the start to the VCF implementation
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1425 348d0f76-0448-11de-a6fe-93d51630548a
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aaron
parent
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8403618846
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package org.broadinstitute.sting.utils.genotype.vcf;
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import org.broadinstitute.sting.utils.Pair;
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import org.broadinstitute.sting.utils.StingException;
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import org.apache.log4j.Logger;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Set;
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import java.util.LinkedHashSet;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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/**
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* @author aaron
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* <p/>
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* Class VCFHeader
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* <p/>
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* A descriptions should go here. Blame aaron if it's missing.
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*/
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public class VCFHeader {
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// the manditory header fields
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public enum HEADER_FIELDS {
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CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO
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}
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// our header field ordering, as a linked hash set to guarantee ordering
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private Set<HEADER_FIELDS> mHeaderFields = new LinkedHashSet<HEADER_FIELDS>();
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// the associated meta data
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private final List<Pair<String, String>> mMetaData = new ArrayList<Pair<String, String>>();
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// the list of auxillary tags
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private final List<String> auxillaryTags = new ArrayList<String>();
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// the character string that indicates meta data
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public static final String METADATA_INDICATOR = "##";
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// the header string indicator
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public static final String HEADER_INDICATOR = "#";
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/**
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* our log, which we want to capture anything from this class
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*/
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private static Logger logger = Logger.getLogger(VCFHeader.class);
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// patterns we use for detecting meta data and header lines
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private static Pattern pMeta = Pattern.compile("^" + METADATA_INDICATOR + "\\s*(\\S+)\\s*=\\s*(\\S+)\\s*$");
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/**
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* create a VCF header, given an array of strings that all start with at least the # character
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*
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* @param headerStrings a list of header strings
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*/
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public VCFHeader(List<String> headerStrings) {
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try {
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Thread.sleep(5000);
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} catch (InterruptedException e) {
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e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
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}
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// iterate over all the passed in strings
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for (String str : headerStrings) {
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Matcher matcher = pMeta.matcher(str);
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if (matcher.matches()) {
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String metaKey = "";
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String metaValue = "";
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if (matcher.groupCount() < 1) continue;
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if (matcher.groupCount() == 2) metaValue = matcher.group(2);
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metaKey = matcher.group(1);
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mMetaData.add(new Pair<String, String>(metaKey, metaValue));
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}
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}
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// iterate over all the passed in strings
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for (String str : headerStrings) {
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if (str.startsWith("#") && !str.startsWith("##")) {
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String[] strings = str.substring(1).split("\\s+");
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for (String s : strings) {
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if (mHeaderFields.contains(s)) throw new StingException("Header field duplication is not allowed");
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try {
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mHeaderFields.add(HEADER_FIELDS.valueOf(s));
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} catch (IllegalArgumentException e) {
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this.auxillaryTags.add(s);
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}
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}
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}
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}
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if (mHeaderFields.size() != HEADER_FIELDS.values().length) {
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throw new StingException("The VCF header is missing " + (HEADER_FIELDS.values().length - mHeaderFields.size()) + " required fields");
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}
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}
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/**
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* get the header fieldsm in order they're presented in the input file
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* @return
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*/
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public Set<HEADER_FIELDS> getHeaderFields() {
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return mHeaderFields;
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}
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/**
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* get the meta data, associated with this header
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* @return
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*/
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public List<Pair<String, String>> getMetaData() {
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return mMetaData;
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}
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/**
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* get the auxillary tags
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* @return
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*/
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public List<String> getAuxillaryTags() {
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return auxillaryTags;
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}
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}
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package org.broadinstitute.sting.utils.genotype.vcf;
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import org.broadinstitute.sting.utils.StingException;
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import java.io.*;
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import java.util.List;
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import java.util.Iterator;
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import java.util.ArrayList;
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import java.nio.ByteBuffer;
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import java.nio.charset.Charset;
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/**
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* The VCFReader class, which given a valid vcf file, parses out the header and VCF records
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*/
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public class VCFReader implements Iterator<VCFRecord> {
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// our VCF header
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private VCFHeader mHeader;
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// our buffered input stream
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private BufferedReader mReader;
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// our next record
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private VCFRecord mNextRecord = null;
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/**
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* Create a VCF reader, given a VCF file
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*
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* @param vcfFile
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*/
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public VCFReader(File vcfFile) {
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Charset utf8 = Charset.forName("UTF-8");
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try {
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mReader = new BufferedReader(
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new InputStreamReader(
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new FileInputStream(vcfFile),
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utf8));
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} catch (FileNotFoundException e) {
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throw new StingException("Unable to find VCF file: " + vcfFile, e);
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}
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String line = null;
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try {
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ArrayList<String> lines = new ArrayList<String>();
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line = mReader.readLine();
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while (line.startsWith("#")) {
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lines.add(line);
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line = mReader.readLine();
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}
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mHeader = new VCFHeader(lines);
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mNextRecord = new VCFRecord(mHeader, line);
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} catch (IOException e) {
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throw new StingException("Failed to parse VCF File on line: " + line, e);
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}
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}
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/**
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*
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* @return true if we have another VCF record to return
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*/
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public boolean hasNext() {
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return (mNextRecord != null);
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}
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/**
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* return the next available VCF record. Make sure to check availability with a call to hasNext!
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* @return a VCFRecord, representing the next record in the file
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*/
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public VCFRecord next() {
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VCFRecord rec = mNextRecord;
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try {
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String line = mReader.readLine();
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if (line == null) mNextRecord = null;
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else mNextRecord = new VCFRecord(mHeader, line);
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} catch (IOException e) {
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mNextRecord = null;
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}
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return rec;
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}
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/**
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* Remove is not supported
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*/
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public void remove() {
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throw new UnsupportedOperationException("Unsupported operation");
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}
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}
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package org.broadinstitute.sting.utils.genotype.vcf;
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import org.broadinstitute.sting.utils.StingException;
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import java.util.HashMap;
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import java.util.Map;
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import java.util.List;
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/**
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* the basic VCF record type
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*/
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public class VCFRecord {
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// required field values
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private Map<VCFHeader.HEADER_FIELDS, String> mValues = new HashMap<VCFHeader.HEADER_FIELDS, String>();
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// our auxillary values
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private Map<String, String> mAuxValues = new HashMap<String, String>();
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/**
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* create a VCFRecord, given a VCF header and the the values in this field
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*
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* @param header the VCF header
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* @param line the line to parse into individual fields
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*/
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public VCFRecord(VCFHeader header, String line) {
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String tokens[] = line.split("\\s+");
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if (tokens.length != (header.getAuxillaryTags().size() + header.getHeaderFields().size())) {
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throw new StingException("Line:" + line + " didn't parse into " + (header.getAuxillaryTags().size() + header.getHeaderFields().size()) + " fields");
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}
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int tokenCount = 0;
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for (VCFHeader.HEADER_FIELDS field : header.getHeaderFields()) {
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mValues.put(field, tokens[tokenCount]);
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tokenCount++;
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}
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for (String aux : header.getAuxillaryTags()) {
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mAuxValues.put(aux, tokens[tokenCount]);
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tokenCount++;
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}
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}
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/**
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* lookup a value, given it's column name
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*
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* @param key the column name, which is looked up in both the set columns and the auxillary columns
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* @return a String representing the column values, or null if the field doesn't exist in this record
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*/
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public String getValue(String key) {
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try {
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return mValues.get(VCFHeader.HEADER_FIELDS.valueOf(key));
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} catch (IllegalArgumentException e) {
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if (this.mAuxValues.containsKey(key)) {
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return mAuxValues.get(key);
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}
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return null;
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}
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}
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/**
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* get a required field, given the field tag
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*
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* @param field
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* @return
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*/
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public String getValue(VCFHeader.HEADER_FIELDS field) {
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return mValues.get(field);
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}
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/**
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* @return the string for the chromosome that this VCF record is associated with
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*/
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public String getChromosome() {
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return this.mValues.get(VCFHeader.HEADER_FIELDS.CHROM);
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}
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/**
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* @return this VCF records position on the specified chromosome
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*/
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public long getPosition() {
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return Long.valueOf(this.mValues.get(VCFHeader.HEADER_FIELDS.POS));
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}
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/**
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* @return the ID value for this record
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*/
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public String getID() {
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return this.mValues.get(VCFHeader.HEADER_FIELDS.ID);
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}
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/**
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* get the reference base
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*
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* @return either A, T, C, G, or N
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*/
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public char getReferenceBase() {
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// TODO: this field isn't validated correctly
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return this.mValues.get(VCFHeader.HEADER_FIELDS.REF).charAt(0);
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}
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/**
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* get the alternate allele strings
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*
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* @return an array of strings representing the alt alleles, or null if there are none
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*/
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public String[] getAlternateAlleles() {
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if (this.mValues.get(VCFHeader.HEADER_FIELDS.ALT).trim().equals(".")) {
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return null;
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}
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return this.mValues.get(VCFHeader.HEADER_FIELDS.ALT).split(",");
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}
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public boolean hasAlternateAllele() {
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return getAlternateAlleles() != null;
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}
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/**
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* @return the phred-scaled quality score
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*/
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public int getQual() {
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return Integer.valueOf(this.mValues.get(VCFHeader.HEADER_FIELDS.QUAL));
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}
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/**
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* get the filter criteria
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*
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* @return an array of strings representing the filtering criteria, or null if none were applied
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*/
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public String[] getFilteringCodes() {
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if (this.mValues.get(VCFHeader.HEADER_FIELDS.FILTER).trim().equals("0")) {
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return null;
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}
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return this.mValues.get(VCFHeader.HEADER_FIELDS.ALT).split(";");
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}
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public boolean hasFilteringCodes() {
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return getAlternateAlleles() != null;
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}
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/**
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* get the information key-value pairs as a Map<>
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* @return a map, of the info key-value pairs
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*/
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public Map<String,String> getInfoValues() {
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Map<String,String> ret = new HashMap<String,String>();
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String infoSplit[] = mValues.get(VCFHeader.HEADER_FIELDS.INFO).split(";");
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for (String s: infoSplit) {
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String keyValue[] = s.split("=");
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if (keyValue.length != 2) throw new StingException("Key value pairs must have both a key and a value; pair: " + s);
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ret.put(keyValue[0],keyValue[1]);
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}
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return ret;
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}
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}
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package org.broadinstitute.sting.utils.genotype.vcf;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.utils.StingException;
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import org.junit.Test;
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import org.junit.Assert;
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import java.io.*;
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import java.util.ArrayList;
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import java.util.List;
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/**
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*
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* @author aaron
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*
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* Class VCFHeaderTest
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*
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* Test the VCF Header class
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*/
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public class VCFHeaderTest extends BaseTest {
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@Test
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public void test1() {
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File in = new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample.vcf");
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if (!in.exists()) throw new StingException("vfc doesn't exist");
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List<String> array = new ArrayList<String>();
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try {
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BufferedReader reader = new BufferedReader(new FileReader("vcfexample.vcf"));
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String line = reader.readLine();
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while (line.startsWith("#")) {
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array.add(line);
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line = reader.readLine();
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}
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VCFHeader header = new VCFHeader(array);
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} catch (FileNotFoundException e) {
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Assert.fail("File not found exception in VCFHeaderTest");
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} catch (IOException e) {
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Assert.fail("IO exception in VCFHeaderTest");
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}
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}
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}
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package org.broadinstitute.sting.utils.genotype.vcf;
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import org.junit.Test;
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import org.junit.Assert;
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import org.broadinstitute.sting.BaseTest;
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import java.io.File;
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/**
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* test the VCFReader class test
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*/
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public class VCFReaderTest extends BaseTest {
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private static File vcfFile = new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample.vcf");
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@Test
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public void testVCFInput() {
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VCFReader reader = new VCFReader(vcfFile);
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int counter = 0;
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while (reader.hasNext()) {
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counter++;
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reader.next();
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System.err.println(counter);
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}
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Assert.assertEquals(5,counter);
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}
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}
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