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var chai = global.chai = require('chai')
var rewire = global.rewire = require('rewire')
var graphql = global.graphql = require('graphql')
var private = global.private = rewire('../index')
var factory = global.factory = require('../index')(graphql)
var expect = global.expect = chai.expect
var utils = require('./utils')
global.logger = {
error: function (log) {
console.log(log)
}
}
var opt = require('node-getopt').create([
['t', 'test=ARG', 'tests to run using comma separated']
]).bindHelp().parseSystem()
// include tests
var unitTests = require('./unit')
// get tests to run
var tests = (opt.options.test || 'all').split(',')
// run appropriate tests
if (utils.hasTest(tests, /^unit/)) unitTests(tests)
#!/usr/bin/env node
var fs = require('fs'),
path = require('path'),
Getopt = require('node-getopt'),
sp = require('./softplus'),
getParams = require('./getparams')
var getopt = Getopt.create([
['p' , 'params=FILE' , 'specify parameters as JSON file'],
['x' , 'inprof=FILE' , 'specify input profile as CSV file'],
['y' , 'outprof=FILE' , 'specify output profile as CSV file'],
['i' , 'inseq=STRING' , 'specify input sequence as string'],
['o' , 'outseq=STRING' , 'specify output sequence as string'],
['h' , 'help' , 'display this help message']
]) // create Getopt instance
.bindHelp() // bind option 'help' to default action
var opt = getopt.parseSystem() // parse command line
var input, output, params
function readCSV (filename) {
var rows = fs.readFileSync(filename).toString().split('\n').filter (function (line) { return line.length }).map (function (line) { return line.split(',') })
return { header: rows[0], row: rows.slice(1).map (function (row) { return row.map (parseFloat) }) }
}
"use strict";
let mongo = require('mongodb').MongoClient,
random = require('randomstring'),
faker = require('faker'),
fs = require('fs'),
optionParser = require('node-getopt').create([
['c', 'customize=[ARG]', 'file to customize the data generation process'],
['m', 'mongourl=[ARG]', 'Mongo DB url'],
['h', 'help', 'Display this help']
]);
let arg = optionParser.bindHelp().parseSystem();
// check preconditions
// we need a mongo url, first check environment variables, then
// parameters and if neither provides a url, exit with an error
let mongoUrl = arg.options.mongourl || process.env.MONGO_URL;
if (!mongoUrl) {
optionParser.showHelp();
console.error('No mongo url found in env or given as parameter.');
(function () {
"use strict";
var modular = require("modular-amd"),
optionsManager = require("node-getopt").create([
["g", "grep=
// Generated by LispyScript v1.0.0
require("./require");
var fs = require("fs"),
path = require("path"),
ls = require("./ls"),
repl = require("./repl"),
watch = require("watch"),
isValidFlag = /-h\b|-r\b|-v\b|-b\b|-s\b/,
error = function(err) {
console.error(err.message);
return process.exit(1);
};
var opt = ((((require('node-getopt')).create([['h', 'help', 'display this help'],
['v', 'version', 'show version'],
['r', 'run', 'run .ls files directly'],
['w', 'watch', 'watch and compile changed files beneath current directory'],
['b', 'browser-bundle', 'create browser-bundle.js in the same directory'],
['m', 'map', 'generate source map files'],
['i', 'include-dir=ARG+', 'add directory to include search path']])).setHelp(("lispy [OPTION] [] []\n\n" + " will default to with '.js' extension\n\n" + "Also compile stdin to stdout\n" + "eg. $ echo '(console.log \"hello\")' | lispy\n\n" + "[[OPTIONS]]\n\n"))).bindHelp()).parseSystem();
(function(___monad) {
var mBind = ___monad.mBind,
mResult = ___monad.mResult,
mZero = ___monad.mZero,
mPlus = ___monad.mPlus;
var ____mResult = function(___arg) {
return (((typeof(___arg) === "undefined") && (!(typeof(mZero) === "undefined"))) ?
mZero :
mResult(___arg));
};
#!/usr/bin/env node
var getopt = require('node-getopt')
var negbin = require('./negbin')
var fast5 = require('./fast5')
var defaultStrand = 0
var defaultKmerLen = 6
var defaultComponents = 1
var minFracInc = 1e-5 // minimum fractional increment for EM negative binomial fit
var minExtendProb = 1e-10
var parser = getopt.create([
['f' , 'fast5=PATH' , 'FAST5 input file'],
['s' , 'strand=N' , 'strand (0, 1, 2; default ' + defaultStrand + ')'],
['g' , 'group=GROUP' , 'group name (000, RN_001, ...)'],
['k' , 'kmerlen=N' , 'kmer length (default ' + defaultKmerLen + ')'],
['c' , 'components=N' , 'negative binomial mixture components (default ' + defaultComponents + ')'],
['a' , 'aggregate' , 'give all kmers the same length distribution'],
['h' , 'help' , 'display this help message']
]) // create Getopt instance
.bindHelp() // bind option 'help' to default action
var opt = parser.parseSystem(); // parse command line
function inputError(err) {
parser.showHelp()
console.warn (err, "\n")
process.exit(1)
}
#!/usr/bin/env node
var getopt = require('node-getopt')
var fasta = require('bionode-fasta')
var colors = require('colors')
var fast5 = require('./fast5')
var defaultStrand = 0
var matchScore = +5, mismatchScore = -4, gapScore = -7
var parser = getopt.create([
['q' , 'query=PATH' , 'FASTA query file'],
['r' , 'reference=PATH' , 'FAST5 reference file'],
['s' , 'strand=N' , 'strand (0, 1, 2; default ' + defaultStrand + ')'],
['g' , 'group=GROUP' , 'group name (000, RN_001, ...)'],
['h' , 'help' , 'display this help message']
]) // create Getopt instance
.bindHelp() // bind option 'help' to default action
var opt = parser.parseSystem(); // parse command line
function inputError(err) {
parser.showHelp()
console.warn (err, "\n")
process.exit(1)
}
var queryFilename = opt.options.query || inputError("Please specify a query file")
// the data model
const ItemSchema = {
name: 'Item',
primaryKey: 'itemId',
properties: {
'itemId': { type: 'string', optional: false },
'body': { type: 'string', optional: false },
'isDone': { type: 'bool', optional: false },
'timestamp': { type: 'date', optional: false }
}
};
// parsing command-line options
let getopt = require('node-getopt').create([
[ 'c', 'create=ARG', 'create a new item' ],
[ 'l', 'list', 'list all items' ],
[ 'm', 'mark=ARG', 'mark a item done' ],
[ 'h', 'help', 'display this text'],
]).bindHelp();
let opt = getopt.parse(process.argv.slice(2));
// open the Realm and perform operations
Realm.Sync.User.login(`https://${SERVER}`, USERNAME, PASSWORD)
.then(user => {
console.log(`${USERNAME} is logged in`);
Realm.open({
sync: {
url: `realms://${SERVER}/~/todo`,
user: user
},
const fs = require('fs');
const path = require('path');
const tl = require('azure-pipelines-task-lib/task');
const util = require('./util');
const { Octokit } = require("@octokit/rest");
const OWNER = 'microsoft';
const REPO = 'azure-pipelines-agent';
const GIT = 'git';
const VALID_RELEASE_RE = /^[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}$/;
const octokit = new Octokit({}); // only read-only operations, no need to auth
process.env.EDITOR = process.env.EDITOR === undefined ? 'code --wait' : process.env.EDITOR;
var opt = require('node-getopt').create([
['', 'dryrun', 'Dry run only, do not actually commit new release'],
['', 'derivedFrom=version', 'Used to get PRs merged since this release was created', 'latest'],
['', 'branch=branch', 'Branch to select PRs merged into', 'master'],
['h', 'help', 'Display this help'],
])
.setHelp(
'Usage: node createReleaseBranch.js [OPTION] \n' +
'\n' +
'[[OPTIONS]]\n'
)
.bindHelp() // bind option 'help' to default action
.parseSystem(); // parse command line
async function verifyNewReleaseTagOk(newRelease)
{
if (!newRelease || !newRelease.match(VALID_RELEASE_RE) || newRelease.endsWith('.999.999'))
#!/usr/bin/env node
// emacs mode -*-JavaScript-*-
// An automata that echoes all DNA sequences except those matching a pattern.
var fs = require('fs'),
getopt = require('node-getopt')
// parse command-line options
var opt = getopt.create([
['m' , 'motif=SEQ' , 'specify motif [ACGTN]+'],
['f' , 'forward' , 'do not check reverse strand'],
['r' , 'repeats' , 'allow homopolymer repeats'],
['h' , 'help' , 'display this help message']
]) // create Getopt instance
.bindHelp() // bind option 'help' to default action
.parseSystem() // parse command line
var motif = opt.options.motif || 'Z', forward = opt.options.forward, repeats = opt.options.repeats
var motifSeq = motif.toUpperCase().split('')
// The state space is indexed (P,M[1],M[2]...M[motif.length-1])
// where
// P is the previous nucleotide (or the empty string if in the initial state),
// M[K] is a binary variable that is true iff the previously-emitted K symbols match the first K characters of the motif.
// We only need to keep 2^(motif.length-1) states because the last bit is never allowed to be 1.