\n","category":"constant"},{"location":"api/public/#XAM.SAM.FLAG_READ1","page":"Public","title":"XAM.SAM.FLAG_READ1","text":"0x0040: this is read1\n\n\n\n\n\n","category":"constant"},{"location":"api/public/#XAM.SAM.FLAG_READ2","page":"Public","title":"XAM.SAM.FLAG_READ2","text":"0x0080: this is read2\n\n\n\n\n\n","category":"constant"},{"location":"api/public/#XAM.SAM.FLAG_REVERSE","page":"Public","title":"XAM.SAM.FLAG_REVERSE","text":"0x0010: the read is mapped to the reverse strand\n\n\n\n\n\n","category":"constant"},{"location":"api/public/#XAM.SAM.FLAG_SECONDARY","page":"Public","title":"XAM.SAM.FLAG_SECONDARY","text":"0x0100: not primary alignment\n\n\n\n\n\n","category":"constant"},{"location":"api/public/#XAM.SAM.FLAG_SUPPLEMENTARY","page":"Public","title":"XAM.SAM.FLAG_SUPPLEMENTARY","text":"0x0800: supplementary alignment\n\n\n\n\n\n","category":"constant"},{"location":"api/public/#XAM.SAM.FLAG_UNMAP","page":"Public","title":"XAM.SAM.FLAG_UNMAP","text":"0x0004: the read itself is unmapped; conflictive with SAM.FLAGPROPERPAIR\n\n\n\n\n\n","category":"constant"},{"location":"api/public/#XAM.SAM.Header-Tuple{}","page":"Public","title":"XAM.SAM.Header","text":"SAM.Header()\n\nCreate an empty header.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.MetaInfo-Tuple{AbstractString,Any}","page":"Public","title":"XAM.SAM.MetaInfo","text":"MetaInfo(tag::AbstractString, value)\n\nCreate a SAM metainfo with tag and value.\n\ntag 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.\n\nExamples\n\njulia> SAM.MetaInfo(\"CO\", \"some comment\")\nBioAlignments.SAM.MetaInfo:\n    tag: CO\n  value: some comment\n\njulia> string(ans)\n\"@CO\tsome comment\"\n\njulia> SAM.MetaInfo(\"SQ\", [\"SN\" => \"chr1\", \"LN\" => 12345])\nBioAlignments.SAM.MetaInfo:\n    tag: SQ\n  value: SN=chr1 LN=12345\n\njulia> string(ans)\n\"@SQ\tSN:chr1\tLN:12345\"\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.MetaInfo-Tuple{AbstractString}","page":"Public","title":"XAM.SAM.MetaInfo","text":"MetaInfo(str::AbstractString)\n\nCreate a SAM metainfo from str.\n\nExamples\n\njulia> SAM.MetaInfo(\"@CO\tsome comment\")\nBioAlignments.SAM.MetaInfo:\n    tag: CO\n  value: some comment\n\njulia> SAM.MetaInfo(\"@SQ\tSN:chr1\tLN:12345\")\nBioAlignments.SAM.MetaInfo:\n    tag: SQ\n  value: SN=chr1 LN=12345\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.Reader-Tuple{IO}","page":"Public","title":"XAM.SAM.Reader","text":"SAM.Reader(input::IO)\n\nCreate a data reader of the SAM file format.\n\nArguments\n\ninput: data source\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.Record-Tuple{AbstractString}","page":"Public","title":"XAM.SAM.Record","text":"SAM.Record(str::AbstractString)\n\nCreate a SAM record from str. This function verifies the format and indexes fields for accessors.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.Record-Tuple{Array{UInt8,1}}","page":"Public","title":"XAM.SAM.Record","text":"SAM.Record(data::Vector{UInt8})\n\nCreate 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.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.Record-Tuple{}","page":"Public","title":"XAM.SAM.Record","text":"SAM.Record()\n\nCreate an unfilled SAM record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.Writer","page":"Public","title":"XAM.SAM.Writer","text":"Writer(output::IO, header::Header=Header())\n\nCreate a data writer of the SAM file format.\n\nArguments\n\noutput: data sink\nheader=Header(): SAM header object\n\n\n\n\n\n","category":"type"},{"location":"api/public/#Base.findall-Tuple{XAM.SAM.Header,AbstractString}","page":"Public","title":"Base.findall","text":"find(header::Header, key::AbstractString)::Vector{MetaInfo}\n\nFind metainfo objects satisfying SAM.tag(metainfo) == key.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#BioCore.header-Tuple{XAM.SAM.Reader}","page":"Public","title":"BioCore.header","text":"header(reader::Reader)::Header\n\nGet the header of reader.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.alignlength-Tuple{XAM.SAM.Record}","page":"Public","title":"XAM.SAM.alignlength","text":"alignlength(record::Record)::Int\n\nGet the alignment length of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.alignment-Tuple{XAM.SAM.Record}","page":"Public","title":"XAM.SAM.alignment","text":"alignment(record::Record)::BioAlignments.Alignment\n\nGet the alignment of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.auxdata-Tuple{XAM.SAM.Record}","page":"Public","title":"XAM.SAM.auxdata","text":"auxdata(record::Record)::Dict{String,Any}\n\nGet the auxiliary data (optional fields) of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.cigar-Tuple{XAM.SAM.Record}","page":"Public","title":"XAM.SAM.cigar","text":"cigar(record::Record)::String\n\nGet the CIGAR string of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.flag-Tuple{XAM.SAM.Record}","page":"Public","title":"XAM.SAM.flag","text":"flag(record::Record)::UInt16\n\nGet the bitwise flag of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.iscomment-Tuple{XAM.SAM.MetaInfo}","page":"Public","title":"XAM.SAM.iscomment","text":"iscomment(metainfo::MetaInfo)::Bool\n\nTest if metainfo is a comment (i.e. its tag is \"CO\").\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.ismapped-Tuple{XAM.SAM.Record}","page":"Public","title":"XAM.SAM.ismapped","text":"ismapped(record::Record)::Bool\n\nTest if record is mapped.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.isnextmapped-Tuple{XAM.SAM.Record}","page":"Public","title":"XAM.SAM.isnextmapped","text":"isnextmapped(record::Record)::Bool\n\nTest if the mate/next read of record is mapped.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.isprimary-Tuple{XAM.SAM.Record}","page":"Public","title":"XAM.SAM.isprimary","text":"isprimary(record::Record)::Bool\n\nTest if record is a primary line of the read.\n\nThis is equivalent to flag(record) & 0x900 == 0.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.keyvalues-Tuple{XAM.SAM.MetaInfo}","page":"Public","title":"XAM.SAM.keyvalues","text":"keyvalues(metainfo::MetaInfo)::Vector{Pair{String,String}}\n\nGet the values of metainfo as string pairs.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.mappingquality-Tuple{XAM.SAM.Record}","page":"Public","title":"XAM.SAM.mappingquality","text":"mappingquality(record::Record)::UInt8\n\nGet the mapping quality of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.nextposition-Tuple{XAM.SAM.Record}","page":"Public","title":"XAM.SAM.nextposition","text":"nextposition(record::Record)::Int\n\nGet the position of the mate/next read of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.nextrefname-Tuple{XAM.SAM.Record}","page":"Public","title":"XAM.SAM.nextrefname","text":"nextrefname(record::Record)::String\n\nGet the reference name of the mate/next read of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.position-Tuple{XAM.SAM.Record}","page":"Public","title":"XAM.SAM.position","text":"position(record::Record)::Int\n\nGet the 1-based leftmost mapping position of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.quality-Tuple{Type{String},XAM.SAM.Record}","page":"Public","title":"XAM.SAM.quality","text":"quality(::Type{String}, record::Record)::String\n\nGet the ASCII-encoded base quality of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.quality-Tuple{XAM.SAM.Record}","page":"Public","title":"XAM.SAM.quality","text":"quality(record::Record)::Vector{UInt8}\n\nGet the Phred-scaled base quality of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.refname-Tuple{XAM.SAM.Record}","page":"Public","title":"XAM.SAM.refname","text":"refname(record::Record)::String\n\nGet the reference sequence name of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.rightposition-Tuple{XAM.SAM.Record}","page":"Public","title":"XAM.SAM.rightposition","text":"rightposition(record::Record)::Int\n\nGet the 1-based rightmost mapping position of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.seqlength-Tuple{XAM.SAM.Record}","page":"Public","title":"XAM.SAM.seqlength","text":"seqlength(record::Record)::Int\n\nGet the sequence length of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.sequence-Tuple{Type{String},XAM.SAM.Record}","page":"Public","title":"XAM.SAM.sequence","text":"sequence(::Type{String}, record::Record)::String\n\nGet the segment sequence of record as String.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.sequence-Tuple{XAM.SAM.Record}","page":"Public","title":"XAM.SAM.sequence","text":"sequence(record::Record)::BioSequences.DNASequence\n\nGet the segment sequence of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.tag-Tuple{XAM.SAM.MetaInfo}","page":"Public","title":"XAM.SAM.tag","text":"tag(metainfo::MetaInfo)::String\n\nGet the tag of metainfo.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.templength-Tuple{XAM.SAM.Record}","page":"Public","title":"XAM.SAM.templength","text":"templength(record::Record)::Int\n\nGet the template length of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.tempname-Tuple{XAM.SAM.Record}","page":"Public","title":"XAM.SAM.tempname","text":"tempname(record::Record)::String\n\nGet the query template name of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.value-Tuple{XAM.SAM.MetaInfo}","page":"Public","title":"XAM.SAM.value","text":"value(metainfo::MetaInfo)::String\n\nGet the value of metainfo as a string.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#BAM-API-1","page":"Public","title":"BAM API","text":"","category":"section"},{"location":"api/public/#","page":"Public","title":"Public","text":"The following methods and types are provided by the BAM submodule for public use.","category":"page"},{"location":"api/public/#","page":"Public","title":"Public","text":"Modules = [XAM.BAM]\nprivate = false","category":"page"},{"location":"api/public/#XAM.BAM.BAI-Tuple{AbstractString}","page":"Public","title":"XAM.BAM.BAI","text":"BAI(filename::AbstractString)\n\nLoad a BAI index from filename.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.BAM.BAI-Tuple{IO}","page":"Public","title":"XAM.BAM.BAI","text":"BAI(input::IO)\n\nLoad a BAI index from input.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.BAM.Reader","page":"Public","title":"XAM.BAM.Reader","text":"BAM.Reader(input::IO; index=nothing)\n\nCreate a data reader of the BAM file format.\n\nArguments\n\ninput: data source\nindex=nothing: filepath to a random access index (currently bai is supported)\n\n\n\n\n\n","category":"type"},{"location":"api/public/#XAM.BAM.Record","page":"Public","title":"XAM.BAM.Record","text":"BAM.Record()\n\nCreate an unfilled BAM record.\n\n\n\n\n\n","category":"type"},{"location":"api/public/#XAM.BAM.Writer","page":"Public","title":"XAM.BAM.Writer","text":"BAM.Writer(output::BGZFStream, header::SAM.Header)\n\nCreate a data writer of the BAM file format.\n\nArguments\n\noutput: data sink\nheader: SAM header object\n\n\n\n\n\n","category":"type"},{"location":"api/public/#BioCore.header-Tuple{XAM.BAM.Reader}","page":"Public","title":"BioCore.header","text":"header(reader::Reader; fillSQ::Bool=false)::SAM.Header\n\nGet the header of reader.\n\nIf fillSQ is true, this function fills missing \"SQ\" metainfo in the header.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.BAM.alignlength-Tuple{XAM.BAM.Record}","page":"Public","title":"XAM.BAM.alignlength","text":"alignlength(record::Record)::Int\n\nGet the alignment length of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.BAM.alignment-Tuple{XAM.BAM.Record}","page":"Public","title":"XAM.BAM.alignment","text":"alignment(record::Record)::BioAlignments.Alignment\n\nGet the alignment of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.BAM.auxdata-Tuple{XAM.BAM.Record}","page":"Public","title":"XAM.BAM.auxdata","text":"auxdata(record::Record)::BAM.AuxData\n\nGet the auxiliary data of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.BAM.cigar","page":"Public","title":"XAM.BAM.cigar","text":"cigar(record::Record)::String\n\nGet the CIGAR string of record.\n\nNote 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.\n\nCalling 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.\n\nIf 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.\n\nSee also BAM.cigar_rle.\n\n\n\n\n\n","category":"function"},{"location":"api/public/#XAM.BAM.cigar_rle","page":"Public","title":"XAM.BAM.cigar_rle","text":"cigar_rle(record::Record, checkCG::Bool = true)::Tuple{Vector{BioAlignments.Operation},Vector{Int}}\n\nGet a run-length encoded tuple (ops, lens) of the CIGAR string in record.\n\nNote 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.\n\nCalling 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.\n\nIf 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.\n\nSee also BAM.cigar.\n\n\n\n\n\n","category":"function"},{"location":"api/public/#XAM.BAM.flag-Tuple{XAM.BAM.Record}","page":"Public","title":"XAM.BAM.flag","text":"flag(record::Record)::UInt16\n\nGet the bitwise flag of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.BAM.ismapped-Tuple{XAM.BAM.Record}","page":"Public","title":"XAM.BAM.ismapped","text":"ismapped(record::Record)::Bool\n\nTest if record is mapped.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.BAM.isnextmapped-Tuple{XAM.BAM.Record}","page":"Public","title":"XAM.BAM.isnextmapped","text":"isnextmapped(record::Record)::Bool\n\nTest if the mate/next read of record is mapped.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.BAM.ispositivestrand-Tuple{XAM.BAM.Record}","page":"Public","title":"XAM.BAM.ispositivestrand","text":"ispositivestrand(record::Record)::Bool\n\nTest if record is aligned to the positive strand.\n\nThis is equivalent to flag(record) & 0x10 == 0.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.BAM.isprimary-Tuple{XAM.BAM.Record}","page":"Public","title":"XAM.BAM.isprimary","text":"isprimary(record::Record)::Bool\n\nTest if record is a primary line of the read.\n\nThis is equivalent to flag(record) & 0x900 == 0.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.BAM.mappingquality-Tuple{XAM.BAM.Record}","page":"Public","title":"XAM.BAM.mappingquality","text":"mappingquality(record::Record)::UInt8\n\nGet the mapping quality of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.BAM.n_cigar_op","page":"Public","title":"XAM.BAM.n_cigar_op","text":"n_cigar_op(record::Record, checkCG::Bool = true)\n\nReturn the number of operations in the CIGAR string of record.\n\nNote 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.\n\nCalling 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.\n\nIf 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.\n\n\n\n\n\n","category":"function"},{"location":"api/public/#XAM.BAM.nextposition-Tuple{XAM.BAM.Record}","page":"Public","title":"XAM.BAM.nextposition","text":"nextposition(record::Record)::Int\n\nGet the 1-based leftmost mapping position of the next/mate read of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.BAM.nextrefid-Tuple{XAM.BAM.Record}","page":"Public","title":"XAM.BAM.nextrefid","text":"nextrefid(record::Record)::Int\n\nGet the next/mate reference sequence ID of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.BAM.nextrefname-Tuple{XAM.BAM.Record}","page":"Public","title":"XAM.BAM.nextrefname","text":"nextrefname(record::Record)::String\n\nGet the reference name of the mate/next read of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.BAM.position-Tuple{XAM.BAM.Record}","page":"Public","title":"XAM.BAM.position","text":"position(record::Record)::Int\n\nGet the 1-based leftmost mapping position of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.BAM.quality-Tuple{XAM.BAM.Record}","page":"Public","title":"XAM.BAM.quality","text":"quality(record::Record)::Vector{UInt8}\n\nGet the base quality of  record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.BAM.refid-Tuple{XAM.BAM.Record}","page":"Public","title":"XAM.BAM.refid","text":"refid(record::Record)::Int\n\nGet the reference sequence ID of record.\n\nThe ID is 1-based (i.e. the first sequence is 1) and is 0 for a record without a mapping position.\n\nSee also: BAM.rname\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.BAM.reflen-Tuple{XAM.BAM.Record}","page":"Public","title":"XAM.BAM.reflen","text":"reflen(record::Record)::Int\n\nGet the length of the reference sequence this record applies to.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.BAM.refname-Tuple{XAM.BAM.Record}","page":"Public","title":"XAM.BAM.refname","text":"refname(record::Record)::String\n\nGet the reference sequence name of record.\n\nSee also: BAM.refid\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.BAM.rightposition-Tuple{XAM.BAM.Record}","page":"Public","title":"XAM.BAM.rightposition","text":"rightposition(record::Record)::Int\n\nGet the 1-based rightmost mapping position of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.BAM.seqlength-Tuple{XAM.BAM.Record}","page":"Public","title":"XAM.BAM.seqlength","text":"seqlength(record::Record)::Int\n\nGet the sequence length of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.BAM.sequence-Tuple{XAM.BAM.Record}","page":"Public","title":"XAM.BAM.sequence","text":"sequence(record::Record)::BioSequences.DNASequence\n\nGet the segment sequence of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.BAM.templength-Tuple{XAM.BAM.Record}","page":"Public","title":"XAM.BAM.templength","text":"templength(record::Record)::Int\n\nGet the template length of record.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.BAM.tempname-Tuple{XAM.BAM.Record}","page":"Public","title":"XAM.BAM.tempname","text":"tempname(record::Record)::String\n\nGet the query template name of record.\n\n\n\n\n\n","category":"method"}]
+}
diff --git a/dev/siteinfo.js b/dev/siteinfo.js
new file mode 100644
index 0000000..3343491
--- /dev/null
+++ b/dev/siteinfo.js
@@ -0,0 +1 @@
+var DOCUMENTER_CURRENT_VERSION = "dev";
diff --git a/latest b/latest
new file mode 120000
index 0000000..9001211
--- /dev/null
+++ b/latest
@@ -0,0 +1 @@
+dev
\ No newline at end of file
diff --git a/versions.js b/versions.js
new file mode 100644
index 0000000..0314857
--- /dev/null
+++ b/versions.js
@@ -0,0 +1,3 @@
+var DOC_VERSIONS = [
+  "dev",
+];