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ChristinaXu2017ChristinaXu2017
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Merge pull request #242 from AdamaJava/newVcfReader
create VcfFileReader based on RecordReader
2 parents d155b8e + 9584c25 commit ca65b51

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‎qio/src/org/qcmg/qio/vcf/VcfFileReader.java

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/**
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* © Copyright The University of Queensland 2010-2014.
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* © Copyright QIMR Berghofer Medical Research Institute 2014-2016.
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*
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* This code is released under the terms outlined in the included LICENSE file.
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*/
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package org.qcmg.qio.vcf;
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import java.io.File;
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import java.io.IOException;
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import org.qcmg.common.util.Constants;
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import org.qcmg.common.util.TabTokenizer;
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import org.qcmg.common.vcf.VcfRecord;
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import org.qcmg.common.vcf.header.VcfHeader;
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import org.qcmg.qio.record.RecordReader;
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/**
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* Contains an `InputStream` so remember to call close() or use in try-with-resources
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*/
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public final class VcfFileReader extends RecordReader<VcfRecord> {
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private static final String HEADER_PREFIX = Constants.HASH_STRING;
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private VcfHeader header;
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public VcfFileReader(final String file) throws IOException {
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this(new File(file));
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}
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public VcfFileReader(final File file) throws IOException {
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super(file, HEADER_PREFIX);
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header = new VcfHeader(getHeader());
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}
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public VcfHeader getVcfHeader() {
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return header;
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}
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@Override
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public VcfRecord getRecord(String line) {
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final String[] params = TabTokenizer.tokenize(line);
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final int arrayLength = params.length;
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if (8 > arrayLength) {
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throw new IllegalArgumentException("Bad VCF format. Insufficient columns: '" + line + "'");
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}
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return new VcfRecord(params);
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}
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}

‎qio/src/org/qcmg/vcf/VCFFileReader.java

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/**
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* Contains an `InputStream` so remember to call close() or use in try-with-resources
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*/
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@Deprecated
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public final class VCFFileReader implements Closeable, Iterable<VcfRecord> {
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private final File file;
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private final InputStream inputStream;

‎qio/src/org/qcmg/vcf/VCFFileWriter.java

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import org.qcmg.common.util.FileUtils;
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import org.qcmg.common.vcf.VcfRecord;
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@Deprecated
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public final class VCFFileWriter implements Closeable {
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private final File file;
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private final OutputStream outputStream;

‎qio/src/org/qcmg/vcf/VCFRecordIterator.java

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import org.qcmg.common.vcf.VcfRecord;
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@Deprecated
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public final class VCFRecordIterator implements Iterator<VcfRecord> {
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private final BufferedReader reader;
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private VcfRecord next;

‎qio/src/org/qcmg/vcf/VCFSerializer.java

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import org.qcmg.common.vcf.VcfRecord;
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import org.qcmg.common.vcf.header.VcfHeader;
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@Deprecated
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public final class VCFSerializer {
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private static final String DEFAULT_HEADER_PREFIX = "#";
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‎qio/test/org/qcmg/qio/vcf/VcfWriterReaderTest.java

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package org.qcmg.qio.vcf;
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import static org.junit.Assert.*;
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import java.io.File;
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import java.io.IOException;
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import java.util.Arrays;
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import java.util.stream.Collectors;
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import org.junit.Assert;
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import org.junit.Rule;
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import org.junit.Test;
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import org.junit.rules.TemporaryFolder;
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import org.qcmg.common.util.FileUtils;
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import org.qcmg.common.vcf.VcfRecord;
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import org.qcmg.common.vcf.header.VcfHeader;
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import org.qcmg.common.vcf.header.VcfHeaderUtils;
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import org.qcmg.qio.vcf.VcfFileReader;
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import org.qcmg.qio.record.RecordWriter;
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public class VcfWriterReaderTest {
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public static final String[] vcfStrings = new String[] {"##test=test", VcfHeaderUtils.STANDARD_FINAL_HEADER_LINE, };
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private final String[] parms = {"chrY","2675826",".","TG","CA"};
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@Rule
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public TemporaryFolder testFolder = new TemporaryFolder();
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@Test
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public void getHeaderFromZippedVcfFile() throws IOException {
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File file = testFolder.newFile("header.vcf.gz");
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try(RecordWriter<VcfRecord> writer = new RecordWriter<>(file) ){
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writer.addHeader(Arrays.stream(vcfStrings).collect(Collectors.joining("\n")));
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}
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assertEquals(true, FileUtils.isInputGZip(file) );
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/*
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* Should be able to get the header back out
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*/
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VcfHeader header = null;
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int num = 0;
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try(VcfFileReader reader = new VcfFileReader(file) ){
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header = reader.getVcfHeader();
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for(VcfRecord re: reader) {
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num ++;
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}
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}
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assertEquals(true, null != header);
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assertEquals(VcfHeaderUtils.STANDARD_FINAL_HEADER_LINE, header.getChrom().toString());
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assertEquals(1, header.getAllMetaRecords().size());
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assertEquals("##test=test", header.getAllMetaRecords().get(0).toString());
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assertEquals(0, num); //no record
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}
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@Test
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public void getHeaderFromInvalidVcfFile() throws IOException {
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File file = testFolder.newFile("header.vcf.gz");
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try(RecordWriter<VcfRecord> writer = new RecordWriter<>(file) ){
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writer.addHeader(Arrays.stream(vcfStrings).collect(Collectors.joining("\n")));
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//add two valide record
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writer.add(new VcfRecord(parms));
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writer.add(new VcfRecord(parms));
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writer.addHeader(Arrays.stream(vcfStrings).collect(Collectors.joining("\n")));
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}
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assertEquals(true, FileUtils.isInputGZip(file) );
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/*
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* Should be able to get the header back out
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*/
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VcfHeader header = null;
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try(VcfFileReader reader = new VcfFileReader(file) ){
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header = reader.getVcfHeader();
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}
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assertEquals(true, null != header);
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assertEquals(1, header.getAllMetaRecords().size());
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int num = 0;
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try(VcfFileReader reader = new VcfFileReader(file) ){
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for(VcfRecord re: reader) {
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num ++;
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System.out.println(re.toSimpleString());
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}
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fail("expected exception should throw here! ");
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}catch(IllegalArgumentException e) {
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//two valid record but exception happed when check next record before create second vcf record
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assertEquals(1, num); //one valid record
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}
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}
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@Test
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public void testValidation() throws IOException {
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String[] fnames = new String[] { "test.output.gz", "test.output" };
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String[] vcfStrings = new String[] {"#testing...", VcfHeaderUtils.STANDARD_FINAL_HEADER_LINE};
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for(int i = 0; i < fnames.length; i ++){
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File file = testFolder.newFile(fnames[i]);
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//create writer
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try(RecordWriter<VcfRecord> writer = new RecordWriter<>(file) ){
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writer.addHeader(vcfStrings[i]);
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} catch (Exception e) { fail(); }
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//check output type
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try {
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if( FileUtils.isFileNameGZip(file) )
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Assert.assertTrue( FileUtils.isInputGZip(file) );
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else
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Assert.assertFalse( FileUtils.isInputGZip(file) );
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} catch (IOException e) { fail(); }
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//read invaid vcf
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try(VcfFileReader reader = new VcfFileReader(file);){
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//file can be deleted here even without close but can't be closed if fail()
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Assert.assertTrue( file.delete());
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if(i == 0 ) fail();
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Assert.assertTrue( reader.getVcfHeader() != null);
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} catch (Exception e) {
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e.printStackTrace();
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if(i == 1 ) fail();
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//delete testing file which is invalid vcf,
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Assert.assertTrue( file.delete());
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}
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}
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}
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@Test
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public void testCreateAppendVcfWriter() throws IOException {
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File file = testFolder.newFile("output.vcf");
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//create new file
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try(RecordWriter<VcfRecord> writer = new RecordWriter<>(file) ){
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writer.addHeader(vcfStrings[0]);
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} catch (Exception e) { fail(); }
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// read throw exception
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try(VcfFileReader reader = new VcfFileReader(file);){
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fail();
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} catch (Exception e) { }
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//append to file
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try(RecordWriter<VcfRecord> writer = new RecordWriter<>(file, true) ){
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writer.addHeader(vcfStrings[1]);
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} catch (Exception e) { fail(); }
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//now it become a valid vcf file
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try(VcfFileReader reader = new VcfFileReader(file);){
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Assert.assertFalse( FileUtils.isInputGZip(file) );
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Assert.assertTrue( reader.getVcfHeader().getAllMetaRecords().size() == 1);
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Assert.assertTrue(file.delete());
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} catch (Exception e) {fail(); }
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}
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}

‎qio/test/org/qcmg/vcf/VcfWriterReaderTest.java

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import org.qcmg.common.vcf.header.VcfHeader;
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import org.qcmg.common.vcf.header.VcfHeaderUtils;
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@Deprecated
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public class VcfWriterReaderTest {
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public static final String[] vcfStrings = new String[] {"##test=test", VcfHeaderUtils.STANDARD_FINAL_HEADER_LINE};

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