404
+ +Page not found
+ + +'+ escapeHtml(title) + '
' + escapeHtml(summary) +'
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+ Deploying Chanjo2 using Docker
+The Dockerfile provided in the chanjo2 repository can be built and runned to deploy the software. Alternatively an image containing chanjo2 and all its dependencies is hosted on Docker Hub.
+Launching a demo using Docker
+The file named Dockerfile is a generic Docker file to run the application. Whenever the app is launched with the ENV param DEMO (check the settings present in file docker-compose.yml) it will create a test SQLite database to work with.
To start the demo via docker, run:
+docker run -d --rm -p 8000:8000 --expose 8000 clinicalgenomics/chanjo2:latest
+The endpoints of the app will be now reachable from any web browser: http://0.0.0.0:8000/docs or http://localhost:8000/docs
+Launching the app connected to a MySQL database via docker-compose
+An example of this setup is provided in the docker-compose-mysql.yml file.
+Here we connect the app to a MySQL (MariaDB) and provide the connection settings to use it.
Note that a file containing environmnent variables is required to run this setup. The template.env file offers an example of the required variables and can be customised according to your local settings.
To check the configuration (env variables passed to the docker-compose file) run:
+docker-compose -f docker-compose-mysql.yml --env-file template.env config
+The docker-compose file contains 2 services:
+- MariaDB database, runned from a Docker file that includes the script to create an empty testdb database
+- The chanjo2 web app, a REST API
To start the demo, run:
+docker-compose -f docker-compose-mysql.yml --env-file template.env up
+The endpoints of the app will be now reachable from any web browser: http://0.0.0.0:8000/docs or http://localhost:8000/docs
+Production settings and .env file
+Keep in mind that Chanjo2 reads the variables necessary for connecting to the database from a default .env file.
+If you run a dockerized version of Chanjo2 and want to connect to a real database, you'll need to replace the default .env file with a custom environment file containing the correct settings to connect to your MySQL database.
+The last line present on the .env file (DEMO=Y) should be removed or commented out.
Given a local database running on localhost and port 3306, a custom .env file like this:
+MYSQL_USER=dbUser
+MYSQL_PASSWORD=dbPassword
+MYSQL_DATABASE_NAME=chanjo2_test
+MYSQL_HOST_NAME=host.docker.internal
+MYSQL_PORT=3306
+Should suffice to override the parameters present in the default .env file of Chanjo2:
+docker run -d --rm -v $(pwd)/.env:/home/worker/app/.env -p 8000:8000 --expose 8000 clinicalgenomics/chanjo2:latest
+Customising the coverage levels used to create coverage reports and genes overview reports
+When generating coverage and genes overview reports, the metrics showcased in these documents are calculated across various coverage levels, such as 10x, 20x, and 50x.
+These specific coverage levels can be directly specified in queries to the /report and /overview endpoints using the completeness_thresholds parameter, which accepts a list of integers.
+For detailed instructions, please refer to the coverage-reports documentation.
+Alternatively, you can define these coverage levels in the .env file by adding the following line:
REPORT_COVERAGE_LEVELS=[100,150,,..]
+If the REPORT_COVERAGE_LEVELS parameter is not present in the .env file and a request does not include a completeness_thresholds value, the report metrics will default to the following coverage level values: [10, 15, 20, 50, 100].
It's important to note that if coverage level values are provided through multiple methods as described above, the application will prioritize them in the following order:
+-
+
- Values specified in the user's request +
- Values included in the .env file +
- Default coverage level values +
Furthermore, it's worth considering that the more coverage levels provided, the longer it will take for the report pages to load.
+ +
+
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+ GitHub
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+ Next »
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diff --git a/deployment/installation/index.html b/deployment/installation/index.html
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+ Installing Chanjo2 in a virtual environment
+Installing the application on a local Conda environment
+Given a conda environment containing Rust, Python >=3.8 with poetry installed, clone the repository from GitHub with the following command:
+git clone https://github.com/Clinical-Genomics/chanjo2.git
+The command will create a folder named chanjo2 in your current working directory. Move inside this directory:
cd chanjo2
+And install the software with poetry:
+poetry install
+If you encounter any difficulties installing the pyd4 library due to its lack of support for PEP 517 builds, simply retry the aforementioned step using a version of poetry that is less than 1.8.
+You can run a demo instance of the web server by typing:
+uvicorn src.chanjo2.main:app --reload
+The server will run on localhost and default port 8000 (http://0.0.0.0:8000)
+Custom settings and the .env file
+The demo server is connecting to a SQLite database whose temporary tables are destroyed and re-created every time the server is started.
+In order to connect to a permanent MYSQL database instance, you'd need to customise the settings present on the .env file:
MYSQL_USER=dbUser
+MYSQL_PASSWORD=dbPassword
+MYSQL_DATABASE_NAME=chanjo2_test
+MYSQL_HOST_NAME=localhost
+MYSQL_PORT=3306
+The last line present on this file (DEMO=Y) should be removed or commented out.
+
+
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+ GitHub
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diff --git a/js/html5shiv.min.js b/js/html5shiv.min.js
new file mode 100644
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--- /dev/null
+++ b/js/html5shiv.min.js
@@ -0,0 +1,4 @@
+/**
+* @preserve HTML5 Shiv 3.7.3 | @afarkas @jdalton @jon_neal @rem | MIT/GPL2 Licensed
+*/
+!function(a,b){function c(a,b){var c=a.createElement("p"),d=a.getElementsByTagName("head")[0]||a.documentElement;return c.innerHTML="x",d.insertBefore(c.lastChild,d.firstChild)}function d(){var a=t.elements;return"string"==typeof a?a.split(" "):a}function e(a,b){var c=t.elements;"string"!=typeof c&&(c=c.join(" ")),"string"!=typeof a&&(a=a.join(" ")),t.elements=c+" "+a,j(b)}function f(a){var b=s[a[q]];return b||(b={},r++,a[q]=r,s[r]=b),b}function g(a,c,d){if(c||(c=b),l)return c.createElement(a);d||(d=f(c));var e;return e=d.cache[a]?d.cache[a].cloneNode():p.test(a)?(d.cache[a]=d.createElem(a)).cloneNode():d.createElem(a),!e.canHaveChildren||o.test(a)||e.tagUrn?e:d.frag.appendChild(e)}function h(a,c){if(a||(a=b),l)return a.createDocumentFragment();c=c||f(a);for(var e=c.frag.cloneNode(),g=0,h=d(),i=h.length;i>g;g++)e.createElement(h[g]);return e}function i(a,b){b.cache||(b.cache={},b.createElem=a.createElement,b.createFrag=a.createDocumentFragment,b.frag=b.createFrag()),a.createElement=function(c){return t.shivMethods?g(c,a,b):b.createElem(c)},a.createDocumentFragment=Function("h,f","return function(){var n=f.cloneNode(),c=n.createElement;h.shivMethods&&("+d().join().replace(/[\w\-:]+/g,function(a){return b.createElem(a),b.frag.createElement(a),'c("'+a+'")'})+");return n}")(t,b.frag)}function j(a){a||(a=b);var d=f(a);return!t.shivCSS||k||d.hasCSS||(d.hasCSS=!!c(a,"article,aside,dialog,figcaption,figure,footer,header,hgroup,main,nav,section{display:block}mark{background:#FF0;color:#000}template{display:none}")),l||i(a,d),a}var k,l,m="3.7.3",n=a.html5||{},o=/^<|^(?:button|map|select|textarea|object|iframe|option|optgroup)$/i,p=/^(?:a|b|code|div|fieldset|h1|h2|h3|h4|h5|h6|i|label|li|ol|p|q|span|strong|style|table|tbody|td|th|tr|ul)$/i,q="_html5shiv",r=0,s={};!function(){try{var a=b.createElement("a");a.innerHTML="
+
+
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+
+
+
+
+ Chanjo2 documentation pages
+Chanjo2 is coverage analysis tool for clinical sequencing data using the d4 (Dense Depth Data Dump) format. +It's implemented in Python FastAPI and provides API endpoints to communicate with a d4tools software in order to +return coverage and coverage completeness over genomic intervals (genes, transcripts, exons as well as custom intervals) over +single d4 files or samples stored in the database with associated d4 files.
+The tool is flexible and can be used in different ways. The simplest use case would be calculating sequencing coverage over one or more intervals for a d4 file stored locally or remotely on the internet.
+Chanjo2 image as a proxy to d4tools to compute coverage stats over genomic intervals of a d4 file
+Chanjo2 image contains d4tools and can be used to directly retrieve statistics over d4 files.
+Executing d4tools
+docker run --entrypoint d4tools --rm clinicalgenomics/chanjo2:latest
+Calculating coverage on specific genomic intervals of a d4 file using d4tools
+docker run --entrypoint d4tools --platform linux/x86_64 --rm -v <path-to-local-d4-files-folder>:/home/worker/infiles clinicalgenomics/chanjo2:latest view /home/worker/infiles/<d4file.d4> 1:1234560-1234580 X:1234560-1234580
+Please note that the d4 file containing the coverage data can be also stored on a remote server. In this case the command above could be replaced by this one:
+docker run --entrypoint d4tools --platform linux/x86_64 --rm clinicalgenomics/chanjo2:latest view <url-to-remote-d4-file.d4> 1:1234560-1234580 X:1234560-1234580
+The coverage computation on a file hosted on a remote server, will be consistently slower than when hosting the file on a local server.
+Chanjo2 as a REST server
+When chanjo2 is launched and runs as a REST server, it is offering many additional features, including:
+-
+
Support for calculating coverage and coverage completeness over genes, transcripts and exons for different genome builds
+- Chanjo2 server can be either installed on a virtual environment using poetry of directly launched using Docker +
Instructions on how to set up and run Chanjo2 as a REST server as well as the functionalities that it offers are better illustrated in these dedicated pages.
+ +
+
+
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+
+ Search Results
+ + + +
+ Searching...
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+ GitHub
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diff --git a/search/lunr.js b/search/lunr.js
new file mode 100644
index 00000000..aca0a167
--- /dev/null
+++ b/search/lunr.js
@@ -0,0 +1,3475 @@
+/**
+ * lunr - http://lunrjs.com - A bit like Solr, but much smaller and not as bright - 2.3.9
+ * Copyright (C) 2020 Oliver Nightingale
+ * @license MIT
+ */
+
+;(function(){
+
+/**
+ * A convenience function for configuring and constructing
+ * a new lunr Index.
+ *
+ * A lunr.Builder instance is created and the pipeline setup
+ * with a trimmer, stop word filter and stemmer.
+ *
+ * This builder object is yielded to the configuration function
+ * that is passed as a parameter, allowing the list of fields
+ * and other builder parameters to be customised.
+ *
+ * All documents _must_ be added within the passed config function.
+ *
+ * @example
+ * var idx = lunr(function () {
+ * this.field('title')
+ * this.field('body')
+ * this.ref('id')
+ *
+ * documents.forEach(function (doc) {
+ * this.add(doc)
+ * }, this)
+ * })
+ *
+ * @see {@link lunr.Builder}
+ * @see {@link lunr.Pipeline}
+ * @see {@link lunr.trimmer}
+ * @see {@link lunr.stopWordFilter}
+ * @see {@link lunr.stemmer}
+ * @namespace {function} lunr
+ */
+var lunr = function (config) {
+ var builder = new lunr.Builder
+
+ builder.pipeline.add(
+ lunr.trimmer,
+ lunr.stopWordFilter,
+ lunr.stemmer
+ )
+
+ builder.searchPipeline.add(
+ lunr.stemmer
+ )
+
+ config.call(builder, builder)
+ return builder.build()
+}
+
+lunr.version = "2.3.9"
+/*!
+ * lunr.utils
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/**
+ * A namespace containing utils for the rest of the lunr library
+ * @namespace lunr.utils
+ */
+lunr.utils = {}
+
+/**
+ * Print a warning message to the console.
+ *
+ * @param {String} message The message to be printed.
+ * @memberOf lunr.utils
+ * @function
+ */
+lunr.utils.warn = (function (global) {
+ /* eslint-disable no-console */
+ return function (message) {
+ if (global.console && console.warn) {
+ console.warn(message)
+ }
+ }
+ /* eslint-enable no-console */
+})(this)
+
+/**
+ * Convert an object to a string.
+ *
+ * In the case of `null` and `undefined` the function returns
+ * the empty string, in all other cases the result of calling
+ * `toString` on the passed object is returned.
+ *
+ * @param {Any} obj The object to convert to a string.
+ * @return {String} string representation of the passed object.
+ * @memberOf lunr.utils
+ */
+lunr.utils.asString = function (obj) {
+ if (obj === void 0 || obj === null) {
+ return ""
+ } else {
+ return obj.toString()
+ }
+}
+
+/**
+ * Clones an object.
+ *
+ * Will create a copy of an existing object such that any mutations
+ * on the copy cannot affect the original.
+ *
+ * Only shallow objects are supported, passing a nested object to this
+ * function will cause a TypeError.
+ *
+ * Objects with primitives, and arrays of primitives are supported.
+ *
+ * @param {Object} obj The object to clone.
+ * @return {Object} a clone of the passed object.
+ * @throws {TypeError} when a nested object is passed.
+ * @memberOf Utils
+ */
+lunr.utils.clone = function (obj) {
+ if (obj === null || obj === undefined) {
+ return obj
+ }
+
+ var clone = Object.create(null),
+ keys = Object.keys(obj)
+
+ for (var i = 0; i < keys.length; i++) {
+ var key = keys[i],
+ val = obj[key]
+
+ if (Array.isArray(val)) {
+ clone[key] = val.slice()
+ continue
+ }
+
+ if (typeof val === 'string' ||
+ typeof val === 'number' ||
+ typeof val === 'boolean') {
+ clone[key] = val
+ continue
+ }
+
+ throw new TypeError("clone is not deep and does not support nested objects")
+ }
+
+ return clone
+}
+lunr.FieldRef = function (docRef, fieldName, stringValue) {
+ this.docRef = docRef
+ this.fieldName = fieldName
+ this._stringValue = stringValue
+}
+
+lunr.FieldRef.joiner = "/"
+
+lunr.FieldRef.fromString = function (s) {
+ var n = s.indexOf(lunr.FieldRef.joiner)
+
+ if (n === -1) {
+ throw "malformed field ref string"
+ }
+
+ var fieldRef = s.slice(0, n),
+ docRef = s.slice(n + 1)
+
+ return new lunr.FieldRef (docRef, fieldRef, s)
+}
+
+lunr.FieldRef.prototype.toString = function () {
+ if (this._stringValue == undefined) {
+ this._stringValue = this.fieldName + lunr.FieldRef.joiner + this.docRef
+ }
+
+ return this._stringValue
+}
+/*!
+ * lunr.Set
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/**
+ * A lunr set.
+ *
+ * @constructor
+ */
+lunr.Set = function (elements) {
+ this.elements = Object.create(null)
+
+ if (elements) {
+ this.length = elements.length
+
+ for (var i = 0; i < this.length; i++) {
+ this.elements[elements[i]] = true
+ }
+ } else {
+ this.length = 0
+ }
+}
+
+/**
+ * A complete set that contains all elements.
+ *
+ * @static
+ * @readonly
+ * @type {lunr.Set}
+ */
+lunr.Set.complete = {
+ intersect: function (other) {
+ return other
+ },
+
+ union: function () {
+ return this
+ },
+
+ contains: function () {
+ return true
+ }
+}
+
+/**
+ * An empty set that contains no elements.
+ *
+ * @static
+ * @readonly
+ * @type {lunr.Set}
+ */
+lunr.Set.empty = {
+ intersect: function () {
+ return this
+ },
+
+ union: function (other) {
+ return other
+ },
+
+ contains: function () {
+ return false
+ }
+}
+
+/**
+ * Returns true if this set contains the specified object.
+ *
+ * @param {object} object - Object whose presence in this set is to be tested.
+ * @returns {boolean} - True if this set contains the specified object.
+ */
+lunr.Set.prototype.contains = function (object) {
+ return !!this.elements[object]
+}
+
+/**
+ * Returns a new set containing only the elements that are present in both
+ * this set and the specified set.
+ *
+ * @param {lunr.Set} other - set to intersect with this set.
+ * @returns {lunr.Set} a new set that is the intersection of this and the specified set.
+ */
+
+lunr.Set.prototype.intersect = function (other) {
+ var a, b, elements, intersection = []
+
+ if (other === lunr.Set.complete) {
+ return this
+ }
+
+ if (other === lunr.Set.empty) {
+ return other
+ }
+
+ if (this.length < other.length) {
+ a = this
+ b = other
+ } else {
+ a = other
+ b = this
+ }
+
+ elements = Object.keys(a.elements)
+
+ for (var i = 0; i < elements.length; i++) {
+ var element = elements[i]
+ if (element in b.elements) {
+ intersection.push(element)
+ }
+ }
+
+ return new lunr.Set (intersection)
+}
+
+/**
+ * Returns a new set combining the elements of this and the specified set.
+ *
+ * @param {lunr.Set} other - set to union with this set.
+ * @return {lunr.Set} a new set that is the union of this and the specified set.
+ */
+
+lunr.Set.prototype.union = function (other) {
+ if (other === lunr.Set.complete) {
+ return lunr.Set.complete
+ }
+
+ if (other === lunr.Set.empty) {
+ return this
+ }
+
+ return new lunr.Set(Object.keys(this.elements).concat(Object.keys(other.elements)))
+}
+/**
+ * A function to calculate the inverse document frequency for
+ * a posting. This is shared between the builder and the index
+ *
+ * @private
+ * @param {object} posting - The posting for a given term
+ * @param {number} documentCount - The total number of documents.
+ */
+lunr.idf = function (posting, documentCount) {
+ var documentsWithTerm = 0
+
+ for (var fieldName in posting) {
+ if (fieldName == '_index') continue // Ignore the term index, its not a field
+ documentsWithTerm += Object.keys(posting[fieldName]).length
+ }
+
+ var x = (documentCount - documentsWithTerm + 0.5) / (documentsWithTerm + 0.5)
+
+ return Math.log(1 + Math.abs(x))
+}
+
+/**
+ * A token wraps a string representation of a token
+ * as it is passed through the text processing pipeline.
+ *
+ * @constructor
+ * @param {string} [str=''] - The string token being wrapped.
+ * @param {object} [metadata={}] - Metadata associated with this token.
+ */
+lunr.Token = function (str, metadata) {
+ this.str = str || ""
+ this.metadata = metadata || {}
+}
+
+/**
+ * Returns the token string that is being wrapped by this object.
+ *
+ * @returns {string}
+ */
+lunr.Token.prototype.toString = function () {
+ return this.str
+}
+
+/**
+ * A token update function is used when updating or optionally
+ * when cloning a token.
+ *
+ * @callback lunr.Token~updateFunction
+ * @param {string} str - The string representation of the token.
+ * @param {Object} metadata - All metadata associated with this token.
+ */
+
+/**
+ * Applies the given function to the wrapped string token.
+ *
+ * @example
+ * token.update(function (str, metadata) {
+ * return str.toUpperCase()
+ * })
+ *
+ * @param {lunr.Token~updateFunction} fn - A function to apply to the token string.
+ * @returns {lunr.Token}
+ */
+lunr.Token.prototype.update = function (fn) {
+ this.str = fn(this.str, this.metadata)
+ return this
+}
+
+/**
+ * Creates a clone of this token. Optionally a function can be
+ * applied to the cloned token.
+ *
+ * @param {lunr.Token~updateFunction} [fn] - An optional function to apply to the cloned token.
+ * @returns {lunr.Token}
+ */
+lunr.Token.prototype.clone = function (fn) {
+ fn = fn || function (s) { return s }
+ return new lunr.Token (fn(this.str, this.metadata), this.metadata)
+}
+/*!
+ * lunr.tokenizer
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/**
+ * A function for splitting a string into tokens ready to be inserted into
+ * the search index. Uses `lunr.tokenizer.separator` to split strings, change
+ * the value of this property to change how strings are split into tokens.
+ *
+ * This tokenizer will convert its parameter to a string by calling `toString` and
+ * then will split this string on the character in `lunr.tokenizer.separator`.
+ * Arrays will have their elements converted to strings and wrapped in a lunr.Token.
+ *
+ * Optional metadata can be passed to the tokenizer, this metadata will be cloned and
+ * added as metadata to every token that is created from the object to be tokenized.
+ *
+ * @static
+ * @param {?(string|object|object[])} obj - The object to convert into tokens
+ * @param {?object} metadata - Optional metadata to associate with every token
+ * @returns {lunr.Token[]}
+ * @see {@link lunr.Pipeline}
+ */
+lunr.tokenizer = function (obj, metadata) {
+ if (obj == null || obj == undefined) {
+ return []
+ }
+
+ if (Array.isArray(obj)) {
+ return obj.map(function (t) {
+ return new lunr.Token(
+ lunr.utils.asString(t).toLowerCase(),
+ lunr.utils.clone(metadata)
+ )
+ })
+ }
+
+ var str = obj.toString().toLowerCase(),
+ len = str.length,
+ tokens = []
+
+ for (var sliceEnd = 0, sliceStart = 0; sliceEnd <= len; sliceEnd++) {
+ var char = str.charAt(sliceEnd),
+ sliceLength = sliceEnd - sliceStart
+
+ if ((char.match(lunr.tokenizer.separator) || sliceEnd == len)) {
+
+ if (sliceLength > 0) {
+ var tokenMetadata = lunr.utils.clone(metadata) || {}
+ tokenMetadata["position"] = [sliceStart, sliceLength]
+ tokenMetadata["index"] = tokens.length
+
+ tokens.push(
+ new lunr.Token (
+ str.slice(sliceStart, sliceEnd),
+ tokenMetadata
+ )
+ )
+ }
+
+ sliceStart = sliceEnd + 1
+ }
+
+ }
+
+ return tokens
+}
+
+/**
+ * The separator used to split a string into tokens. Override this property to change the behaviour of
+ * `lunr.tokenizer` behaviour when tokenizing strings. By default this splits on whitespace and hyphens.
+ *
+ * @static
+ * @see lunr.tokenizer
+ */
+lunr.tokenizer.separator = /[\s\-]+/
+/*!
+ * lunr.Pipeline
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/**
+ * lunr.Pipelines maintain an ordered list of functions to be applied to all
+ * tokens in documents entering the search index and queries being ran against
+ * the index.
+ *
+ * An instance of lunr.Index created with the lunr shortcut will contain a
+ * pipeline with a stop word filter and an English language stemmer. Extra
+ * functions can be added before or after either of these functions or these
+ * default functions can be removed.
+ *
+ * When run the pipeline will call each function in turn, passing a token, the
+ * index of that token in the original list of all tokens and finally a list of
+ * all the original tokens.
+ *
+ * The output of functions in the pipeline will be passed to the next function
+ * in the pipeline. To exclude a token from entering the index the function
+ * should return undefined, the rest of the pipeline will not be called with
+ * this token.
+ *
+ * For serialisation of pipelines to work, all functions used in an instance of
+ * a pipeline should be registered with lunr.Pipeline. Registered functions can
+ * then be loaded. If trying to load a serialised pipeline that uses functions
+ * that are not registered an error will be thrown.
+ *
+ * If not planning on serialising the pipeline then registering pipeline functions
+ * is not necessary.
+ *
+ * @constructor
+ */
+lunr.Pipeline = function () {
+ this._stack = []
+}
+
+lunr.Pipeline.registeredFunctions = Object.create(null)
+
+/**
+ * A pipeline function maps lunr.Token to lunr.Token. A lunr.Token contains the token
+ * string as well as all known metadata. A pipeline function can mutate the token string
+ * or mutate (or add) metadata for a given token.
+ *
+ * A pipeline function can indicate that the passed token should be discarded by returning
+ * null, undefined or an empty string. This token will not be passed to any downstream pipeline
+ * functions and will not be added to the index.
+ *
+ * Multiple tokens can be returned by returning an array of tokens. Each token will be passed
+ * to any downstream pipeline functions and all will returned tokens will be added to the index.
+ *
+ * Any number of pipeline functions may be chained together using a lunr.Pipeline.
+ *
+ * @interface lunr.PipelineFunction
+ * @param {lunr.Token} token - A token from the document being processed.
+ * @param {number} i - The index of this token in the complete list of tokens for this document/field.
+ * @param {lunr.Token[]} tokens - All tokens for this document/field.
+ * @returns {(?lunr.Token|lunr.Token[])}
+ */
+
+/**
+ * Register a function with the pipeline.
+ *
+ * Functions that are used in the pipeline should be registered if the pipeline
+ * needs to be serialised, or a serialised pipeline needs to be loaded.
+ *
+ * Registering a function does not add it to a pipeline, functions must still be
+ * added to instances of the pipeline for them to be used when running a pipeline.
+ *
+ * @param {lunr.PipelineFunction} fn - The function to check for.
+ * @param {String} label - The label to register this function with
+ */
+lunr.Pipeline.registerFunction = function (fn, label) {
+ if (label in this.registeredFunctions) {
+ lunr.utils.warn('Overwriting existing registered function: ' + label)
+ }
+
+ fn.label = label
+ lunr.Pipeline.registeredFunctions[fn.label] = fn
+}
+
+/**
+ * Warns if the function is not registered as a Pipeline function.
+ *
+ * @param {lunr.PipelineFunction} fn - The function to check for.
+ * @private
+ */
+lunr.Pipeline.warnIfFunctionNotRegistered = function (fn) {
+ var isRegistered = fn.label && (fn.label in this.registeredFunctions)
+
+ if (!isRegistered) {
+ lunr.utils.warn('Function is not registered with pipeline. This may cause problems when serialising the index.\n', fn)
+ }
+}
+
+/**
+ * Loads a previously serialised pipeline.
+ *
+ * All functions to be loaded must already be registered with lunr.Pipeline.
+ * If any function from the serialised data has not been registered then an
+ * error will be thrown.
+ *
+ * @param {Object} serialised - The serialised pipeline to load.
+ * @returns {lunr.Pipeline}
+ */
+lunr.Pipeline.load = function (serialised) {
+ var pipeline = new lunr.Pipeline
+
+ serialised.forEach(function (fnName) {
+ var fn = lunr.Pipeline.registeredFunctions[fnName]
+
+ if (fn) {
+ pipeline.add(fn)
+ } else {
+ throw new Error('Cannot load unregistered function: ' + fnName)
+ }
+ })
+
+ return pipeline
+}
+
+/**
+ * Adds new functions to the end of the pipeline.
+ *
+ * Logs a warning if the function has not been registered.
+ *
+ * @param {lunr.PipelineFunction[]} functions - Any number of functions to add to the pipeline.
+ */
+lunr.Pipeline.prototype.add = function () {
+ var fns = Array.prototype.slice.call(arguments)
+
+ fns.forEach(function (fn) {
+ lunr.Pipeline.warnIfFunctionNotRegistered(fn)
+ this._stack.push(fn)
+ }, this)
+}
+
+/**
+ * Adds a single function after a function that already exists in the
+ * pipeline.
+ *
+ * Logs a warning if the function has not been registered.
+ *
+ * @param {lunr.PipelineFunction} existingFn - A function that already exists in the pipeline.
+ * @param {lunr.PipelineFunction} newFn - The new function to add to the pipeline.
+ */
+lunr.Pipeline.prototype.after = function (existingFn, newFn) {
+ lunr.Pipeline.warnIfFunctionNotRegistered(newFn)
+
+ var pos = this._stack.indexOf(existingFn)
+ if (pos == -1) {
+ throw new Error('Cannot find existingFn')
+ }
+
+ pos = pos + 1
+ this._stack.splice(pos, 0, newFn)
+}
+
+/**
+ * Adds a single function before a function that already exists in the
+ * pipeline.
+ *
+ * Logs a warning if the function has not been registered.
+ *
+ * @param {lunr.PipelineFunction} existingFn - A function that already exists in the pipeline.
+ * @param {lunr.PipelineFunction} newFn - The new function to add to the pipeline.
+ */
+lunr.Pipeline.prototype.before = function (existingFn, newFn) {
+ lunr.Pipeline.warnIfFunctionNotRegistered(newFn)
+
+ var pos = this._stack.indexOf(existingFn)
+ if (pos == -1) {
+ throw new Error('Cannot find existingFn')
+ }
+
+ this._stack.splice(pos, 0, newFn)
+}
+
+/**
+ * Removes a function from the pipeline.
+ *
+ * @param {lunr.PipelineFunction} fn The function to remove from the pipeline.
+ */
+lunr.Pipeline.prototype.remove = function (fn) {
+ var pos = this._stack.indexOf(fn)
+ if (pos == -1) {
+ return
+ }
+
+ this._stack.splice(pos, 1)
+}
+
+/**
+ * Runs the current list of functions that make up the pipeline against the
+ * passed tokens.
+ *
+ * @param {Array} tokens The tokens to run through the pipeline.
+ * @returns {Array}
+ */
+lunr.Pipeline.prototype.run = function (tokens) {
+ var stackLength = this._stack.length
+
+ for (var i = 0; i < stackLength; i++) {
+ var fn = this._stack[i]
+ var memo = []
+
+ for (var j = 0; j < tokens.length; j++) {
+ var result = fn(tokens[j], j, tokens)
+
+ if (result === null || result === void 0 || result === '') continue
+
+ if (Array.isArray(result)) {
+ for (var k = 0; k < result.length; k++) {
+ memo.push(result[k])
+ }
+ } else {
+ memo.push(result)
+ }
+ }
+
+ tokens = memo
+ }
+
+ return tokens
+}
+
+/**
+ * Convenience method for passing a string through a pipeline and getting
+ * strings out. This method takes care of wrapping the passed string in a
+ * token and mapping the resulting tokens back to strings.
+ *
+ * @param {string} str - The string to pass through the pipeline.
+ * @param {?object} metadata - Optional metadata to associate with the token
+ * passed to the pipeline.
+ * @returns {string[]}
+ */
+lunr.Pipeline.prototype.runString = function (str, metadata) {
+ var token = new lunr.Token (str, metadata)
+
+ return this.run([token]).map(function (t) {
+ return t.toString()
+ })
+}
+
+/**
+ * Resets the pipeline by removing any existing processors.
+ *
+ */
+lunr.Pipeline.prototype.reset = function () {
+ this._stack = []
+}
+
+/**
+ * Returns a representation of the pipeline ready for serialisation.
+ *
+ * Logs a warning if the function has not been registered.
+ *
+ * @returns {Array}
+ */
+lunr.Pipeline.prototype.toJSON = function () {
+ return this._stack.map(function (fn) {
+ lunr.Pipeline.warnIfFunctionNotRegistered(fn)
+
+ return fn.label
+ })
+}
+/*!
+ * lunr.Vector
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/**
+ * A vector is used to construct the vector space of documents and queries. These
+ * vectors support operations to determine the similarity between two documents or
+ * a document and a query.
+ *
+ * Normally no parameters are required for initializing a vector, but in the case of
+ * loading a previously dumped vector the raw elements can be provided to the constructor.
+ *
+ * For performance reasons vectors are implemented with a flat array, where an elements
+ * index is immediately followed by its value. E.g. [index, value, index, value]. This
+ * allows the underlying array to be as sparse as possible and still offer decent
+ * performance when being used for vector calculations.
+ *
+ * @constructor
+ * @param {Number[]} [elements] - The flat list of element index and element value pairs.
+ */
+lunr.Vector = function (elements) {
+ this._magnitude = 0
+ this.elements = elements || []
+}
+
+
+/**
+ * Calculates the position within the vector to insert a given index.
+ *
+ * This is used internally by insert and upsert. If there are duplicate indexes then
+ * the position is returned as if the value for that index were to be updated, but it
+ * is the callers responsibility to check whether there is a duplicate at that index
+ *
+ * @param {Number} insertIdx - The index at which the element should be inserted.
+ * @returns {Number}
+ */
+lunr.Vector.prototype.positionForIndex = function (index) {
+ // For an empty vector the tuple can be inserted at the beginning
+ if (this.elements.length == 0) {
+ return 0
+ }
+
+ var start = 0,
+ end = this.elements.length / 2,
+ sliceLength = end - start,
+ pivotPoint = Math.floor(sliceLength / 2),
+ pivotIndex = this.elements[pivotPoint * 2]
+
+ while (sliceLength > 1) {
+ if (pivotIndex < index) {
+ start = pivotPoint
+ }
+
+ if (pivotIndex > index) {
+ end = pivotPoint
+ }
+
+ if (pivotIndex == index) {
+ break
+ }
+
+ sliceLength = end - start
+ pivotPoint = start + Math.floor(sliceLength / 2)
+ pivotIndex = this.elements[pivotPoint * 2]
+ }
+
+ if (pivotIndex == index) {
+ return pivotPoint * 2
+ }
+
+ if (pivotIndex > index) {
+ return pivotPoint * 2
+ }
+
+ if (pivotIndex < index) {
+ return (pivotPoint + 1) * 2
+ }
+}
+
+/**
+ * Inserts an element at an index within the vector.
+ *
+ * Does not allow duplicates, will throw an error if there is already an entry
+ * for this index.
+ *
+ * @param {Number} insertIdx - The index at which the element should be inserted.
+ * @param {Number} val - The value to be inserted into the vector.
+ */
+lunr.Vector.prototype.insert = function (insertIdx, val) {
+ this.upsert(insertIdx, val, function () {
+ throw "duplicate index"
+ })
+}
+
+/**
+ * Inserts or updates an existing index within the vector.
+ *
+ * @param {Number} insertIdx - The index at which the element should be inserted.
+ * @param {Number} val - The value to be inserted into the vector.
+ * @param {function} fn - A function that is called for updates, the existing value and the
+ * requested value are passed as arguments
+ */
+lunr.Vector.prototype.upsert = function (insertIdx, val, fn) {
+ this._magnitude = 0
+ var position = this.positionForIndex(insertIdx)
+
+ if (this.elements[position] == insertIdx) {
+ this.elements[position + 1] = fn(this.elements[position + 1], val)
+ } else {
+ this.elements.splice(position, 0, insertIdx, val)
+ }
+}
+
+/**
+ * Calculates the magnitude of this vector.
+ *
+ * @returns {Number}
+ */
+lunr.Vector.prototype.magnitude = function () {
+ if (this._magnitude) return this._magnitude
+
+ var sumOfSquares = 0,
+ elementsLength = this.elements.length
+
+ for (var i = 1; i < elementsLength; i += 2) {
+ var val = this.elements[i]
+ sumOfSquares += val * val
+ }
+
+ return this._magnitude = Math.sqrt(sumOfSquares)
+}
+
+/**
+ * Calculates the dot product of this vector and another vector.
+ *
+ * @param {lunr.Vector} otherVector - The vector to compute the dot product with.
+ * @returns {Number}
+ */
+lunr.Vector.prototype.dot = function (otherVector) {
+ var dotProduct = 0,
+ a = this.elements, b = otherVector.elements,
+ aLen = a.length, bLen = b.length,
+ aVal = 0, bVal = 0,
+ i = 0, j = 0
+
+ while (i < aLen && j < bLen) {
+ aVal = a[i], bVal = b[j]
+ if (aVal < bVal) {
+ i += 2
+ } else if (aVal > bVal) {
+ j += 2
+ } else if (aVal == bVal) {
+ dotProduct += a[i + 1] * b[j + 1]
+ i += 2
+ j += 2
+ }
+ }
+
+ return dotProduct
+}
+
+/**
+ * Calculates the similarity between this vector and another vector.
+ *
+ * @param {lunr.Vector} otherVector - The other vector to calculate the
+ * similarity with.
+ * @returns {Number}
+ */
+lunr.Vector.prototype.similarity = function (otherVector) {
+ return this.dot(otherVector) / this.magnitude() || 0
+}
+
+/**
+ * Converts the vector to an array of the elements within the vector.
+ *
+ * @returns {Number[]}
+ */
+lunr.Vector.prototype.toArray = function () {
+ var output = new Array (this.elements.length / 2)
+
+ for (var i = 1, j = 0; i < this.elements.length; i += 2, j++) {
+ output[j] = this.elements[i]
+ }
+
+ return output
+}
+
+/**
+ * A JSON serializable representation of the vector.
+ *
+ * @returns {Number[]}
+ */
+lunr.Vector.prototype.toJSON = function () {
+ return this.elements
+}
+/* eslint-disable */
+/*!
+ * lunr.stemmer
+ * Copyright (C) 2020 Oliver Nightingale
+ * Includes code from - http://tartarus.org/~martin/PorterStemmer/js.txt
+ */
+
+/**
+ * lunr.stemmer is an english language stemmer, this is a JavaScript
+ * implementation of the PorterStemmer taken from http://tartarus.org/~martin
+ *
+ * @static
+ * @implements {lunr.PipelineFunction}
+ * @param {lunr.Token} token - The string to stem
+ * @returns {lunr.Token}
+ * @see {@link lunr.Pipeline}
+ * @function
+ */
+lunr.stemmer = (function(){
+ var step2list = {
+ "ational" : "ate",
+ "tional" : "tion",
+ "enci" : "ence",
+ "anci" : "ance",
+ "izer" : "ize",
+ "bli" : "ble",
+ "alli" : "al",
+ "entli" : "ent",
+ "eli" : "e",
+ "ousli" : "ous",
+ "ization" : "ize",
+ "ation" : "ate",
+ "ator" : "ate",
+ "alism" : "al",
+ "iveness" : "ive",
+ "fulness" : "ful",
+ "ousness" : "ous",
+ "aliti" : "al",
+ "iviti" : "ive",
+ "biliti" : "ble",
+ "logi" : "log"
+ },
+
+ step3list = {
+ "icate" : "ic",
+ "ative" : "",
+ "alize" : "al",
+ "iciti" : "ic",
+ "ical" : "ic",
+ "ful" : "",
+ "ness" : ""
+ },
+
+ c = "[^aeiou]", // consonant
+ v = "[aeiouy]", // vowel
+ C = c + "[^aeiouy]*", // consonant sequence
+ V = v + "[aeiou]*", // vowel sequence
+
+ mgr0 = "^(" + C + ")?" + V + C, // [C]VC... is m>0
+ meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$", // [C]VC[V] is m=1
+ mgr1 = "^(" + C + ")?" + V + C + V + C, // [C]VCVC... is m>1
+ s_v = "^(" + C + ")?" + v; // vowel in stem
+
+ var re_mgr0 = new RegExp(mgr0);
+ var re_mgr1 = new RegExp(mgr1);
+ var re_meq1 = new RegExp(meq1);
+ var re_s_v = new RegExp(s_v);
+
+ var re_1a = /^(.+?)(ss|i)es$/;
+ var re2_1a = /^(.+?)([^s])s$/;
+ var re_1b = /^(.+?)eed$/;
+ var re2_1b = /^(.+?)(ed|ing)$/;
+ var re_1b_2 = /.$/;
+ var re2_1b_2 = /(at|bl|iz)$/;
+ var re3_1b_2 = new RegExp("([^aeiouylsz])\\1$");
+ var re4_1b_2 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+
+ var re_1c = /^(.+?[^aeiou])y$/;
+ var re_2 = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
+
+ var re_3 = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
+
+ var re_4 = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
+ var re2_4 = /^(.+?)(s|t)(ion)$/;
+
+ var re_5 = /^(.+?)e$/;
+ var re_5_1 = /ll$/;
+ var re3_5 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+
+ var porterStemmer = function porterStemmer(w) {
+ var stem,
+ suffix,
+ firstch,
+ re,
+ re2,
+ re3,
+ re4;
+
+ if (w.length < 3) { return w; }
+
+ firstch = w.substr(0,1);
+ if (firstch == "y") {
+ w = firstch.toUpperCase() + w.substr(1);
+ }
+
+ // Step 1a
+ re = re_1a
+ re2 = re2_1a;
+
+ if (re.test(w)) { w = w.replace(re,"$1$2"); }
+ else if (re2.test(w)) { w = w.replace(re2,"$1$2"); }
+
+ // Step 1b
+ re = re_1b;
+ re2 = re2_1b;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ re = re_mgr0;
+ if (re.test(fp[1])) {
+ re = re_1b_2;
+ w = w.replace(re,"");
+ }
+ } else if (re2.test(w)) {
+ var fp = re2.exec(w);
+ stem = fp[1];
+ re2 = re_s_v;
+ if (re2.test(stem)) {
+ w = stem;
+ re2 = re2_1b_2;
+ re3 = re3_1b_2;
+ re4 = re4_1b_2;
+ if (re2.test(w)) { w = w + "e"; }
+ else if (re3.test(w)) { re = re_1b_2; w = w.replace(re,""); }
+ else if (re4.test(w)) { w = w + "e"; }
+ }
+ }
+
+ // Step 1c - replace suffix y or Y by i if preceded by a non-vowel which is not the first letter of the word (so cry -> cri, by -> by, say -> say)
+ re = re_1c;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ w = stem + "i";
+ }
+
+ // Step 2
+ re = re_2;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ suffix = fp[2];
+ re = re_mgr0;
+ if (re.test(stem)) {
+ w = stem + step2list[suffix];
+ }
+ }
+
+ // Step 3
+ re = re_3;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ suffix = fp[2];
+ re = re_mgr0;
+ if (re.test(stem)) {
+ w = stem + step3list[suffix];
+ }
+ }
+
+ // Step 4
+ re = re_4;
+ re2 = re2_4;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = re_mgr1;
+ if (re.test(stem)) {
+ w = stem;
+ }
+ } else if (re2.test(w)) {
+ var fp = re2.exec(w);
+ stem = fp[1] + fp[2];
+ re2 = re_mgr1;
+ if (re2.test(stem)) {
+ w = stem;
+ }
+ }
+
+ // Step 5
+ re = re_5;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = re_mgr1;
+ re2 = re_meq1;
+ re3 = re3_5;
+ if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) {
+ w = stem;
+ }
+ }
+
+ re = re_5_1;
+ re2 = re_mgr1;
+ if (re.test(w) && re2.test(w)) {
+ re = re_1b_2;
+ w = w.replace(re,"");
+ }
+
+ // and turn initial Y back to y
+
+ if (firstch == "y") {
+ w = firstch.toLowerCase() + w.substr(1);
+ }
+
+ return w;
+ };
+
+ return function (token) {
+ return token.update(porterStemmer);
+ }
+})();
+
+lunr.Pipeline.registerFunction(lunr.stemmer, 'stemmer')
+/*!
+ * lunr.stopWordFilter
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/**
+ * lunr.generateStopWordFilter builds a stopWordFilter function from the provided
+ * list of stop words.
+ *
+ * The built in lunr.stopWordFilter is built using this generator and can be used
+ * to generate custom stopWordFilters for applications or non English languages.
+ *
+ * @function
+ * @param {Array} token The token to pass through the filter
+ * @returns {lunr.PipelineFunction}
+ * @see lunr.Pipeline
+ * @see lunr.stopWordFilter
+ */
+lunr.generateStopWordFilter = function (stopWords) {
+ var words = stopWords.reduce(function (memo, stopWord) {
+ memo[stopWord] = stopWord
+ return memo
+ }, {})
+
+ return function (token) {
+ if (token && words[token.toString()] !== token.toString()) return token
+ }
+}
+
+/**
+ * lunr.stopWordFilter is an English language stop word list filter, any words
+ * contained in the list will not be passed through the filter.
+ *
+ * This is intended to be used in the Pipeline. If the token does not pass the
+ * filter then undefined will be returned.
+ *
+ * @function
+ * @implements {lunr.PipelineFunction}
+ * @params {lunr.Token} token - A token to check for being a stop word.
+ * @returns {lunr.Token}
+ * @see {@link lunr.Pipeline}
+ */
+lunr.stopWordFilter = lunr.generateStopWordFilter([
+ 'a',
+ 'able',
+ 'about',
+ 'across',
+ 'after',
+ 'all',
+ 'almost',
+ 'also',
+ 'am',
+ 'among',
+ 'an',
+ 'and',
+ 'any',
+ 'are',
+ 'as',
+ 'at',
+ 'be',
+ 'because',
+ 'been',
+ 'but',
+ 'by',
+ 'can',
+ 'cannot',
+ 'could',
+ 'dear',
+ 'did',
+ 'do',
+ 'does',
+ 'either',
+ 'else',
+ 'ever',
+ 'every',
+ 'for',
+ 'from',
+ 'get',
+ 'got',
+ 'had',
+ 'has',
+ 'have',
+ 'he',
+ 'her',
+ 'hers',
+ 'him',
+ 'his',
+ 'how',
+ 'however',
+ 'i',
+ 'if',
+ 'in',
+ 'into',
+ 'is',
+ 'it',
+ 'its',
+ 'just',
+ 'least',
+ 'let',
+ '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',
+ 'where',
+ 'which',
+ 'while',
+ 'who',
+ 'whom',
+ 'why',
+ 'will',
+ 'with',
+ 'would',
+ 'yet',
+ 'you',
+ 'your'
+])
+
+lunr.Pipeline.registerFunction(lunr.stopWordFilter, 'stopWordFilter')
+/*!
+ * lunr.trimmer
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/**
+ * lunr.trimmer is a pipeline function for trimming non word
+ * characters from the beginning and end of tokens before they
+ * enter the index.
+ *
+ * This implementation may not work correctly for non latin
+ * characters and should either be removed or adapted for use
+ * with languages with non-latin characters.
+ *
+ * @static
+ * @implements {lunr.PipelineFunction}
+ * @param {lunr.Token} token The token to pass through the filter
+ * @returns {lunr.Token}
+ * @see lunr.Pipeline
+ */
+lunr.trimmer = function (token) {
+ return token.update(function (s) {
+ return s.replace(/^\W+/, '').replace(/\W+$/, '')
+ })
+}
+
+lunr.Pipeline.registerFunction(lunr.trimmer, 'trimmer')
+/*!
+ * lunr.TokenSet
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/**
+ * A token set is used to store the unique list of all tokens
+ * within an index. Token sets are also used to represent an
+ * incoming query to the index, this query token set and index
+ * token set are then intersected to find which tokens to look
+ * up in the inverted index.
+ *
+ * A token set can hold multiple tokens, as in the case of the
+ * index token set, or it can hold a single token as in the
+ * case of a simple query token set.
+ *
+ * Additionally token sets are used to perform wildcard matching.
+ * Leading, contained and trailing wildcards are supported, and
+ * from this edit distance matching can also be provided.
+ *
+ * Token sets are implemented as a minimal finite state automata,
+ * where both common prefixes and suffixes are shared between tokens.
+ * This helps to reduce the space used for storing the token set.
+ *
+ * @constructor
+ */
+lunr.TokenSet = function () {
+ this.final = false
+ this.edges = {}
+ this.id = lunr.TokenSet._nextId
+ lunr.TokenSet._nextId += 1
+}
+
+/**
+ * Keeps track of the next, auto increment, identifier to assign
+ * to a new tokenSet.
+ *
+ * TokenSets require a unique identifier to be correctly minimised.
+ *
+ * @private
+ */
+lunr.TokenSet._nextId = 1
+
+/**
+ * Creates a TokenSet instance from the given sorted array of words.
+ *
+ * @param {String[]} arr - A sorted array of strings to create the set from.
+ * @returns {lunr.TokenSet}
+ * @throws Will throw an error if the input array is not sorted.
+ */
+lunr.TokenSet.fromArray = function (arr) {
+ var builder = new lunr.TokenSet.Builder
+
+ for (var i = 0, len = arr.length; i < len; i++) {
+ builder.insert(arr[i])
+ }
+
+ builder.finish()
+ return builder.root
+}
+
+/**
+ * Creates a token set from a query clause.
+ *
+ * @private
+ * @param {Object} clause - A single clause from lunr.Query.
+ * @param {string} clause.term - The query clause term.
+ * @param {number} [clause.editDistance] - The optional edit distance for the term.
+ * @returns {lunr.TokenSet}
+ */
+lunr.TokenSet.fromClause = function (clause) {
+ if ('editDistance' in clause) {
+ return lunr.TokenSet.fromFuzzyString(clause.term, clause.editDistance)
+ } else {
+ return lunr.TokenSet.fromString(clause.term)
+ }
+}
+
+/**
+ * Creates a token set representing a single string with a specified
+ * edit distance.
+ *
+ * Insertions, deletions, substitutions and transpositions are each
+ * treated as an edit distance of 1.
+ *
+ * Increasing the allowed edit distance will have a dramatic impact
+ * on the performance of both creating and intersecting these TokenSets.
+ * It is advised to keep the edit distance less than 3.
+ *
+ * @param {string} str - The string to create the token set from.
+ * @param {number} editDistance - The allowed edit distance to match.
+ * @returns {lunr.Vector}
+ */
+lunr.TokenSet.fromFuzzyString = function (str, editDistance) {
+ var root = new lunr.TokenSet
+
+ var stack = [{
+ node: root,
+ editsRemaining: editDistance,
+ str: str
+ }]
+
+ while (stack.length) {
+ var frame = stack.pop()
+
+ // no edit
+ if (frame.str.length > 0) {
+ var char = frame.str.charAt(0),
+ noEditNode
+
+ if (char in frame.node.edges) {
+ noEditNode = frame.node.edges[char]
+ } else {
+ noEditNode = new lunr.TokenSet
+ frame.node.edges[char] = noEditNode
+ }
+
+ if (frame.str.length == 1) {
+ noEditNode.final = true
+ }
+
+ stack.push({
+ node: noEditNode,
+ editsRemaining: frame.editsRemaining,
+ str: frame.str.slice(1)
+ })
+ }
+
+ if (frame.editsRemaining == 0) {
+ continue
+ }
+
+ // insertion
+ if ("*" in frame.node.edges) {
+ var insertionNode = frame.node.edges["*"]
+ } else {
+ var insertionNode = new lunr.TokenSet
+ frame.node.edges["*"] = insertionNode
+ }
+
+ if (frame.str.length == 0) {
+ insertionNode.final = true
+ }
+
+ stack.push({
+ node: insertionNode,
+ editsRemaining: frame.editsRemaining - 1,
+ str: frame.str
+ })
+
+ // deletion
+ // can only do a deletion if we have enough edits remaining
+ // and if there are characters left to delete in the string
+ if (frame.str.length > 1) {
+ stack.push({
+ node: frame.node,
+ editsRemaining: frame.editsRemaining - 1,
+ str: frame.str.slice(1)
+ })
+ }
+
+ // deletion
+ // just removing the last character from the str
+ if (frame.str.length == 1) {
+ frame.node.final = true
+ }
+
+ // substitution
+ // can only do a substitution if we have enough edits remaining
+ // and if there are characters left to substitute
+ if (frame.str.length >= 1) {
+ if ("*" in frame.node.edges) {
+ var substitutionNode = frame.node.edges["*"]
+ } else {
+ var substitutionNode = new lunr.TokenSet
+ frame.node.edges["*"] = substitutionNode
+ }
+
+ if (frame.str.length == 1) {
+ substitutionNode.final = true
+ }
+
+ stack.push({
+ node: substitutionNode,
+ editsRemaining: frame.editsRemaining - 1,
+ str: frame.str.slice(1)
+ })
+ }
+
+ // transposition
+ // can only do a transposition if there are edits remaining
+ // and there are enough characters to transpose
+ if (frame.str.length > 1) {
+ var charA = frame.str.charAt(0),
+ charB = frame.str.charAt(1),
+ transposeNode
+
+ if (charB in frame.node.edges) {
+ transposeNode = frame.node.edges[charB]
+ } else {
+ transposeNode = new lunr.TokenSet
+ frame.node.edges[charB] = transposeNode
+ }
+
+ if (frame.str.length == 1) {
+ transposeNode.final = true
+ }
+
+ stack.push({
+ node: transposeNode,
+ editsRemaining: frame.editsRemaining - 1,
+ str: charA + frame.str.slice(2)
+ })
+ }
+ }
+
+ return root
+}
+
+/**
+ * Creates a TokenSet from a string.
+ *
+ * The string may contain one or more wildcard characters (*)
+ * that will allow wildcard matching when intersecting with
+ * another TokenSet.
+ *
+ * @param {string} str - The string to create a TokenSet from.
+ * @returns {lunr.TokenSet}
+ */
+lunr.TokenSet.fromString = function (str) {
+ var node = new lunr.TokenSet,
+ root = node
+
+ /*
+ * Iterates through all characters within the passed string
+ * appending a node for each character.
+ *
+ * When a wildcard character is found then a self
+ * referencing edge is introduced to continually match
+ * any number of any characters.
+ */
+ for (var i = 0, len = str.length; i < len; i++) {
+ var char = str[i],
+ final = (i == len - 1)
+
+ if (char == "*") {
+ node.edges[char] = node
+ node.final = final
+
+ } else {
+ var next = new lunr.TokenSet
+ next.final = final
+
+ node.edges[char] = next
+ node = next
+ }
+ }
+
+ return root
+}
+
+/**
+ * Converts this TokenSet into an array of strings
+ * contained within the TokenSet.
+ *
+ * This is not intended to be used on a TokenSet that
+ * contains wildcards, in these cases the results are
+ * undefined and are likely to cause an infinite loop.
+ *
+ * @returns {string[]}
+ */
+lunr.TokenSet.prototype.toArray = function () {
+ var words = []
+
+ var stack = [{
+ prefix: "",
+ node: this
+ }]
+
+ while (stack.length) {
+ var frame = stack.pop(),
+ edges = Object.keys(frame.node.edges),
+ len = edges.length
+
+ if (frame.node.final) {
+ /* In Safari, at this point the prefix is sometimes corrupted, see:
+ * https://github.com/olivernn/lunr.js/issues/279 Calling any
+ * String.prototype method forces Safari to "cast" this string to what
+ * it's supposed to be, fixing the bug. */
+ frame.prefix.charAt(0)
+ words.push(frame.prefix)
+ }
+
+ for (var i = 0; i < len; i++) {
+ var edge = edges[i]
+
+ stack.push({
+ prefix: frame.prefix.concat(edge),
+ node: frame.node.edges[edge]
+ })
+ }
+ }
+
+ return words
+}
+
+/**
+ * Generates a string representation of a TokenSet.
+ *
+ * This is intended to allow TokenSets to be used as keys
+ * in objects, largely to aid the construction and minimisation
+ * of a TokenSet. As such it is not designed to be a human
+ * friendly representation of the TokenSet.
+ *
+ * @returns {string}
+ */
+lunr.TokenSet.prototype.toString = function () {
+ // NOTE: Using Object.keys here as this.edges is very likely
+ // to enter 'hash-mode' with many keys being added
+ //
+ // avoiding a for-in loop here as it leads to the function
+ // being de-optimised (at least in V8). From some simple
+ // benchmarks the performance is comparable, but allowing
+ // V8 to optimize may mean easy performance wins in the future.
+
+ if (this._str) {
+ return this._str
+ }
+
+ var str = this.final ? '1' : '0',
+ labels = Object.keys(this.edges).sort(),
+ len = labels.length
+
+ for (var i = 0; i < len; i++) {
+ var label = labels[i],
+ node = this.edges[label]
+
+ str = str + label + node.id
+ }
+
+ return str
+}
+
+/**
+ * Returns a new TokenSet that is the intersection of
+ * this TokenSet and the passed TokenSet.
+ *
+ * This intersection will take into account any wildcards
+ * contained within the TokenSet.
+ *
+ * @param {lunr.TokenSet} b - An other TokenSet to intersect with.
+ * @returns {lunr.TokenSet}
+ */
+lunr.TokenSet.prototype.intersect = function (b) {
+ var output = new lunr.TokenSet,
+ frame = undefined
+
+ var stack = [{
+ qNode: b,
+ output: output,
+ node: this
+ }]
+
+ while (stack.length) {
+ frame = stack.pop()
+
+ // NOTE: As with the #toString method, we are using
+ // Object.keys and a for loop instead of a for-in loop
+ // as both of these objects enter 'hash' mode, causing
+ // the function to be de-optimised in V8
+ var qEdges = Object.keys(frame.qNode.edges),
+ qLen = qEdges.length,
+ nEdges = Object.keys(frame.node.edges),
+ nLen = nEdges.length
+
+ for (var q = 0; q < qLen; q++) {
+ var qEdge = qEdges[q]
+
+ for (var n = 0; n < nLen; n++) {
+ var nEdge = nEdges[n]
+
+ if (nEdge == qEdge || qEdge == '*') {
+ var node = frame.node.edges[nEdge],
+ qNode = frame.qNode.edges[qEdge],
+ final = node.final && qNode.final,
+ next = undefined
+
+ if (nEdge in frame.output.edges) {
+ // an edge already exists for this character
+ // no need to create a new node, just set the finality
+ // bit unless this node is already final
+ next = frame.output.edges[nEdge]
+ next.final = next.final || final
+
+ } else {
+ // no edge exists yet, must create one
+ // set the finality bit and insert it
+ // into the output
+ next = new lunr.TokenSet
+ next.final = final
+ frame.output.edges[nEdge] = next
+ }
+
+ stack.push({
+ qNode: qNode,
+ output: next,
+ node: node
+ })
+ }
+ }
+ }
+ }
+
+ return output
+}
+lunr.TokenSet.Builder = function () {
+ this.previousWord = ""
+ this.root = new lunr.TokenSet
+ this.uncheckedNodes = []
+ this.minimizedNodes = {}
+}
+
+lunr.TokenSet.Builder.prototype.insert = function (word) {
+ var node,
+ commonPrefix = 0
+
+ if (word < this.previousWord) {
+ throw new Error ("Out of order word insertion")
+ }
+
+ for (var i = 0; i < word.length && i < this.previousWord.length; i++) {
+ if (word[i] != this.previousWord[i]) break
+ commonPrefix++
+ }
+
+ this.minimize(commonPrefix)
+
+ if (this.uncheckedNodes.length == 0) {
+ node = this.root
+ } else {
+ node = this.uncheckedNodes[this.uncheckedNodes.length - 1].child
+ }
+
+ for (var i = commonPrefix; i < word.length; i++) {
+ var nextNode = new lunr.TokenSet,
+ char = word[i]
+
+ node.edges[char] = nextNode
+
+ this.uncheckedNodes.push({
+ parent: node,
+ char: char,
+ child: nextNode
+ })
+
+ node = nextNode
+ }
+
+ node.final = true
+ this.previousWord = word
+}
+
+lunr.TokenSet.Builder.prototype.finish = function () {
+ this.minimize(0)
+}
+
+lunr.TokenSet.Builder.prototype.minimize = function (downTo) {
+ for (var i = this.uncheckedNodes.length - 1; i >= downTo; i--) {
+ var node = this.uncheckedNodes[i],
+ childKey = node.child.toString()
+
+ if (childKey in this.minimizedNodes) {
+ node.parent.edges[node.char] = this.minimizedNodes[childKey]
+ } else {
+ // Cache the key for this node since
+ // we know it can't change anymore
+ node.child._str = childKey
+
+ this.minimizedNodes[childKey] = node.child
+ }
+
+ this.uncheckedNodes.pop()
+ }
+}
+/*!
+ * lunr.Index
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/**
+ * An index contains the built index of all documents and provides a query interface
+ * to the index.
+ *
+ * Usually instances of lunr.Index will not be created using this constructor, instead
+ * lunr.Builder should be used to construct new indexes, or lunr.Index.load should be
+ * used to load previously built and serialized indexes.
+ *
+ * @constructor
+ * @param {Object} attrs - The attributes of the built search index.
+ * @param {Object} attrs.invertedIndex - An index of term/field to document reference.
+ * @param {Object' + noResultsText + '
'); + } +} + +function doSearch () { + var query = document.getElementById('mkdocs-search-query').value; + if (query.length > min_search_length) { + if (!window.Worker) { + displayResults(search(query)); + } else { + searchWorker.postMessage({query: query}); + } + } else { + // Clear results for short queries + displayResults([]); + } +} + +function initSearch () { + var search_input = document.getElementById('mkdocs-search-query'); + if (search_input) { + search_input.addEventListener("keyup", doSearch); + } + var term = getSearchTermFromLocation(); + if (term) { + search_input.value = term; + doSearch(); + } +} + +function onWorkerMessage (e) { + if (e.data.allowSearch) { + initSearch(); + } else if (e.data.results) { + var results = e.data.results; + displayResults(results); + } else if (e.data.config) { + min_search_length = e.data.config.min_search_length-1; + } +} + +if (!window.Worker) { + console.log('Web Worker API not supported'); + // load index in main thread + $.getScript(joinUrl(base_url, "search/worker.js")).done(function () { + console.log('Loaded worker'); + init(); + window.postMessage = function (msg) { + onWorkerMessage({data: msg}); + }; + }).fail(function (jqxhr, settings, exception) { + console.error('Could not load worker.js'); + }); +} else { + // Wrap search in a web worker + var searchWorker = new Worker(joinUrl(base_url, "search/worker.js")); + searchWorker.postMessage({init: true}); + searchWorker.onmessage = onWorkerMessage; +} diff --git a/search/search_index.json b/search/search_index.json new file mode 100644 index 00000000..8f0d005a --- /dev/null +++ b/search/search_index.json @@ -0,0 +1 @@ +{"config":{"indexing":"full","lang":["en"],"min_search_length":3,"prebuild_index":false,"separator":"[\\s\\-]+"},"docs":[{"location":"","text":"Chanjo2 documentation pages Chanjo2 is coverage analysis tool for clinical sequencing data using the d4 (Dense Depth Data Dump) format . It's implemented in Python FastAPI and provides API endpoints to communicate with a d4tools software in order to return coverage and coverage completeness over genomic intervals (genes, transcripts, exons as well as custom intervals) over single d4 files or samples stored in the database with associated d4 files. The tool is flexible and can be used in different ways. The simplest use case would be calculating sequencing coverage over one or more intervals for a d4 file stored locally or remotely on the internet. Chanjo2 image as a proxy to d4tools to compute coverage stats over genomic intervals of a d4 file Chanjo2 image contains d4tools and can be used to directly retrieve statistics over d4 files. Executing d4tools docker run --entrypoint d4tools --rm clinicalgenomics/chanjo2:latest Calculating coverage on specific genomic intervals of a d4 file using d4tools docker run --entrypoint d4tools --platform linux/x86_64 --rm -v
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Creating a coverage report for one or more samples based on a list of genes
+An example of this report is shown by the demo report endpoint: http://0.0.0.0:8000/report/demo (requires all genes and gene transcripts in build GRCh37 loaded into the database).
+The statistics from the report above are computed using the transcripts intervals present in the provided genes.
+Given an application running in production settings, with genes, transcripts and exons loaded into the database, a coverage report like the one above can be created taking into account one of these types of intervals from any gene of choice.
+The gene list might be provided as a list of Ensembl gene IDs, HGNC gene IDs or HGNC gene symbols.
+Here is what the request data of a POST request to the /report endpoint looks like:
{
+ "build": "GRCh37",
+ "completeness_thresholds": [
+ 10,
+ 15,
+ 20,
+ 50,
+ 100
+ ],
+ "ensembl_gene_ids": [],
+ "hgnc_gene_ids": [],
+ "hgnc_gene_symbols": [],
+ "interval_type": "genes",
+ "default_level": 10,
+ "panel_name": "Custom panel",
+ "case_display_name": "internal_id",
+ "samples": [
+ {
+ "name": "string",
+ "coverage_file_path": "string",
+ "case_name": "string",
+ "analysis_date": "2023-10-04T08:22:06.980106"
+ }
+ ]
+}
+Mandatory parameters
+-
+
- build either "GRCh37" or "GRCh38" +
- ensembl_gene_ids OR hgnc_gene_ids OR hgnc_gene_symbols either a list of strings (for Ensembl IDs or HGNC symbols or a list of integers for HGNC IDs +
- interval_type either "genes", "transcripts" or "exons", depending on the analysis type (WGS, WES, WTS) +
- default_level default coverage threshold level to take into account for displaying the number of fully covered or partially covered intervals +
- samples mandatory parameters are name and either coverage_file_path or case_name +
Optional parameters
+-
+
- completeness_thresholds the list of different coverage thresholds that will be used to calculate gene coverage completeness. If not provided, the default threshold values will be: 10, 15, 20, 50, 100 +
- panel_name Add a name only if the provided genes are part of a gene panel +
- case_display_name provide this string parameter if the case belong to the same case / group +
- samples analysis_date if not provided with be set to current date +
Creating a genes coverage overview report to show incompletely covered genomic intervals
+This type of report contains stats from incompletely covered genomic intervals at different coverage thresholds and is basically the same as the genes overview report provided by chanjo-report.
+A demo genes overview report based on genes transcripts from the demo PanelApp genes is available at the demo overview endpoint: http://0.0.0.0:8000/overview/demo (requires all genes and gene transcripts in build GRCh37 loaded into the database).
+To create a custom genes coverage overview report, send a POST request to the /overview endpoint containing the same request data described above for the /report endpoint.
Creating coverage overview over MANE transcripts for a list of genes
+This report contains statistics over all MANE Select and Mane Plus Clinical transcripts for a list of genes provided by the user.
+The /mane_overview endpoint accepts POST request with the same data described for the 2 reports above.
Note that MANE overview reports are available only for analyses run with genome build GRCh38.
+ +
+
+
+
+ GitHub
+
+
+
+ « Previous
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/usage/loading-intervals/index.html b/usage/loading-intervals/index.html
new file mode 100644
index 00000000..b8d6d185
--- /dev/null
+++ b/usage/loading-intervals/index.html
@@ -0,0 +1,224 @@
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+ Loading genetic intervals: genes, transcripts and exons into the database
+Genes, transcripts and exons should be loaded and updated at regular intervals of time. Depending on the type of sequencing data analysed using chanjo2, loading of transcripts and exons might not be required. +For instance, gene coordinates should be enough for whole genome sequencing (WGS) experiments, while transcripts and exons data are necessary to return statistics from transcripts and exons-based experiments.
+Genes, transcripts and exons are retrieved from the Ensembl Biomart using the Schug[shug] library and loaded into the database in three distinct tables.
+Genes should be loaded into the database before transcripts and exons intervals. Depending on the hardware in use and the HTML connection speed, the process of loading these intervals might take some time. For this reason requests sent to these endpoints are asynchronous, so that they don't time out while processing the information.
+Loading/updating database genes
+Loading of genes in a given genome build can be achieved by sending a POST request to the /intervals/load/genes/{<genome-build} endpoint:
curl -X 'POST' \
+ 'http://localhost:8000/intervals/load/genes/GRCh38' \
+ -H 'accept: application/json' \
+ -d ''
+Please note that the process of loading genes into the database will erase eventual transcripts and exons with the same genome build that are already present in the database. This ensures that transcripts and exons intervals will be up-to-date with the latest definitions of the genes loaded into the database.
+Loading/updating transcripts
+Transcripts can be loaded/updated by using the /intervals/load/transcripts/{<genome-build} endpoint:
curl -X 'POST' \
+ 'http://localhost:8000/intervals/load/transcripts/GRCh38' \
+ -H 'accept: application/json' \
+ -d ''
+Loading/updating exons:
+As for the previous endpoints, exons are loaded by sending a POST request to the /intervals/load/exons/{<genome-build} endpoint.
curl -X 'POST' \
+ 'http://localhost:8000/intervals/load/transcripts/GRCh38' \
+ -H 'accept: application/json' \
+ -d ''
+Genes, transcripts and exons queries
+Once the database is populated with genomic intervals data, it is possible to run queries to retrieve its content.
+Genomic intervals can be queried using genes definitions. Genes can be provided as a parameter to the query in the following formats
+-
+
- Ensembl gene IDs (use parameter
ensembl_ids)
+ - HGNC ids (use parameter
hgnc_ids)
+ - HGNC symbols (use parameter
hgnc_symbols)
+
Genome build is always a required parameter in these queries.
+Examples:
+-
+
- Send a POST request to Retrieve information on a list of genes using HGNC symbols: +
{
+ "build": "GRCh37",
+ "hgnc_symbols": ["LAMA1","LAMA2"]
+}
+-
+
- Retrieve transcripts available for one of more genes described by Ensembl IDs: +
curl -X 'POST' \
+ 'http://localhost:8000/intervals/transcripts' \
+ -H 'accept: application/json' \
+ -H 'Content-Type: application/json' \
+ -d '{
+ "build": "GRCh37",
+ "ensembl_gene_ids": [
+ "ENSG00000101680", "ENSG00000196569"
+ ]
+}'
+-
+
- Retrieve all exons for genes with HGNC IDs: 6481 and 6482: +
curl -X 'POST' \
+ 'http://localhost:8000/intervals/exons' \
+ -H 'accept: application/json' \
+ -H 'Content-Type: application/json' \
+ -d '{
+ "build": "GRCh37",
+ "hgnc_ids": [
+ 6481, 6482
+ ]
+}'
+Whenever ensembl_ids, hgnc_ids, hgnc_symbols parameter is not provided, these endpoints will return a list of 100 default genes, transcripts or exons. To increase the number of returned entries you can specify a custom value for the query limit parameter.
+
+
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+ Coverage queries on d4 files or data contained in the database
+Chanjo2 can be used to quickly access average coverage depth statistics for an interval from a list of genomic intervals on a custom d4 coverage file.
+Coverage completeness
+When querying the server for sample coverage statistics, it is also possible to specify a custom list of numbers (example 30, 20, 10) representing the coverage thresholds that should be used to calculate the coverage completeness for each genomic interval. +This number describes the percentage of bases (as a decimal number) meeting the user-defined coverage threshold for each genomic interval.
+Direct coverage query over a single genomic interval
+Coverage and coverage completeness over a genomic interval can be computed by sending a POST request to the /coverage/d4/interval/ endpoint.
The entrypoint accepts a json query with the following parameters:
+-
+
- coverage_file_path # (required). Path to a d4 file that is stored on the local drive or on a remote server (slower computation) +
- chromosome # (required). Genomic interval chromosome +
- completeness_thresholds # Threshold values for computing coverage completeness. Example [50, 30, 10] +
- start # Genomic interval start position +
- stop # Genomic interval end position +
Note that start and stop coordinates are not required and whenever they are omitted coverage statistics will be computer over the entire chromosome.
+Query example:
+curl -X 'POST' \
+ 'http://localhost:8000/coverage/d4/interval/' \
+ -H 'accept: application/json' \
+ -H 'Content-Type: application/json' \
+ -d '{
+ "coverage_file_path": "https://d4-format-testing.s3.us-west-1.amazonaws.com/hg002.d4",
+ "chromosome": "7",
+ "start": 124822386,
+ "end": 124929983,
+ "completeness_thresholds": [
+ 10,20,30
+ ]
+}'
+This query wll return a response, where the mean coverage over the single interval is present under the mean_coverage key. +Coverage completeness values will be additionally returned if the query sent to the server contains values for the completeness_thresholds key. +A response from the server to the query above will return for instance a mean interval coverage of 27.2 and coverage completeness of 99.6%, 85% and 33.4% using threshold values of respectively 10, 20 and 30.
+{
+ "mean_coverage": 27.19804455514559,
+ "completeness": {
+ "10": 1,
+ "20": 0.85,
+ "30": 0.33
+ },
+ "interval_id": null,
+ "interval_type": null
+}
+Direct coverage query over the intervals present in a bed file
+Mean coverage can be also calculated for a list of intervals using the /coverage/d4/interval_file endpoint. The intervals list should be provided as the path to a bed-formatted file.
The entrypoint accepts a json query with the following parameters:
+-
+
- coverage_file_path # (required). Path to a d4 file that is stored on the local drive or on a remote server (slower computation) +
- intervals_bed_path # (required). Path to a .bed file present on the local drive. +
- completeness_thresholds # Threshold values for computing coverage completeness. Example [50, 30, 10] +
If we were to use the demo bed file provided in this repository, the query would look like this:
+curl -X 'POST' \
+ 'http://localhost:8000/coverage/d4/interval_file/' \
+ -H 'accept: application/json' \
+ -H 'Content-Type: application/json' \
+ -d '{
+ "coverage_file_path": "https://d4-format-testing.s3.us-west-1.amazonaws.com/hg002.d4",
+ "intervals_bed_path": "<path-to-109_green.bed>",
+ "completeness_thresholds": [
+ 10,20,30
+ ]
+}'
+And it would return the following result:
+[
+ {
+ "mean_coverage": 22.17115629570222,
+ "completeness": {
+ "10": 1,
+ "20": 0.69,
+ "30": 0.08
+ },
+ "interval_id": null,
+ "interval_type": null
+ },
+ {
+ "mean_coverage": 83.1338549817423,
+ "completeness": {
+ "10": 1,
+ "20": 0.84,
+ "30": 0.24
+ },
+ "interval_id": null,
+ "interval_type": null
+ },
+ {
+ "mean_coverage": 252.63072816253893,
+ "completeness": {
+ "10": 1,
+ "20": 0.78,
+ "30": 0.03
+ },
+ "interval_id": null,
+ "interval_type": null
+ },
+ {
+ "mean_coverage": 141.35853114545165,
+ "completeness": {
+ "10": 0.99,
+ "20": 0.7,
+ "30": 0.09
+ },
+ "interval_id": null,
+ "interval_type": null
+ }
+]
+Condensed summary stats for one or more samples over a list of HGNC IDs
+To obtain condensed statistics for one or more samples, use the /coverage/d4/genes/summary endpoint.
+Send a request with a list of HGNC gene IDs, the path to the d4 files for the samples, and the coverage threshold for computing coverage completeness.
+The endpoint will return the average coverage and coverage completeness for all the genes included in the query.
+You need to provide a parameter interval_type to specify whether the statistics should be computed over entire genes, gene transcripts, or exons.
Request example:
+curl -X 'POST' \
+ 'https://chanjo2-stage.scilifelab.se/coverage/d4/genes/summary' \
+ -H 'accept: application/json' \
+ -H 'Content-Type: application/json' \
+ -d '{
+ "build": "GRCh37",
+ "samples": [
+ {
+ "name": "TestSample",
+ "coverage_file_path": "<path-to-d4-file.d4>"
+ }
+ ],
+ "hgnc_gene_ids": [
+ 2861, 3791, 6481, 7436, 30521
+ ],
+ "coverage_threshold": 10,
+ "interval_type": "genes"
+}'
+Response from chanjo2:
+{"TestSample":{"mean_coverage":54.38,"coverage_completeness_percent":33.03}}
+
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