File jquery-3.5.1.js has 6902 lines of code (exceeds 250 allowed). Consider refactoring.

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/*!
 * jQuery JavaScript Library v3.5.1
 * https://jquery.com/
 *
 * Includes Sizzle.js

Function Sizzle has 1510 lines of code (exceeds 25 allowed). Consider refactoring.

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( function( window ) {
var i,
    support,
    Expr,
    getText,

File underscore-1.13.1.js has 1445 lines of code (exceeds 250 allowed). Consider refactoring.

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(function (global, factory) {
  typeof exports === 'object' && typeof module !== 'undefined' ? module.exports = factory() :
  typeof define === 'function' && define.amd ? define('underscore', factory) :
  (global = typeof globalThis !== 'undefined' ? globalThis : global || self, (function () {
    var current = global._;

File parsers.py has 983 lines of code (exceeds 250 allowed). Consider refactoring.

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# parsers.py

import argparse
import sys

Function setDocument has 262 lines of code (exceeds 25 allowed). Consider refactoring.

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setDocument = Sizzle.setDocument = function( node ) {
    var hasCompare, subWindow,
        doc = node ? node.ownerDocument || node : preferredDoc;

    // Return early if doc is invalid or already selected

Function ajax has 257 lines of code (exceeds 25 allowed). Consider refactoring.

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    ajax: function( url, options ) {

        // If url is an object, simulate pre-1.5 signature
        if ( typeof url === "object" ) {
            options = url;

File map.py has 566 lines of code (exceeds 250 allowed). Consider refactoring.

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# map.py

import sys
from collections import Counter, defaultdict
from multiprocessing import cpu_count

Function Stemmer has a Cognitive Complexity of 58 (exceeds 5 allowed). Consider refactoring.

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var Stemmer = function() {

  var step2list = {
    ational: 'ate',
    tional: 'tion',

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File qc.py has 498 lines of code (exceeds 250 allowed). Consider refactoring.

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# qc.py

from itertools import cycle, islice
from pathlib import Path

Function query has a Cognitive Complexity of 49 (exceeds 5 allowed). Consider refactoring.

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  query : function(query) {
    var i;

    // stem the searchterms and add them to the correct list
    var stemmer = new Stemmer();

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Function Deferred has 178 lines of code (exceeds 25 allowed). Consider refactoring.

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    Deferred: function( func ) {
        var tuples = [

                // action, add listener, callbacks,
                // ... .then handlers, argument index, [final state]

Function performObjectSearch has a Cognitive Complexity of 45 (exceeds 5 allowed). Consider refactoring.

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  performObjectSearch : function(object, otherterms) {
    var filenames = this._index.filenames;
    var docnames = this._index.docnames;
    var objects = this._index.objects;
    var objnames = this._index.objnames;

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Function extract_feature_barcoding_regex has a Cognitive Complexity of 44 (exceeds 5 allowed). Consider refactoring.

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def extract_feature_barcoding_regex(
    read1_file,
    read2_file,
    cb_file,
    fb_file,

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Function Stemmer has 151 lines of code (exceeds 25 allowed). Consider refactoring.

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var Stemmer = function() {

  var step2list = {
    ational: 'ate',
    tional: 'tion',

File demultiplex.py has 415 lines of code (exceeds 250 allowed). Consider refactoring.

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# demulitplex.py

import re
import sys
import hdbscan

Function performTermsSearch has a Cognitive Complexity of 36 (exceeds 5 allowed). Consider refactoring.

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  performTermsSearch : function(searchterms, excluded, terms, titleterms) {
    var docnames = this._index.docnames;
    var filenames = this._index.filenames;
    var titles = this._index.titles;

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File searchtools.js has 381 lines of code (exceeds 250 allowed). Consider refactoring.

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/*
 * searchtools.js
 * ~~~~~~~~~~~~~~~~
 *
 * Sphinx JavaScript utilities for the full-text search.

Function filter_matching has a Cognitive Complexity of 34 (exceeds 5 allowed). Consider refactoring.

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def filter_matching(
    matching_file,
    filtered_matching_file,
    cb_pos_start=0,
    cb_num_mismatches=1,

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Function defaultPrefilter has 122 lines of code (exceeds 25 allowed). Consider refactoring.

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function defaultPrefilter( elem, props, opts ) {
    var prop, value, toggle, hooks, oldfire, propTween, restoreDisplay, display,
        isBox = "width" in props || "height" in props,
        anim = this,
        orig = {},

Function Callbacks has 121 lines of code (exceeds 25 allowed). Consider refactoring.

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jQuery.Callbacks = function( options ) {

    // Convert options from String-formatted to Object-formatted if needed
    // (we check in cache first)
    options = typeof options === "string" ?