sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
e55a1bce4bd34e840ba5034c9201cd1937bb7aaf70f6a826abc14f3361988ce2 | Java | 4,764 | 151 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlpermutationtranscriptionfactoranalysis;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.M... |
cc9a3303b4dd5857d4293cd520e116f927f8a0eb9c34101210720a59ce3b19b7 | Java | 4,819 | 170 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
0e87d528ad546aed79a5451633ab23d6e38af36222fc7c34c7933a39cfef4efe | Java | 4,825 | 131 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
35e1b4e4ff9b4470e7bf3a0e42cb56562d095f46f7fcd29030d2ceaaffa733f7 | Java | 4,826 | 161 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.gadocommandline;
import com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.opencsv.CSVR... |
a04389d6f05433792adead773a4bcaa23e87abe0265243c8def2d0b7a5248a90 | Java | 4,826 | 171 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.interactionanalysis;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.LinkedHashSet;
import umcg.genetica.containers.Pair;
import umcg.genetica... |
cee6df93ccbc981da854b17938a77edbe463b10a173d0c520c4bcadf86c37cb0 | Java | 4,827 | 157 | package mbqtl.stat;
import JSci.maths.statistics.NormalDistribution;
import cern.jet.stat.tdouble.Probability;
import umcg.genetica.math.stats.ZScores;
public class FisherWeightedMetaAnalysis {
NormalDistribution d = new NormalDistribution();
public double[] metaAnalyzeCorrelationsFixedEffect(double[] corre... |
ef8fed80f8ab96574c3ce51772e12cb0090d53d7aea6726af127740af7170618 | Java | 4,838 | 162 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
0e07d449bfc5221d1246e0e13ee73de2b39d86e7406070e7a187aeea797824c0 | Java | 4,853 | 144 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlpermutationtranscriptionfactoranalysis;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.u... |
8493f8f9f441716e6301bf88abc02c4e920603a3b7912dd76b6b454f3037013a | Java | 4,858 | 145 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.mixupmapper;
import eqtlmappingpipeline.metaqtl3.FDR;
import eqtlmappingpipeline.metaqtl3.containers.Settings;
import org.apache.commons.configuration.ConfigurationException;
import umcg.gene... |
c6ee0f9b49c8b558853004565065fc9f68616f4cd1a4546f56473050da9fb0cb | Java | 4,875 | 133 | /*-
* #%L
* Utility classes for BoneJ1 plugins
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must ret... |
afc4f34ddb9335f98275dac1e4bb03bfbdd1d0d68801115bb0f6e4588cfdbf8d | Java | 4,878 | 138 | package org.molgenis.genotype.plink;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.assertTrue;
import java.io.IOException;
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
imp... |
ae4f61ecfb867d14ef7d4da051d9af4b6a4c3c4ff94dcb8854135590c6cd7f25 | Java | 4,880 | 161 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.matrix2;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java... |
af6f8c3ec81c6908d0907aa1c973a228e2dddb56bbf2605558d8b5c1d2af3061 | Java | 4,895 | 151 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
6b23edce63aabc7135f1140d6595e6325442d819dc530a5ccab936d6f67674bf | Java | 4,896 | 114 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper.util;
import umcg.genetica.io.trityper.SNP;
/**
*
* @author harmjan
*/
public class CompareAllelicDirections {
public static Boolean[] compare(SNP[] snps) {
int firstDa... |
d3cd8cc30e7754a177e30b1c68290e44d3e65952747215c73c1f167b949c1d14 | Java | 4,929 | 135 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats.concurrent;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import cern.colt.matrix.tdouble.impl.DenseDoubleMatrix2D;
import cern.colt.matrix.tdouble.impl.DenseLargeDoubleMatrix2D;
impor... |
eb01b313789a79ab4a5682ecb8140d0e2db23927ec1207b131998a5f35eca7e7 | Java | 4,950 | 140 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
0fa1476af469c0522286cfd77b12b17c3bf5c78f61c198c40c84b13bccf5f595 | Java | 4,957 | 145 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.matrix2;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import cern.colt.matrix.tdouble.impl.DenseDoubleMatrix2D;
import no.uib.cipr.matrix.DenseMatrix;
import org.apache.commons.math3.stat.r... |
69181d2702cab371d1c8b47d4bebff6a79ba366d475e110f5520d3c49c865c32 | Java | 4,960 | 161 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
13aca38bba93a8853d9f2e946fd35bf8e4e40018f861a543bb4db6139745b1d1 | Java | 4,961 | 147 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
14ee4edb9f590e381aa709fa1bbd550786307868a56433c434014a97ce8a4447 | Java | 4,962 | 190 | package umcg.genetica.io.bedgraph;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.Iterator;
import java.util.NoSuchElementException;
import java.util.regex.Matcher;
... |
9effd8e68fea933653653dc6254b23178bf6b99f5dc11cb00519e74fdbfbcd23 | Java | 4,977 | 121 | /*
* Copyright (C) 2016 adriaan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distribute... |
66b463e7f8ed0f073e766113b0f536d03dedfbe373f4f5249a289478f7625435 | Java | 4,987 | 152 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.cellTypeSpecificAlleleSpecificExpression;
import java.io.BufferedReader;
import java.io.File;
import java.i... |
cae47bc78bdcbf150a710b57af31fce4a8f34dbc96f35f5c04bb50dffc67883d | Java | 4,997 | 156 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
40b67bef06aa744163d95261a8fcc0cdd06cadef16f91aa9598453619e5f9c37 | Java | 5,006 | 129 | /*-
* #%L
* Utility classes for BoneJ1 plugins
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must ret... |
644c841364bdcce59d5fcc8d08c73f742b42d67fd9b5bb1a2460293b551e10ae | Java | 5,048 | 270 | /*
* as taken from http://pastebin.com/f57ae8d47
*/
package umcg.genetica.util;
import java.util.ArrayList;
import java.util.List;
/**
*
*
*/
public class Primitives {
public static double max(double[] values) {
double max = -Double.MAX_VALUE;
for (double value : values) {
if (!Double.isNaN(value) && v... |
59f32fbae100998eac22a21c2587b0a3c7e9da1f15016b69ae4160497d9ad2d8 | Java | 5,049 | 197 | package mbqtl.vcf;
import mbqtl.vcf.filter.genotypefilters.VCFGenotypeFilter;
import umcg.genetica.io.text.TextFile;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.Iterator;
import java.util.Set;
/**
* Created by hwestra on 5/11/15.
*/
public class VCFGenotypeDat... |
c523e60974dd2f5d9e899cce0f5e28b11113c00d6cf2fb10971ce90abfd601e3 | Java | 5,049 | 198 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.enums;
import umcg.genetica.features.Feature;
/**
* @author Harm-Jan
*/
public enum Chromosome {
ONE(1, "... |
ce1fce3f953ba12d7f2f8e8691677ccb2e067e6cd02d4d780d3ce78a14f71060 | Java | 5,059 | 250 | package nl.systemsgenetics.downstreamer.summarystatistic;
import org.molgenis.genotype.variant.GeneticVariant;
import java.io.Serializable;
/**
* Created by olivier on 06/12/2017.
*/
public class SummaryStatisticRecord extends SNP {
//TODO: refactoring to more appropriate names
private double beta;
private do... |
ffb4c335f1fa3c2cedae1d586761cd41731314e8aa1417c821bc7785f8794e7a | Java | 5,068 | 141 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
03f2a66488a6dbdf998a474ef20238902fcebcc67d0cfb33887d92bafbedc538 | Java | 5,076 | 191 | package umcg.genetica.io.pileup;
import gnu.trove.map.hash.TObjectDoubleHashMap;
import gnu.trove.map.hash.TObjectIntHashMap;
import org.molgenis.genotype.Allele;
/**
*
* @author Patrick Deelen
*/
public class PileupEntry {
private final String chr;
private final int pos;
private final Allele refAllele;
priva... |
4f285877af1d1b0d6353c03c3a62f1ea1def357f0928fefd9fa2a527674cd0a8 | Java | 5,088 | 161 | package mbqtl.stat;
import JSci.maths.ArrayMath;
import cern.colt.GenericSorting;
import cern.colt.Swapper;
import cern.colt.function.tint.IntComparator;
import org.apache.commons.collections.primitives.ArrayDoubleList;
import org.apache.commons.math3.stat.ranking.NaNStrategy;
import org.apache.commons.math3.stat.rank... |
f2cb6a7805629b7c1165ec507a7dcfb087bb61ec5f90c672d67884ae618ab34b | Java | 5,099 | 214 | /* Copyright (c) 2019 Thomas Braschler <thomas.braschler@unige.ch>
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation; either version 3 of the License, or
## (at your option) any later version... |
1e0e0afd9c91394e1948f9ecc2593c51fd0bf42875f0c3fad611955ae5f960d8 | Java | 5,110 | 117 | /*-
* #%L
* Ops created for BoneJ2
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the abov... |
a04db499350d1c7dd272b30ffb585f3bbc0ebfd6f5301356bc37f1b62998f49e | Java | 5,110 | 117 | /*-
* #%L
* Ops created for BoneJ2
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the abov... |
d06ccdddb920adb4a59c6691987c3c923c06c5122527c3ad877a1bdd549fce0b | Java | 5,123 | 191 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.oxford;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.io.Writer;
import jav... |
fee4e036f70b1e130d5e5ed8b58e2e32856035dde7582f3a7c0c550f8c97b446 | Java | 5,126 | 150 | /*-
* #%L
* Utility methods for BoneJ2
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the ... |
33c068b587aea126fe40662e1545a821e4b9f73352c8ad0a4bb11dca0d427072 | Java | 5,134 | 174 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.bgen;
import java.io.File;
import java.net.URISyntaxException;
import java.sql.SQLException;
import sta... |
30d45f046f3d01dd3c61f782d50213fedd4185bcbdd425601c8f0a0387b07976 | Java | 5,139 | 149 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
4ba4cc397edbb10f4eca9dee80ebba2103bc150b7a4a19b7d4373cfc07102a82 | Java | 5,150 | 142 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
ee9d748c58e1d053e63786c23ceda7a1a310b05b6a31bfcfdd8c79d465b214f5 | Java | 5,152 | 169 | package edu.cmu.cs.eyetrack.gui.shapes;
import java.awt.Color;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.HeadlessException;
import java.awt.Shape;
import java.awt.image.BufferedImage;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Ar... |
9cbdf54dc91796fef1916981d132c8905dac629ae537aba34eff9a2ec0d91bb0 | Java | 5,154 | 170 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.genenetworkbackend.div;
import com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.openc... |
26a7951c1fa3931aeae8166d965e2902cbef4ee275ce8885e4d0335549187055 | Java | 5,159 | 133 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
e3348469d83cfeb7fb61d86b3cb3ad340d37651c8243896cb6fe691bf1204166 | Java | 5,177 | 122 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.genenetworkbackend.hpo;
import com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.openc... |
456340062b1f51bb8ee79affdf48eb68dd41b2b83b0b30aff5eb5c417c56b593 | Java | 5,182 | 162 | package org.molgenis.genotype.variant.sampleProvider;
import java.util.List;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.util.Cache;
import org.molgenis.genotype.util.FixedSizeIterable;
import org.molgenis.genotype.variant.GeneticVariant;
import org.molgenis.genotype.variant.GenotypeRecord;
/*... |
91ffed9f65a1b0b70ac2a4980dde266b5778006b2f56003bf91ee834f9972a4c | Java | 5,207 | 141 | package mbqtl.datastructures;
import umcg.genetica.enums.Chromosome;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.text.Strings;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Set;
public class SNPAnnotation {
HashMap... |
d7a6f46f4ce6255d2bfa29692b7b5c632d45313adf165b7619b10ab66c7fe31e | Java | 5,208 | 159 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package transeqtlcrossmap;
import umcg.genetica.features.Exon;
import umcg.genetica.features.FeatureType;
import umcg.genetica.featur... |
08835e2b65a794a69f2f5bee3615222cd9923a36130be07c9b85845b934f2754 | Java | 5,214 | 233 | /* Copyright (c) 2019 Thomas Braschler <thomas.braschler@unige.ch>
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation; either version 3 of the License, or
## (at your option) any later version... |
27f14f21ccbbbb1d74a8546d2c7b6f83013c071a5794b4642275f8d80fcfeeaa | Java | 5,215 | 126 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.util;
import java.io.IOException;
import java.util.zip.DataFormatException;
import umcg.genetica.console.ProgressBar;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.text.TextFile;
impo... |
05cbdebad64377f269896ccecf7e781c3763199afdacb0979a886285e45f5fe1 | Java | 5,219 | 158 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
3346d50b0969b7e0e039b4c8de7e5e9896d72c77bc18a807fd4705a77d2da90d | Java | 5,223 | 156 | /*-
* #%L
* Mavenized version of the BoneJ1 plugins
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code mus... |
dfc0ab6db1e67e31163b3f2bbf25258b52ec9bc77747101ef39ab7d09d0d75fa | Java | 5,223 | 156 | /*-
* #%L
* Mavenized version of the BoneJ1 plugins
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code mus... |
4d73212f69b53cefb3343a58ccde9fd3cb4ad01d9f2b0383bc38b2bd59ac8aec | Java | 5,235 | 178 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
5fe8549fd86867fe6ead185f5cbbabb8eddf4dde524e7b0bd251319bc30c1c48 | Java | 5,248 | 183 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.gadocommandline;
import com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.opencsv.CSVR... |
a743028564c7c88186c53c85fe6a0ee64976202be63f23595cdbf3e3c4da8bcd | Java | 5,254 | 138 | /*-
* #%L
* Utility methods for BoneJ2
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the ... |
5e965b20eff50f43cc1991a08a529c0376251f6e7ec3e6d267d63428330019ad | Java | 5,255 | 148 | package org.molgenis.genotype.oxford;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.nio.charset.Charset;
import java.util.HashMap;
import java.util.List;
import org.apache.logging.log4j.Logger;
import org.... |
ff5ba2f8a94d65b24e3338a0cc538d7daf8f3586d91e4d3c3304e894431fb0df | Java | 5,255 | 141 | package mbqtl;
import mbqtl.vcf.DetermineLDVCF;
import mbqtl.vcf.VCFTabix;
import mbqtl.vcf.VCFVariant;
import umcg.genetica.containers.Pair;
import umcg.genetica.enums.Chromosome;
import umcg.genetica.features.Feature;
import umcg.genetica.io.text.TextFile;
import java.io.IOException;
import java.util.HashMap;
impor... |
8eb98571ce380b6dd5354db5f534ebef78c49e68f6cc85e601dea31c81392b2d | Java | 5,256 | 201 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
e0ea1a2acd81e1d8949da4f64e8ebfb63a8daf149e82bf4f7519616423c8b966 | Java | 5,257 | 172 | package umcg.genetica.math.matrix2;
import org.apache.commons.io.input.CountingInputStream;
import java.io.*;
import java.nio.Buffer;
import java.nio.ByteBuffer;
import java.nio.DoubleBuffer;
import java.nio.channels.Channels;
import java.nio.channels.FileChannel;
import java.util.ArrayList;
import java.util.LinkedHa... |
b5ca4d91991749c6fa713b757ec4e8fe770bf6959aaf0cbd65b08a5834033273 | Java | 5,263 | 162 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
01a355762e00acb111a3faeb9460b4b4327f0c147610ea99f15744f7e5631d29 | Java | 5,279 | 139 | /*-
* #%L
* Utility classes for BoneJ1 plugins
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must ret... |
895a5e68c5115ff70c03a0fc4c1f931f5e107faf695f893a8457cb3603443425 | Java | 5,279 | 168 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.examples;
import java.io.IOException;
import java.util.HashMap;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.molgenis.genotype.Allele;
impo... |
cc4405a42ef2bdd960a6f79e7a662b60f635ed2892c0e9adaf60e45532a8f407 | Java | 5,279 | 139 | /*-
* #%L
* Utility classes for BoneJ1 plugins
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must ret... |
423a35d8379185e3a1577270a8efe67c4801a854b33b4a34134a1d8536126a33 | Java | 5,282 | 168 | package umcg.genetica.math.stats;
import java.util.ArrayList;
/*
This is an adaptation of https://github.com/secastel/aFC/blob/master/aFC.py
originally written by Pejman Mohammadi and Stephane Castel
*/
public class AllelicFoldChange {
// expect un-centered genotypes as input (i.e. variable between 0,1,2 and -1 ... |
8ad2c69f49b6dce8e67d106ab418cea876548f5b8d66f0c8baa2f2cddb0d198b | Java | 5,291 | 155 | package nl.systemsgenetics.downstreamer.runners.options;
import org.apache.commons.cli.*;
import org.molgenis.genotype.RandomAccessGenotypeDataReaderFormats;
import java.io.File;
import java.util.Collection;
public class OptionsModeConvert extends OptionsBase implements GenotypeFileProvider {
// TODO: refactor ... |
9da3c38819700a95f2fa6bd326d19ab70f7a85acdbb53e670c50f443323f8038 | Java | 5,300 | 145 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta.meta.graphics;
import java.awt.Color;
import java.awt.Graphics2D;
import java.awt.image.BufferedImage;
import java.text.DecimalFormat;
import java.util.concurrent.ArrayBlockingQueu... |
e8957e6bde55bc3b53f7543584ab05c8bc3f2165ca4fe12e904e73669e21b8dc | Java | 5,302 | 179 | package nl.systemsgenetics.genenetworkbackend.predictions;
/**
*
* @author ludefranke
*/
public class WilcoxonMannWhitney {
private double k, n, kn, auc;
public double getAUC() {
return auc;
}
private double abs(double value) {
return Math.abs(value);
}
private double k_o... |
7bce58e0880f6807fd8a362bf05540a4d246727d759aec4cf2dc721eb3fa3b8f | Java | 5,320 | 145 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
c2a6a5dfa1742bd5a13d4bc903619cdb68acd8357fb0b0b419ac73df529c721e | Java | 5,325 | 147 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
9b414b79986fa2fbb2efe56434037cce03490f4601ce734a1074db0b2e2f6261 | Java | 5,331 | 141 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
c1a4358cfb763c0a39cc0901098cd9814d1677438aa85d6c33625d709f00d514 | Java | 5,331 | 153 | /*
* Copyright (C) 2016 adriaan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distribute... |
670d00d55c2c24e6e2c9ae2384605224bdfe9ca147a96b56a70d2429112f22d3 | Java | 5,345 | 167 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
f797c50e21daa0638193a1228147f5d078f2b56876cbcb29265c69df1812ccba | Java | 5,348 | 118 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlinteractionanalyser.eqtlinteractionanalyser;
import gnu.trove.set.hash.TIntHashSet;
import java.util.co... |
1abd0ee5e3b44f0ef9adb2ae6f8aa3352d48f9bbd03b6e442c0bfe695fc7aa3c | Java | 5,350 | 148 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.chromosomeyexpressionplotter;
import eqtlmappingpipeline.metaqtl3.containers.Settings;
import umcg.genetica.console.ConsoleGUIElems;
import umcg.genetica.io.trityper.TriTyperGeneticalGenomics... |
3a76e999b4b5c611ed7cb4522b0580b4d9e747fab57262dbf62e184723209023 | Java | 5,356 | 127 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.ase;
import java.io.BufferedReader;
import java.io.FileReader;
import java.text.NumberFormat;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.... |
d04574736a091b17fd9d24f4ace7ca65fd5bf1e559791ebb43df3afd665629a2 | Java | 5,356 | 143 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
842114077aeae1ad115ee49e74ec7558a1f5c9c00916a36fdff8f53c9a70613b | Java | 5,374 | 190 | package eqtlmappingpipeline.util;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.util.BaseAnnot;
import umcg.genetica.text.Strings;
import java.io.IOException;
import java.util.HashMap;
public class ConvertTOSMRFormat {
public static void main(String[] args) {
String file = "D:\\snpqc\\... |
f43a7a0ac514dbe79cc2e3085f3b024bd958dfd810d13ac698c49df46a7b0ee9 | Java | 5,377 | 165 | package eqtlmappingpipeline.metaqtl3;
import gnu.trove.map.hash.TDoubleIntHashMap;
import gnu.trove.set.hash.THashSet;
import umcg.genetica.console.MultiThreadProgressBar;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.QTLTextFile;
import umcg.genetica.text.String... |
7c212756b5daa400d36309427479d829b5ac95bf6624534754fde9b0dd376d66 | Java | 5,418 | 230 | package eqtlmappingpipeline.ase;
import cern.colt.list.tdouble.DoubleArrayList;
import cern.colt.list.tint.IntArrayList;
import cern.jet.stat.tdouble.Probability;
import java.util.ArrayList;
import org.apache.commons.math3.stat.inference.AlternativeHypothesis;
import org.apache.commons.math3.stat.inference.BinomialTes... |
603a2c91f1f29947dcc7e5e06c35362acc5c6bef5f033c207c9f0a8456134894 | Java | 5,451 | 210 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import cern.jet.random.tdouble.StudentT;
import cern... |
ced4db8d4e739971db38f5ad9fe38ae72ea3a9d6645306ee442c403f7187d670 | Java | 5,456 | 150 | package nl.systemsgenetics.downstreamer.summarystatistic;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.molgenis.genotype.RandomAccessGenotypeData;
import org.molgenis.genotype.util.LdCalculatorException;
import org.molgenis.genotype.variant.GeneticVariant;
import org.m... |
87100cdefd9d98124af54cb4f42d261702fca5bc05ba1a7ce16b91c51923cfaf | Java | 5,463 | 139 | /*-
* #%L
* Ops created for BoneJ2
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the abov... |
adb7e308698eedce9cdbce6acf81d6870e46aa4bf80e91eb45f7908cba613065 | Java | 5,475 | 202 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats;
import static org.testng.Assert.*;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import umcg.genetica.containers.Pair;
/**
*
* @author MarcJan
*/
p... |
7916559a8015d5bdf124c0fd726a4f41562153de4d06606d190f2190913a743d | Java | 5,507 | 193 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype;
import java.io.File;
import java.util.Arrays;
import java.util.EnumMap;
import java.util.EnumSet;
import java.util.List;
import org.apache.logging.log4j.Logger;
import org.apache.logging.l... |
bd04d9739931fb30a643445e56259302f097f0dbe8a585e1cb2d077384b6395c | Java | 5,521 | 172 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.downstreamer.development;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import cern.colt.matrix.tdouble.D... |
0b51bb8bc7ad14aeb63711e4dc7f3b199b5b0f980def12edcf90215eac8204bf | Java | 5,557 | 144 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
b648a2378c37839ba3cd58c1fe12857cf19932bb131cb74d438836ce937db909 | Java | 5,560 | 224 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper;
import umcg.genetica.collections.ChrPosTreeMap;
import umcg.genetica.io.text.TextFile;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Iterator;
import java.u... |
0dbaca10251c44fbcb9b79e02b0fb63aff08b3beb86ade7ef9fd53c05b61b1b4 | Java | 5,569 | 166 | package org.molgenis.genotype.bgen;
import java.io.File;
import java.io.IOException;
import java.sql.Connection;
import java.sql.DatabaseMetaData;
import java.sql.DriverManager;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.LinkedHashSet;
import org.molge... |
8e8b2dc991b8459129d504deb3daea7be3585165a89a1a0a00f9d7c2a345b80d | Java | 5,580 | 169 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
290c0826d70e52dafcd24660759f4477b489f17a9e3fa4f6d6075105dec919a3 | Java | 5,589 | 169 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.ncbi.dbsnp;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map.Entry;
import java.util.Set;
import java.util.HashSet;
import umcg.genetica.io.tex... |
7dfcbf0ebfd57107ac20fbf89042e8d21f5e91bd4d2aec6b87c8dd0e029f2653 | Java | 5,599 | 129 | package org.molgenis.genotype.modifiable;
import static org.mockito.Mockito.mock;
import static org.testng.Assert.assertEquals;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.Iterator;
import org.molgenis.genotype.variant.GeneticVariant;
import org.molgenis.genotype.variant.GeneticVariantMeta... |
115e0e3057551304a0a2927c79531bab70b674a5947ac1c3fd248cfb26935d67 | Java | 5,620 | 140 | /*-
* #%L
* Utility methods for BoneJ2
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the ... |
9d6d34d78221c43302543a4bd3b19c436c3aa23677edc2722ee288ce458f5717 | Java | 5,622 | 141 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl4;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Set;
import java.util.TreeSet;
impo... |
b4987cafeb2e1acb13bf4dd33ff18c860cabae4e4432f00ad9cd12ae4da3db66 | Java | 5,633 | 180 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.util;
import org.testng.Assert;
import static org.testng.Assert.fail;
/**
*
* @author Patrick Deelen
*/
public class AssertExtended extends Assert {
/**
* Asserts that two float arr... |
ad59507348a3c8d5f833c408eb0ab9781d2b90054cd9b693d29456ae38b0a9ab | Java | 5,642 | 161 | /*-
* #%L
* Ops created for BoneJ2
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the abov... |
a4c0188dca065cfdf2a4dcbf0ebf5bfd49b801125fc7e53c3a5f76ad0e62f6f0 | Java | 5,644 | 172 | package nl.systemsgenetics.cellTypeSpecificAlleleSpecificExpression;
/*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
import java.io.File;
import java.io.FileNotFoundException;
impo... |
d414d8671645b9bda8b27e897a90e42f2065f4b65c5024b1078081cc72a0bc2d | Java | 5,649 | 158 | package nl.systemsgenetics.downstreamer.runners.options;
import org.apache.commons.cli.*;
import java.io.File;
import static nl.systemsgenetics.downstreamer.runners.options.DownstreamerMode.*;
public class OptionsModeCoreg extends OptionsBase {
// TODO: refactor to input file
private final File gwasZscoreM... |
11a32c0f6149e068c817c2e3bbd44808882c8739f28f96471586d1b41c6a63c9 | Java | 5,651 | 149 | /*-
* #%L
* Utility classes for BoneJ1 plugins
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must ret... |
058dace7c79e5578ce493eab0821c18eafc28e4770f46c09d4cfd316158d4324 | Java | 5,666 | 192 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
3a3e376f4876a9abc74fda1d4b8e16c3d68ab02b4bd3959adb7e947a40f22041 | Java | 5,668 | 114 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetics.tableAdaption;
import java.io.File;
import java.io.IOException;
import java.util.HashSet;
import java.util.loggi... |
cd9bc6aad53a970a6f38e00c4fd3467d8f13dccca227708d2fcdcd01846ad8dd | Java | 5,668 | 155 | /**
* This class defines a quicksort method which sorts an array of comparable objects in place using multiple threads to
* parallelize the sorting.
*
* @author Kenneth Powers
*/
package umcg.genetica.util;
import java.util.concurrent.Executor;
import java.util.concurrent.Executors;
import java.util.concurrent.a... |
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