172 lines
7.8 KiB
Java
172 lines
7.8 KiB
Java
/*
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* Copyright (c) 2012 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.variant.vcf;
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import org.broad.tribble.readers.AsciiLineReader;
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import org.broad.tribble.readers.PositionalBufferedStream;
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import org.broadinstitute.variant.VariantBaseTest;
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import org.testng.Assert;
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import org.testng.annotations.Test;
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import java.io.*;
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import java.math.BigInteger;
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import java.security.MessageDigest;
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import java.security.NoSuchAlgorithmException;
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/**
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* Created by IntelliJ IDEA.
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* User: aaron
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* Date: Jun 30, 2010
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* Time: 3:32:08 PM
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* To change this template use File | Settings | File Templates.
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*/
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public class VCFHeaderUnitTest extends VariantBaseTest {
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private VCFHeader createHeader(String headerStr) {
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VCFCodec codec = new VCFCodec();
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VCFHeader header = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(headerStr))));
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Assert.assertEquals(header.getMetaDataInInputOrder().size(), VCF4headerStringCount);
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return header;
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}
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@Test
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public void testVCF4ToVCF4() {
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VCFHeader header = createHeader(VCF4headerStrings);
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checkMD5ofHeaderFile(header, "f05a57053a0c6a5bac15dba566f7f7ff");
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}
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@Test
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public void testVCF4ToVCF4_alternate() {
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VCFHeader header = createHeader(VCF4headerStrings_with_negativeOne);
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checkMD5ofHeaderFile(header, "b1d71cc94261053131f8d239d65a8c9f");
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}
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/**
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* a little utility function for all tests to md5sum a file
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* Shameless taken from:
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*
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* http://www.javalobby.org/java/forums/t84420.html
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*
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* @param file the file
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* @return a string
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*/
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private static String md5SumFile(File file) {
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MessageDigest digest;
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try {
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digest = MessageDigest.getInstance("MD5");
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} catch (NoSuchAlgorithmException e) {
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throw new RuntimeException("Unable to find MD5 digest");
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}
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InputStream is;
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try {
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is = new FileInputStream(file);
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} catch (FileNotFoundException e) {
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throw new RuntimeException("Unable to open file " + file);
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}
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byte[] buffer = new byte[8192];
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int read;
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try {
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while ((read = is.read(buffer)) > 0) {
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digest.update(buffer, 0, read);
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}
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byte[] md5sum = digest.digest();
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BigInteger bigInt = new BigInteger(1, md5sum);
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return bigInt.toString(16);
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}
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catch (IOException e) {
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throw new RuntimeException("Unable to process file for MD5", e);
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}
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finally {
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try {
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is.close();
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}
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catch (IOException e) {
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throw new RuntimeException("Unable to close input stream for MD5 calculation", e);
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}
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}
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}
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private void checkMD5ofHeaderFile(VCFHeader header, String md5sum) {
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File myTempFile = null;
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PrintWriter pw = null;
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try {
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myTempFile = File.createTempFile("VCFHeader","vcf");
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myTempFile.deleteOnExit();
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pw = new PrintWriter(myTempFile);
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} catch (IOException e) {
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Assert.fail("Unable to make a temp file!");
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}
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for (VCFHeaderLine line : header.getMetaDataInSortedOrder())
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pw.println(line);
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pw.close();
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Assert.assertEquals(md5SumFile(myTempFile), md5sum);
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}
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public static int VCF4headerStringCount = 16;
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public static String VCF4headerStrings =
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"##fileformat=VCFv4.0\n"+
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"##filedate=2010-06-21\n"+
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"##reference=NCBI36\n"+
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"##INFO=<ID=GC, Number=0, Type=Flag, Description=\"Overlap with Gencode CCDS coding sequence\">\n"+
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"##INFO=<ID=DP, Number=1, Type=Integer, Description=\"Total number of reads in haplotype window\">\n"+
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"##INFO=<ID=AF, Number=A, Type=Float, Description=\"Dindel estimated population allele frequency\">\n"+
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"##INFO=<ID=CA, Number=1, Type=String, Description=\"Pilot 1 callability mask\">\n"+
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"##INFO=<ID=HP, Number=1, Type=Integer, Description=\"Reference homopolymer tract length\">\n"+
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"##INFO=<ID=NS, Number=1, Type=Integer, Description=\"Number of samples with data\">\n"+
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"##INFO=<ID=DB, Number=0, Type=Flag, Description=\"dbSNP membership build 129 - type match and indel sequence length match within 25 bp\">\n"+
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"##INFO=<ID=NR, Number=1, Type=Integer, Description=\"Number of reads covering non-ref variant on reverse strand\">\n"+
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"##INFO=<ID=NF, Number=1, Type=Integer, Description=\"Number of reads covering non-ref variant on forward strand\">\n"+
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"##FILTER=<ID=NoQCALL, Description=\"Variant called by Dindel but not confirmed by QCALL\">\n"+
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"##FORMAT=<ID=GT, Number=1, Type=String, Description=\"Genotype\">\n"+
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"##FORMAT=<ID=HQ, Number=2, Type=Integer, Description=\"Haplotype quality\">\n"+
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"##FORMAT=<ID=GQ, Number=1, Type=Integer, Description=\"Genotype quality\">\n"+
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"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n";
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public static String VCF4headerStrings_with_negativeOne =
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"##fileformat=VCFv4.0\n"+
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"##filedate=2010-06-21\n"+
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"##reference=NCBI36\n"+
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"##INFO=<ID=GC, Number=0, Type=Flag, Description=\"Overlap with Gencode CCDS coding sequence\">\n"+
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"##INFO=<ID=YY, Number=., Type=Integer, Description=\"Some weird value that has lots of parameters\">\n"+
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"##INFO=<ID=AF, Number=A, Type=Float, Description=\"Dindel estimated population allele frequency\">\n"+
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"##INFO=<ID=CA, Number=1, Type=String, Description=\"Pilot 1 callability mask\">\n"+
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"##INFO=<ID=HP, Number=1, Type=Integer, Description=\"Reference homopolymer tract length\">\n"+
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"##INFO=<ID=NS, Number=1, Type=Integer, Description=\"Number of samples with data\">\n"+
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"##INFO=<ID=DB, Number=0, Type=Flag, Description=\"dbSNP membership build 129 - type match and indel sequence length match within 25 bp\">\n"+
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"##INFO=<ID=NR, Number=1, Type=Integer, Description=\"Number of reads covering non-ref variant on reverse strand\">\n"+
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"##INFO=<ID=NF, Number=1, Type=Integer, Description=\"Number of reads covering non-ref variant on forward strand\">\n"+
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"##FILTER=<ID=NoQCALL, Description=\"Variant called by Dindel but not confirmed by QCALL\">\n"+
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"##FORMAT=<ID=GT, Number=1, Type=String, Description=\"Genotype\">\n"+
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"##FORMAT=<ID=HQ, Number=2, Type=Integer, Description=\"Haplotype quality\">\n"+
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"##FORMAT=<ID=TT, Number=., Type=Integer, Description=\"Lots of TTs\">\n"+
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"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n";
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}
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