create VcfFileReader based on RecordReader

Author: ChristinaXu2017

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

@@ -0,0 +1,50 @@
+/**
+ * © Copyright The University of Queensland 2010-2014.
+ * © Copyright QIMR Berghofer Medical Research Institute 2014-2016.
+ *
+ * This code is released under the terms outlined in the included LICENSE file.
+ */
+package org.qcmg.qio.vcf;
+
+import java.io.File;
+import java.io.IOException;
+
+import org.qcmg.common.util.Constants;
+import org.qcmg.common.util.TabTokenizer;
+import org.qcmg.common.vcf.VcfRecord;
+import org.qcmg.common.vcf.header.VcfHeader;
+import org.qcmg.qio.record.RecordReader;
+
+/**
+ * Contains an `InputStream` so remember to call close() or use in try-with-resources
+ */
+public final class VcfFileReader extends RecordReader<VcfRecord> {
+	private static final String HEADER_PREFIX = Constants.HASH_STRING;
+   
+    private VcfHeader header;
+    
+    public VcfFileReader(final String file) throws IOException {
+    	this(new File(file));
+    }
+
+    public VcfFileReader(final File file) throws IOException {
+    	super(file, HEADER_PREFIX);     
+    	header = new VcfHeader(getHeader());       
+    }
+
+	public VcfHeader getVcfHeader() {
+		return header;
+	}
+
+	@Override
+	public VcfRecord getRecord(String line) {
+		final String[] params = TabTokenizer.tokenize(line);
+		final int arrayLength = params.length; 
+		if (8 > arrayLength) {
+			throw new IllegalArgumentException("Bad VCF format. Insufficient columns: '" + line + "'");
+		}
+		
+		return new VcfRecord(params);		
+	}
+	
+}

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

@@ -0,0 +1,139 @@
+package org.qcmg.qio.vcf;
+
+import static org.junit.Assert.*;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.stream.Collectors;
+
+import org.junit.Assert;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
+import org.qcmg.common.util.FileUtils;
+import org.qcmg.common.vcf.VcfRecord;
+import org.qcmg.common.vcf.header.VcfHeader;
+import org.qcmg.common.vcf.header.VcfHeaderUtils;
+import org.qcmg.qio.vcf.VcfFileReader;
+import org.qcmg.qio.record.RecordWriter;
+
+public class VcfWriterReaderTest {
+	
+	public static final String[] vcfStrings = new String[] {"##test=test", VcfHeaderUtils.STANDARD_FINAL_HEADER_LINE};
+	
+	@Rule
+	public  TemporaryFolder testFolder = new TemporaryFolder();
+	
+	@Test
+	public void getHeaderFromZippedVcfFileUsingStreams() throws IOException {
+		File file =  testFolder.newFile("header.vcf.gz");
+		
+		try(RecordWriter<VcfRecord> writer = new RecordWriter<>(file) ){
+			 writer.addHeader(Arrays.stream(vcfStrings).collect(Collectors.joining("\n")));
+		}
+		assertEquals(true, FileUtils.isInputGZip(file) );
+		
+		/*
+		 * Should be able to get the header back out
+		 */
+		VcfHeader header = null;
+		try(VcfFileReader reader = new VcfFileReader(file) ){
+			header = reader.getVcfHeader();
+		}
+		assertEquals(true, null != header);
+		assertEquals(VcfHeaderUtils.STANDARD_FINAL_HEADER_LINE, header.getChrom().toString());
+		assertEquals(1, header.getAllMetaRecords().size());
+		assertEquals("##test=test", header.getAllMetaRecords().get(0).toString());
+	}
+	
+	@Test
+	public void getHeaderFromZippedVcfFile() throws IOException {
+		File file =  testFolder.newFile("header.vcf.gz");
+		
+		try(RecordWriter<VcfRecord> writer = new RecordWriter<>(file) ){
+			writer.addHeader(Arrays.stream(vcfStrings).collect(Collectors.joining("\n")));
+		}
+		assertEquals(true, FileUtils.isInputGZip(file) );
+		
+		
+		/*
+		 * Should be able to get the header back out
+		 */
+		VcfHeader header = null;
+		
+		try(VcfFileReader reader = new VcfFileReader(file) ){
+			header = reader.getVcfHeader();
+		}
+		assertEquals(true, null != header);
+		assertEquals(VcfHeaderUtils.STANDARD_FINAL_HEADER_LINE, header.getChrom().toString());
+		assertEquals(1, header.getAllMetaRecords().size());
+		assertEquals("##test=test", header.getAllMetaRecords().get(0).toString());
+	}
+	
+	@Test
+	public void testValidation() throws IOException  {
+		String[] fnames = new String[] { "test.output.gz", "test.output" };
+		String[] vcfStrings = new String[] {"#testing...", VcfHeaderUtils.STANDARD_FINAL_HEADER_LINE};
+		for(int i = 0; i < fnames.length; i ++){ 
+			File file = testFolder.newFile(fnames[i]);
+			//create writer
+			try(RecordWriter<VcfRecord> writer = new RecordWriter<>(file) ){
+				 writer.addHeader(vcfStrings[i]);				
+			} catch (Exception e) { fail(); }
+			
+			//check output type
+			try {
+				if( FileUtils.isFileNameGZip(file) )				
+					Assert.assertTrue( FileUtils.isInputGZip(file) );
+				else
+					Assert.assertFalse( FileUtils.isInputGZip(file) );				
+			} catch (IOException e) { fail(); }
+			
+			//read invaid vcf
+			try(VcfFileReader reader = new VcfFileReader(file);){
+				//file can be deleted here even without close but can't be closed if fail()	
+				Assert.assertTrue( file.delete());				
+				if(i == 0 ) fail();
+				Assert.assertTrue( reader.getVcfHeader() != null);
+			
+			} catch (Exception e) {				 
+				e.printStackTrace();
+				if(i == 1 ) fail();
+				//delete testing file which is invalid vcf, 
+				Assert.assertTrue( file.delete());
+			}						
+		}			
+	}
+
+	@Test
+	public void testCreateAppendVcfWriter() throws IOException {
+		File file =  testFolder.newFile("output.vcf");
+		
+		//create new file 
+		try(RecordWriter<VcfRecord> writer = new RecordWriter<>(file) ){
+			 writer.addHeader(vcfStrings[0]);				
+		} catch (Exception e) { fail(); }
+		
+		// read throw exception
+		try(VcfFileReader reader = new VcfFileReader(file);){
+			fail();
+		} catch (Exception e) { }
+		
+		
+		//append to file
+		try(RecordWriter<VcfRecord> writer = new RecordWriter<>(file, true)   ){
+			 writer.addHeader(vcfStrings[1]);				
+		} catch (Exception e) { fail(); }
+		
+		//now it become a valid vcf file
+		try(VcfFileReader reader = new VcfFileReader(file);){ 
+			Assert.assertFalse( FileUtils.isInputGZip(file) );	
+			Assert.assertTrue( reader.getVcfHeader().getAllMetaRecords().size() == 1);	
+			Assert.assertTrue(file.delete());
+			
+		} catch (Exception e) {fail(); }		
+		
+	}
+
+}