removing some out-of-date RODs and some unused genotype writer formats
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3304 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron
parent
c998c48a23
commit
6bbcc47b5d
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@ -1,24 +0,0 @@
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package org.broadinstitute.sting.gatk.refdata;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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public class CleanedOutSNPROD extends TabularROD {
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private static final String REAL_SNP_STRING = "SAME_SNP";
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private static final String FALSE_SNP_STRING = "NOT_SNP";
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public CleanedOutSNPROD(String name) {
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super(name);
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}
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public GenomeLoc getLocation() {
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return GenomeLocParser.parseGenomeLoc(this.get("0"));
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}
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public boolean isRealSNP() {
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String s = this.get("1");
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return s != null && s.equals(REAL_SNP_STRING);
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}
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}
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@ -1,15 +0,0 @@
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package org.broadinstitute.sting.gatk.refdata;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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public class PointIndelROD extends SimpleIndelROD {
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public PointIndelROD(String name) {
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super(name);
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}
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public GenomeLoc getLocation() {
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return GenomeLocParser.createGenomeLoc(this.get("0"), Long.parseLong(this.get("1")));
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}
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}
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@ -1,275 +0,0 @@
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package org.broadinstitute.sting.gatk.refdata;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.StingException;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
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import java.util.*;
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import java.util.regex.MatchResult;
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import java.util.regex.Pattern;
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/**
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* Class for representing arbitrary reference ordered data sets
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*
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* User: mdepristo
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* Date: Feb 27, 2009
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* Time: 10:47:14 AM
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* To change this template use File | Settings | File Templates.
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*/
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public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum {
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private String contig, source, feature, strand, frame;
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private long start, stop;
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private double score;
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private HashMap<String, String> attributes;
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// ----------------------------------------------------------------------
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//
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// Constructors
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//
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// ----------------------------------------------------------------------
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public RodGenotypeChipAsGFF(final String name) {
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super(name);
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}
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public void setValues(final String contig, final String source, final String feature,
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final long start, final long stop, final double score,
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final String strand, final String frame, HashMap<String, String> attributes) {
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this.contig = contig;
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this.source = source;
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this.feature = feature;
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this.start = start;
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this.stop= stop;
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this.score = score;
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this.strand = strand;
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this.frame = frame;
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this.attributes = attributes;
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}
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// ----------------------------------------------------------------------
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//
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// Accessors
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//
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// ----------------------------------------------------------------------
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public String getSource() {
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return source;
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}
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public String getFeature() {
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return feature;
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}
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public String getStrand() {
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return strand;
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}
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public String getFrame() {
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return frame;
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}
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public double getScore() {
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return score;
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}
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public GenomeLoc getLocation() {
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return GenomeLocParser.parseGenomeLoc(contig, start, stop);
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}
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/**
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* get the reference base(s) at this position
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*
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* @return the reference base or bases, as a string
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*/
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public String getReference() {
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throw new IllegalStateException("Chip data is unable to determine the reference");
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}
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/**
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* get the -1 * (log 10 of the error value)
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*
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* @return the log based error estimate
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*/
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public double getNegLog10PError() {
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return 4; // 1/10000 error
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}
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/**
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* gets the alternate alleles. This method should return all the alleles present at the location,
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* NOT including the reference base. This is returned as a string list with no guarantee ordering
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* of alleles (i.e. the first alternate allele is not always going to be the allele with the greatest
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* frequency).
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*
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* @return an alternate allele list
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*/
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public List<String> getAlternateAlleleList() {
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throw new StingException("Hapmap is unable to provide an alternate allele list; the reference is unknown");
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}
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/**
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* gets the alleles. This method should return all the alleles present at the location,
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* including the reference base. The first allele should always be the reference allele, followed
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* by an unordered list of alternate alleles.
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*
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* @return an alternate allele list
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*/
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public List<String> getAlleleList() {
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List<String> ret = new ArrayList<String>();
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for (char c : feature.toCharArray())
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ret.add(String.valueOf(c));
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return ret;
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}
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public String getAttribute(final String key) {
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return attributes.get(key);
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}
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public boolean containsAttribute(final String key) {
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return attributes.containsKey(key);
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}
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public HashMap<String,String> getAttributes() {
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return attributes;
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}
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public String getAttributeString() {
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String[] strings = new String[attributes.size()];
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int i = 0;
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for ( Map.Entry<String, String> pair : attributes.entrySet() ) {
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strings[i++] = pair.getKey() + " " + pair.getValue();
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//strings[i++] = "(" + pair.getKey() + ") (" + pair.getValue() + ")";
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}
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return Utils.join(" ; ", strings);
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}
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// ----------------------------------------------------------------------
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//
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// formatting
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//
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// ----------------------------------------------------------------------
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public String toString() {
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return String.format("%s\t%s\t%s\t%d\t%d\t%f\t%s\t%s\t%s", contig, source, feature, start, stop+1, score, strand, frame, getAttributeString());
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}
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public String repl() {
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return this.toString();
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}
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public String toSimpleString() {
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return String.format("chip-genotype: %s", feature);
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}
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private static Pattern GFF_DELIM = Pattern.compile("\\s+;\\s*");
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private static Pattern GFF_ATTRIBUTE_PATTERN = Pattern.compile("([A-Za-z][A-Za-z0-9_]*)((?:\\s+\\S+)+)");
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final private HashMap<String, String> parseAttributes( final String attributeLine ) {
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HashMap<String, String> attributes = new HashMap<String, String>();
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Scanner scanner = new Scanner(attributeLine);
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scanner.useDelimiter(GFF_DELIM);
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while ( scanner.hasNext(GFF_ATTRIBUTE_PATTERN) ) {
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MatchResult result = scanner.match();
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String key = result.group(1);
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String value = result.group(2).replace("\"", "").trim();
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//System.out.printf(" Adding %s / %s (total %d)%n", key, value, result.groupCount());
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attributes.put(key, value);
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String n = scanner.next();
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//System.out.printf(" next is %s%n", n);
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}
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return attributes;
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}
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public boolean parseLine(final Object header, final String[] parts) {
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//System.out.printf("Parsing GFFLine %s%n", Utils.join(" ", parts));
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final String contig = parts[0];
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final String source = parts[1];
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final String feature = parts[2];
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final long start = Long.parseLong(parts[3]);
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final long stop = Long.parseLong(parts[4])-1;
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double score = Double.NaN;
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if ( ! parts[5].equals(".") )
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score = Double.parseDouble(parts[5]);
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final String strand = parts[6];
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final String frame = parts[7];
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final String attributeParts = Utils.join(" ", parts, 8, parts.length);
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HashMap<String, String> attributes = parseAttributes(attributeParts);
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setValues(contig, source, feature, start, stop, score, strand, frame, attributes);
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return true;
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}
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public String getRefBasesFWD() { return null; }
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public char getRefSnpFWD() throws IllegalStateException { return 0; }
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public String getAltBasesFWD() { return null; }
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public char getAltSnpFWD() throws IllegalStateException { return 0; }
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public boolean isReference() { return ! isSNP(); }
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/**
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* get the frequency of this variant
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*
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* @return VariantFrequency with the stored frequency
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*/
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public double getNonRefAlleleFrequency() {
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return this.getMAF();
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}
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public boolean isSNP() { return false; }
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public boolean isInsertion() { return false; }
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public boolean isDeletion() { return false; }
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public boolean isIndel() { return false; }
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/**
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* gets the alternate base is the case of a SNP. Throws an IllegalStateException in the case
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* of
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*
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* @return a char, representing the alternate base
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*/
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public char getAlternativeBaseForSNP() {
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return this.getAltSnpFWD();
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}
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/**
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* gets the reference base is the case of a SNP. Throws an IllegalStateException if we're not a SNP
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*
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* @return a char, representing the alternate base
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*/
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public char getReferenceForSNP() {
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return this.getRefSnpFWD();
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}
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public double getMAF() { return 0; }
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public double getHeterozygosity() { return 0; }
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public boolean isGenotype() { return true; }
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public double getVariationConfidence() { return score; }
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public double getConsensusConfidence() { return score; }
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public List<String> getGenotype() throws IllegalStateException {
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//System.out.printf("feature = %s%n", feature);
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return Arrays.asList(feature);
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}
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public int getPloidy() throws IllegalStateException { return 2; }
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public boolean isBiallelic() { return true; }
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public int length() { return 1; }
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/**
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* do we have the specified genotype? not all backedByGenotypes
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* have all the genotype data.
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*
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* @param x the genotype
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*
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* @return true if available, false otherwise
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*/
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public boolean hasGenotype(DiploidGenotype x) {
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if (!x.toString().equals(this.getAltBasesFWD())) return false;
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return true;
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}
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}
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@ -1,174 +0,0 @@
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package org.broadinstitute.sting.gatk.refdata;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import java.util.Arrays;
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import java.util.List;
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public class SimpleIndelROD extends TabularROD {
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private boolean KGENOMES_FORMAT = false, checkedFormat = false;
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public SimpleIndelROD(String name) {
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super(name);
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}
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public GenomeLoc getLocation() {
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long pos = Long.parseLong(this.get("1"));
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return GenomeLocParser.createGenomeLoc(this.get("0"), pos, (isDeletion() ? pos+length() : pos+1));
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}
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/**
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* get the reference base(s) at this position
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*
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* @return the reference base or bases, as a string
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*/
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public String getReference() {
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return String.valueOf(getRef());
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}
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public List<String> getFWDAlleles() {
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if ( is1KGFormat() )
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return Arrays.asList(this.get("4"));
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String str = this.get("3");
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int pos = str.indexOf(":");
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if ( pos == -1 ) {
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return Arrays.asList(str.substring(1));
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}
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return Arrays.asList(str.substring(1, pos));
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}
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public String getFWDRefBases() { return ""; }
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public String getAltBasesFWD() { return getFWDAlleles().get(0); }
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public String getRefBasesFWD() { return ""; }
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public char getRefSnpFWD() { throw new IllegalStateException("I'm an indel, not a SNP"); }
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public char getAltSnpFWD() { throw new IllegalStateException("I'm an indel, not a SNP"); }
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public char getRef() { return 'N'; }
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public List<String> getGenotype() { return getFWDAlleles(); }
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public boolean isGenotype() { return false; }
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public boolean isPointGenotype() { return false; }
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public boolean isIndelGenotype() { return true; }
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/**
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* get the frequency of this variant
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*
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* @return VariantFrequency with the stored frequency
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*/
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public double getNonRefAlleleFrequency() {
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return 0.0;
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}
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public boolean isSNP() { return false; }
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public boolean isReference() { return false; }
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public boolean isInsertion() {
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if ( is1KGFormat() )
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return this.get("3").equals("I");
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return this.get("3").charAt(0) == '+';
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}
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public boolean isDeletion() {
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if ( is1KGFormat() )
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return this.get("3").equals("D");
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return this.get("3").charAt(0) == '-';
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}
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public boolean isIndel() { return true; }
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/**
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* gets the alternate base is the case of a SNP. Throws an IllegalStateException if we're not a SNP
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* of
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*
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* @return a char, representing the alternate base
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*/
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public char getAlternativeBaseForSNP() {
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return getAltSnpFWD();
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}
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||||||
/**
|
|
||||||
* gets the reference base is the case of a SNP. Throws an IllegalStateException if we're not a SNP
|
|
||||||
*
|
|
||||||
* @return a char, representing the alternate base
|
|
||||||
*/
|
|
||||||
public char getReferenceForSNP() {
|
|
||||||
return getRefSnpFWD();
|
|
||||||
}
|
|
||||||
|
|
||||||
public double getVariantConfidence() { return 0.0; }
|
|
||||||
public double getVariationConfidence() { return 0.0; }
|
|
||||||
public double getConsensusConfidence() { return 0.0; }
|
|
||||||
public boolean isBiallelic() { return true; }
|
|
||||||
|
|
||||||
/**
|
|
||||||
* get the -1 * (log 10 of the error value)
|
|
||||||
*
|
|
||||||
* @return the log based error estimate
|
|
||||||
*/
|
|
||||||
public double getNegLog10PError() {
|
|
||||||
return getVariationConfidence();
|
|
||||||
}
|
|
||||||
|
|
||||||
/**
|
|
||||||
* gets the alternate alleles. This method should return all the alleles present at the location,
|
|
||||||
* NOT including the reference base. This is returned as a string list with no guarantee ordering
|
|
||||||
* of alleles (i.e. the first alternate allele is not always going to be the allele with the greatest
|
|
||||||
* frequency).
|
|
||||||
*
|
|
||||||
* @return an alternate allele list
|
|
||||||
*/
|
|
||||||
public List<String> getAlternateAlleleList() {
|
|
||||||
List<String> ret = getAlleleList();
|
|
||||||
for (String val : ret) {
|
|
||||||
if (val.equals(this.getReference())) ret.remove(val);
|
|
||||||
}
|
|
||||||
return ret;
|
|
||||||
}
|
|
||||||
|
|
||||||
/**
|
|
||||||
* gets the alleles. This method should return all the alleles present at the location,
|
|
||||||
* including the reference base. The first allele should always be the reference allele, followed
|
|
||||||
* by an unordered list of alternate alleles.
|
|
||||||
*
|
|
||||||
* @return an alternate allele list
|
|
||||||
*/
|
|
||||||
public List<String> getAlleleList() {
|
|
||||||
return this.getFWDAlleles();
|
|
||||||
}
|
|
||||||
|
|
||||||
public boolean isHom() { return false; }
|
|
||||||
public boolean isHet() { return false; }
|
|
||||||
public double getHeterozygosity() { return 0.0; }
|
|
||||||
public double getMAF() { return 0.0; }
|
|
||||||
public int getPloidy() { return 2; }
|
|
||||||
public int length() {
|
|
||||||
if ( is1KGFormat() )
|
|
||||||
return Integer.parseInt(this.get("2"));
|
|
||||||
return getFWDAlleles().get(0).length();
|
|
||||||
}
|
|
||||||
|
|
||||||
public boolean allowIncompleteRecords() {
|
|
||||||
return true;
|
|
||||||
}
|
|
||||||
|
|
||||||
public String getSamplesString() {
|
|
||||||
return (is1KGFormat() && this.get("5") != null ? this.get("5") : "");
|
|
||||||
}
|
|
||||||
|
|
||||||
public String toString() {
|
|
||||||
StringBuffer sb = new StringBuffer();
|
|
||||||
sb.append(getLocation().getContig() + "\t" + getLocation().getStart() + "\t");
|
|
||||||
sb.append(length() + "\t" + (isInsertion() ? "I" : "D") + "\t" + getFWDAlleles().get(0));
|
|
||||||
String samples = getSamplesString();
|
|
||||||
if ( samples.length() > 0 )
|
|
||||||
sb.append("\t" + samples);
|
|
||||||
return sb.toString();
|
|
||||||
}
|
|
||||||
|
|
||||||
private boolean is1KGFormat() {
|
|
||||||
if ( !checkedFormat ) {
|
|
||||||
checkedFormat = true;
|
|
||||||
KGENOMES_FORMAT = this.get("3").equals("D") || this.get("3").equals("I");
|
|
||||||
}
|
|
||||||
return KGENOMES_FORMAT;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
@ -54,15 +54,11 @@ public class RODTrackBuilder implements RMDTrackBuilder {
|
||||||
|
|
||||||
static {
|
static {
|
||||||
// All known ROD types
|
// All known ROD types
|
||||||
Types.put("GFF", RodGenotypeChipAsGFF.class);
|
|
||||||
Types.put("SAMPileup", rodSAMPileup.class);
|
Types.put("SAMPileup", rodSAMPileup.class);
|
||||||
Types.put("GELI", rodGELI.class);
|
Types.put("GELI", rodGELI.class);
|
||||||
Types.put("RefSeq", rodRefSeq.class);
|
Types.put("RefSeq", rodRefSeq.class);
|
||||||
Types.put("Table", TabularROD.class);
|
Types.put("Table", TabularROD.class);
|
||||||
Types.put("AnnotatorInputTable", AnnotatorROD.class);
|
Types.put("AnnotatorInputTable", AnnotatorROD.class);
|
||||||
Types.put("CleanedOutSNP", CleanedOutSNPROD.class);
|
|
||||||
Types.put("SimpleIndel", SimpleIndelROD.class);
|
|
||||||
Types.put("PointIndel", PointIndelROD.class);
|
|
||||||
Types.put("HapMap", HapMapROD.class);
|
Types.put("HapMap", HapMapROD.class);
|
||||||
Types.put("Intervals", IntervalRod.class);
|
Types.put("Intervals", IntervalRod.class);
|
||||||
Types.put("GLF", RodGLF.class);
|
Types.put("GLF", RodGLF.class);
|
||||||
|
|
|
||||||
|
|
@ -22,7 +22,7 @@ import java.util.Set;
|
||||||
public class GenotypeWriterFactory {
|
public class GenotypeWriterFactory {
|
||||||
/** available genotype writers */
|
/** available genotype writers */
|
||||||
public enum GENOTYPE_FORMAT {
|
public enum GENOTYPE_FORMAT {
|
||||||
GELI, GLF, GFF, TABULAR, GELI_BINARY, VCF
|
GELI, GLF, GELI_BINARY, VCF
|
||||||
}
|
}
|
||||||
|
|
||||||
/**
|
/**
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue