VariantFiltration can now filter specific samples.
This is *NOT* an ideal implementation. One day when we have lots of free time (or a greater desire), we will implement this correctly and sophisticatedly using all the power of JEXL. For now, though, this will have to do. Docs coming tonight. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3060 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
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parent
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0097106938
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@ -496,7 +496,7 @@ public class VariantContext {
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return ref;
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}
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/** Private helper routine that grabs the reference allele but doesn't through an error if there's no such allele */
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/** Private helper routine that grabs the reference allele but doesn't throw an error if there's no such allele */
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private Allele getReferenceWithoutError() {
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for ( Allele allele : getAlleles() )
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if ( allele.isReference() )
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@ -123,6 +123,31 @@ public class VariantContextUtils {
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}
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/**
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* Returns true if exp match VC. See collection<> version for full docs.
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* @param g genotype
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* @param exp expression
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* @return true if there is a match
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*/
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public static boolean match(Genotype g, JexlVCMatchExp exp) {
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return match(g,Arrays.asList(exp)).get(exp);
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}
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/**
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* Matches each JexlVCMatchExp exp against the data contained in vc, and returns a map from these
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* expressions to true (if they matched) or false (if they didn't). This the best way to apply JEXL
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* expressions to VariantContext records. Use initializeMatchExps() to create the list of JexlVCMatchExp
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* expressions.
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*
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* @param g genotype
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* @param exps expressions
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* @return true if there is a match
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*/
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public static Map<JexlVCMatchExp, Boolean> match(Genotype g, Collection<JexlVCMatchExp> exps) {
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return new VariantJEXLContext(exps,g).getVars();
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}
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private static void addAttributesToMap(Map<String, String> infoMap, Map<String, ?> attributes, String prefix ) {
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for (Map.Entry<String, ?> e : attributes.entrySet()) {
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infoMap.put(prefix + String.valueOf(e.getKey()), String.valueOf(e.getValue()));
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@ -50,12 +50,14 @@ class VariantJEXLContext implements JexlContext {
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map = new JEXLMap(jexl, vc);
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}
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@Override
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public VariantJEXLContext(Collection<VariantContextUtils.JexlVCMatchExp> jexl, Genotype g) {
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map = new JEXLMap(jexl, g);
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}
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public void setVars(Map map) {
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throw new UnsupportedOperationException("this operation is unsupported");
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}
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@Override
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public Map getVars() {
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return map;
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}
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@ -72,18 +74,32 @@ class VariantJEXLContext implements JexlContext {
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*/
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class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
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// our variant context
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// our variant context and/or Genotype
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private final VariantContext vc;
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private final Genotype g;
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// our context
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private JexlContext jContext = null;
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// our mapping from JEXLVCMatchExp to Booleans, which will be set to NULL for previously uncached JexlVCMatchExp
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private final Map<VariantContextUtils.JexlVCMatchExp,Boolean> jexl;
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private Map<VariantContextUtils.JexlVCMatchExp,Boolean> jexl;
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public JEXLMap(Collection<VariantContextUtils.JexlVCMatchExp> jexlCollection, VariantContext vc, Genotype g) {
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this.vc = vc;
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this.g = g;
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initialize(jexlCollection);
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}
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public JEXLMap(Collection<VariantContextUtils.JexlVCMatchExp> jexlCollection, VariantContext vc) {
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this.vc = vc;
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this(jexlCollection, vc, null);
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}
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public JEXLMap(Collection<VariantContextUtils.JexlVCMatchExp> jexlCollection, Genotype g) {
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this(jexlCollection, null, g);
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}
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private void initialize(Collection<VariantContextUtils.JexlVCMatchExp> jexlCollection) {
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jexl = new HashMap<VariantContextUtils.JexlVCMatchExp,Boolean>();
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for (VariantContextUtils.JexlVCMatchExp exp: jexlCollection) {
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jexl.put(exp, null);
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@ -94,38 +110,49 @@ class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
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* create the internal JexlContext, only when required. This code is where new JEXL context variables
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* should get added.
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*
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* @param vc the VariantContext
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*
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*/
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private void createContext(VariantContext vc) {
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// create a mapping of what we know about the variant context, its Chromosome, positions, etc.
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private void createContext() {
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Map<String, String> infoMap = new HashMap<String, String>();
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infoMap.put("CHROM", vc.getLocation().getContig());
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infoMap.put("POS", String.valueOf(vc.getLocation().getStart()));
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infoMap.put("TYPE", vc.getType().toString());
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infoMap.put("QUAL", String.valueOf(10 * vc.getNegLog10PError()));
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// add alleles
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infoMap.put("ALLELES", Utils.join(";", vc.getAlleles()));
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infoMap.put("N_ALLELES", String.valueOf(vc.getNAlleles()));
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if ( vc != null ) {
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// create a mapping of what we know about the variant context, its Chromosome, positions, etc.
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infoMap.put("CHROM", vc.getLocation().getContig());
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infoMap.put("POS", String.valueOf(vc.getLocation().getStart()));
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infoMap.put("TYPE", vc.getType().toString());
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infoMap.put("QUAL", String.valueOf(10 * vc.getNegLog10PError()));
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// add attributes
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addAttributesToMap(infoMap, vc.getAttributes());
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// add alleles
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infoMap.put("ALLELES", Utils.join(";", vc.getAlleles()));
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infoMap.put("N_ALLELES", String.valueOf(vc.getNAlleles()));
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// add filter fields
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infoMap.put("FILTER", String.valueOf(vc.isFiltered() ? "1" : "0"));
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for ( Object filterCode : vc.getFilters() ) {
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infoMap.put(String.valueOf(filterCode), "1");
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// add attributes
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addAttributesToMap(infoMap, vc.getAttributes());
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// add filter fields
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infoMap.put("FILTER", vc.isFiltered() ? "1" : "0");
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for ( Object filterCode : vc.getFilters() ) {
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infoMap.put(String.valueOf(filterCode), "1");
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}
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// add genotype-specific fields
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// TODO -- implement me when we figure out a good way to represent this
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// for ( Genotype g : vc.getGenotypes().values() ) {
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// String prefix = g.getSampleName() + ".";
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// addAttributesToMap(infoMap, g.getAttributes(), prefix);
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// infoMap.put(prefix + "GT", g.getGenotypeString());
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// }
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}
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// add specific genotype if one is provided
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if ( g != null ) {
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infoMap.put("GT", g.getGenotypeString());
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infoMap.put("isHomRef", g.isHomRef() ? "1" : "0");
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infoMap.put("isHet", g.isHet() ? "1" : "0");
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infoMap.put("isHomVar", g.isHomVar() ? "1" : "0");
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for ( Map.Entry<String, Object> e : g.getAttributes().entrySet() )
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infoMap.put(e.getKey(), String.valueOf(e.getValue()));
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}
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// add genotypes
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// todo -- comment this back in when we figure out how to represent it nicely
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// for ( Genotype g : vc.getGenotypes().values() ) {
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// String prefix = g.getSampleName() + ".";
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// addAttributesToMap(infoMap, g.getAttributes(), prefix);
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// infoMap.put(prefix + "GT", g.getGenotypeString());
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// }
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// create the internal context that we can evaluate expressions against
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jContext = JexlHelper.createContext();
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@ -135,7 +162,6 @@ class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
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/**
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* @return the size of the internal data structure
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*/
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@Override
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public int size() {
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return jexl.size();
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}
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@ -143,7 +169,6 @@ class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
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/**
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* @return true if we're empty
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*/
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@Override
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public boolean isEmpty() { return this.jexl.isEmpty(); }
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/**
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@ -151,10 +176,8 @@ class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
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* @param o the key
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* @return true if we have a value for that key
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*/
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@Override
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public boolean containsKey(Object o) { return jexl.containsKey(o); }
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@Override
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public Boolean get(Object o) {
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// if we've already determined the value, return it
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if (jexl.containsKey(o) && jexl.get(o) != null) return jexl.get(o);
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@ -169,7 +192,6 @@ class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
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* get the keyset of map
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* @return a set of keys of type JexlVCMatchExp
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*/
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@Override
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public Set<VariantContextUtils.JexlVCMatchExp> keySet() {
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return jexl.keySet();
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}
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@ -180,7 +202,6 @@ class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
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* the keys you want, you would be better off using get() to get them by name.
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* @return a collection of boolean values, representing the results of all the variants evaluated
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*/
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@Override
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public Collection<Boolean> values() {
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// this is an expensive call
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for (VariantContextUtils.JexlVCMatchExp exp : jexl.keySet())
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@ -195,7 +216,7 @@ class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
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*/
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private void evaulateExpression(VariantContextUtils.JexlVCMatchExp exp) {
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// if the context is null, we need to create it to evaluate the JEXL expression
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if (this.jContext == null) createContext(vc);
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if (this.jContext == null) createContext();
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try {
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jexl.put (exp, (Boolean) exp.exp.evaluate(jContext));
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} catch (Exception e) {
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@ -210,16 +231,14 @@ class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
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*/
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private static void addAttributesToMap(Map<String, String> infoMap, Map<String, ?> attributes ) {
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for (Map.Entry<String, ?> e : attributes.entrySet()) {
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infoMap.put(String.valueOf(e.getKey()), String.valueOf(e.getValue()));
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infoMap.put(e.getKey(), String.valueOf(e.getValue()));
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}
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}
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@Override
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public Boolean put(VariantContextUtils.JexlVCMatchExp jexlVCMatchExp, Boolean aBoolean) {
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return jexl.put(jexlVCMatchExp,aBoolean);
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}
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@Override
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public void putAll(Map<? extends VariantContextUtils.JexlVCMatchExp, ? extends Boolean> map) {
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jexl.putAll(map);
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}
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@ -230,25 +249,21 @@ class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
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// this doesn't make much sense to implement, boolean doesn't offer too much variety to deal
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// with evaluating every key in the internal map.
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@Override
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public boolean containsValue(Object o) {
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throw new UnsupportedOperationException("containsValue() not supported on a JEXLMap");
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}
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// this doesn't make much sense
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@Override
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public Boolean remove(Object o) {
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throw new UnsupportedOperationException("remove() not supported on a JEXLMap");
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}
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@Override
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public Set<Entry<VariantContextUtils.JexlVCMatchExp, Boolean>> entrySet() {
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throw new UnsupportedOperationException("clear() not supported on a JEXLMap");
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}
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// nope
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@Override
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public void clear() {
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throw new UnsupportedOperationException("clear() not supported on a JEXLMap");
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}
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@ -217,10 +217,10 @@ public class VariantContextAdaptors {
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}
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public static VCFRecord toVCF(VariantContext vc, char vcfRefBase) {
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return toVCF(vc, vcfRefBase, null, true);
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return toVCF(vc, vcfRefBase, null, true, false);
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}
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public static VCFRecord toVCF(VariantContext vc, char vcfRefBase, List<String> allowedGenotypeAttributeKeys, boolean filtersWereAppliedToContext) {
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public static VCFRecord toVCF(VariantContext vc, char vcfRefBase, List<String> allowedGenotypeAttributeKeys, boolean filtersWereAppliedToContext, boolean filtersWereAppliedToGenotypes) {
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// deal with the reference
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String referenceBases = new String(vc.getReference().getBases());
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@ -284,6 +284,8 @@ public class VariantContextAdaptors {
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if ( allowedGenotypeAttributeKeys == null || allowedGenotypeAttributeKeys.contains(key) )
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vcfGenotypeAttributeKeys.add(key);
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}
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if ( filtersWereAppliedToGenotypes )
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vcfGenotypeAttributeKeys.add(VCFGenotypeRecord.GENOTYPE_FILTER_KEY);
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}
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String genotypeFormatString = Utils.join(VCFRecord.GENOTYPE_FIELD_SEPERATOR, vcfGenotypeAttributeKeys);
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@ -313,6 +315,8 @@ public class VariantContextAdaptors {
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ReadBackedPileup pileup = (ReadBackedPileup)g.getAttribute(CalledGenotype.READBACKEDPILEUP_ATTRIBUTE_KEY);
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if ( pileup != null )
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val = pileup.size();
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} else if ( key.equals(VCFGenotypeRecord.GENOTYPE_FILTER_KEY) ) {
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val = g.isFiltered() ? Utils.join(";", Utils.sorted(g.getFilters())) : VCFRecord.PASSES_FILTERS;
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}
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String outputValue = formatVCFField(key, val);
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@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.filters;
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import org.broadinstitute.sting.gatk.contexts.*;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
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import org.broadinstitute.sting.gatk.refdata.*;
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import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
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import org.broadinstitute.sting.gatk.walkers.*;
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@ -25,16 +26,22 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
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@Argument(fullName="filterName", shortName="filterName", doc="Names to use for the list of filters (must be a 1-to-1 mapping); this name is put in the FILTER field for variants that get filtered", required=false)
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protected String[] FILTER_NAMES = new String[]{};
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@Argument(fullName="clusterSize", shortName="cluster", doc="The number of SNPs which make up a cluster (see also --clusterWindowSize)", required=false)
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@Argument(fullName="genotypeFilterExpression", shortName="G_filter", doc="One or more expression used with FORMAT (sample/genotype-level) fields to filter (see wiki docs for more info)", required=false)
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protected String[] GENOTYPE_FILTER_EXPS = new String[]{};
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@Argument(fullName="genotypeFilterName", shortName="G_filterName", doc="Names to use for the list of sample/genotype filters (must be a 1-to-1 mapping); this name is put in the FILTER field for variants that get filtered", required=false)
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protected String[] GENOTYPE_FILTER_NAMES = new String[]{};
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@Argument(fullName="clusterSize", shortName="cluster", doc="The number of SNPs which make up a cluster (see also --clusterWindowSize); [default:3]", required=false)
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protected Integer clusterSize = 3;
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@Argument(fullName="clusterWindowSize", shortName="window", doc="The window size (in bases) in which to evaluate clustered SNPs (to disable the clustered SNP filter, set this value to less than 1)", required=false)
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@Argument(fullName="clusterWindowSize", shortName="window", doc="The window size (in bases) in which to evaluate clustered SNPs (to disable the clustered SNP filter, set this value to less than 1); [default:0]", required=false)
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protected Integer clusterWindow = 0;
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@Argument(fullName="maskName", shortName="mask", doc="The text to put in the FILTER field if a 'mask' rod is provided and overlaps with a variant call", required=false)
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@Argument(fullName="maskName", shortName="mask", doc="The text to put in the FILTER field if a 'mask' rod is provided and overlaps with a variant call; [default:'Mask']", required=false)
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protected String MASK_NAME = "Mask";
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// JEXL expressions for the filters
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List<VariantContextUtils.JexlVCMatchExp> filterExps;
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List<VariantContextUtils.JexlVCMatchExp> genotypeFilterExps;
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public static final String CLUSTERED_SNP_FILTER_NAME = "SnpCluster";
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@ -70,9 +77,13 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
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if ( clusterWindow > 0 )
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hInfo.add(new VCFFilterHeaderLine(CLUSTERED_SNP_FILTER_NAME, "SNPs found in clusters"));
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for ( VariantContextUtils.JexlVCMatchExp exp : filterExps ) {
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for ( VariantContextUtils.JexlVCMatchExp exp : filterExps )
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hInfo.add(new VCFFilterHeaderLine(exp.name, exp.exp.toString()));
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}
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for ( VariantContextUtils.JexlVCMatchExp exp : genotypeFilterExps )
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hInfo.add(new VCFFilterHeaderLine(exp.name, exp.exp.toString()));
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if ( genotypeFilterExps.size() > 0 )
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hInfo.add(new VCFFormatHeaderLine(VCFGenotypeRecord.GENOTYPE_FILTER_KEY, 1, VCFFormatHeaderLine.FORMAT_TYPE.String, "Genotype-level filter"));
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List<ReferenceOrderedDataSource> dataSources = getToolkit().getRodDataSources();
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for ( ReferenceOrderedDataSource source : dataSources ) {
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@ -91,6 +102,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
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clusteredSNPs = new ClusteredSnps(clusterSize, clusterWindow);
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filterExps = VariantContextUtils.initializeMatchExps(FILTER_NAMES, FILTER_EXPS);
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genotypeFilterExps = VariantContextUtils.initializeMatchExps(GENOTYPE_FILTER_NAMES, GENOTYPE_FILTER_EXPS);
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}
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public Integer reduceInit() { return 0; }
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@ -136,45 +148,53 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
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if ( context == null )
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return;
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StringBuilder filterString = new StringBuilder();
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VariantContext vc = context.getVariantContext();
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// make new Genotypes based on filters
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Map<String, Genotype> genotypes;
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if ( genotypeFilterExps.size() == 0 ) {
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genotypes = vc.getGenotypes();
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} else {
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genotypes = new HashMap<String, Genotype>(vc.getGenotypes().size());
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// for each genotype, check filters then create a new object
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for ( Map.Entry<String, Genotype> genotype : vc.getGenotypes().entrySet() ) {
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Genotype g = genotype.getValue();
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Set<String> filters = new LinkedHashSet<String>(g.getFilters());
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for ( VariantContextUtils.JexlVCMatchExp exp : genotypeFilterExps ) {
|
||||
if ( VariantContextUtils.match(g, exp) )
|
||||
filters.add(exp.name);
|
||||
}
|
||||
|
||||
genotypes.put(genotype.getKey(), new Genotype(genotype.getKey(), g.getAlleles(), g.getNegLog10PError(), filters, g.getAttributes(), g.genotypesArePhased()));
|
||||
}
|
||||
}
|
||||
|
||||
// make a new variant context based on filters
|
||||
Set<String> filters = new LinkedHashSet<String>(vc.getFilters());
|
||||
|
||||
// test for SNP mask, if present
|
||||
RODRecordList mask = context.getTracker().getTrackData("mask", null);
|
||||
if ( mask != null && mask.size() > 0 )
|
||||
addFilter(filterString, MASK_NAME);
|
||||
filters.add(MASK_NAME);
|
||||
|
||||
// test for clustered SNPs if requested
|
||||
if ( clusteredSNPs != null && clusteredSNPs.filter(variantContextWindow) )
|
||||
addFilter(filterString, CLUSTERED_SNP_FILTER_NAME);
|
||||
filters.add(CLUSTERED_SNP_FILTER_NAME);
|
||||
|
||||
VariantContext vc = context.getVariantContext();
|
||||
for ( VariantContextUtils.JexlVCMatchExp exp : filterExps ) {
|
||||
if ( VariantContextUtils.match(vc, exp) )
|
||||
addFilter(filterString, exp.name);
|
||||
filters.add(exp.name);
|
||||
}
|
||||
|
||||
writeVCF(VariantContextAdaptors.toVCF(vc, context.getReferenceContext().getBase(), null, true), filterString);
|
||||
VariantContext filteredVC = new VariantContext(vc.getName(), vc.getLocation(), vc.getAlleles(), genotypes, vc.getNegLog10PError(), filters, vc.getAttributes());
|
||||
|
||||
writeVCF(VariantContextAdaptors.toVCF(filteredVC, context.getReferenceContext().getBase(), null, true, genotypeFilterExps.size() > 0));
|
||||
}
|
||||
|
||||
private static void addFilter(StringBuilder sb, String filter) {
|
||||
if ( sb.length() > 0 )
|
||||
sb.append(";");
|
||||
sb.append(filter);
|
||||
}
|
||||
|
||||
private void writeVCF(VCFRecord rec, StringBuilder filterString) {
|
||||
|
||||
if ( filterString.length() != 0 ) {
|
||||
// if the record is already filtered, don't destroy those filters
|
||||
if ( rec.isFiltered() )
|
||||
filterString.append(";" + rec.getFilterString());
|
||||
rec.setFilterString(filterString.toString());
|
||||
}
|
||||
// otherwise, if it's not already filtered, set it to "passing filters"
|
||||
else if ( !rec.isFiltered() ) {
|
||||
rec.setFilterString(VCFRecord.PASSES_FILTERS);
|
||||
}
|
||||
|
||||
private void writeVCF(VCFRecord rec) {
|
||||
if ( writer == null )
|
||||
initializeVcfWriter(rec);
|
||||
writer.addRecord(rec);
|
||||
|
|
|
|||
|
|
@ -28,6 +28,7 @@ public class VCFGenotypeRecord {
|
|||
public static final int MISSING_GENOTYPE_QUALITY = -1;
|
||||
public static final int MISSING_DEPTH = -1;
|
||||
public static final int MISSING_HAPLOTYPE_QUALITY = -1;
|
||||
public static final String PASSES_FILTERS = "0";
|
||||
public static final String UNFILTERED = ".";
|
||||
|
||||
public static final double MAX_QUAL_VALUE = 99.0;
|
||||
|
|
@ -199,7 +200,9 @@ public class VCFGenotypeRecord {
|
|||
}
|
||||
|
||||
public boolean isFiltered() {
|
||||
return ( mFields.get(GENOTYPE_FILTER_KEY) != null && ! mFields.get(GENOTYPE_FILTER_KEY).equals("0"));
|
||||
return ( mFields.get(GENOTYPE_FILTER_KEY) != null &&
|
||||
!mFields.get(GENOTYPE_FILTER_KEY).equals(UNFILTERED) &&
|
||||
!mFields.get(GENOTYPE_FILTER_KEY).equals(PASSES_FILTERS));
|
||||
}
|
||||
|
||||
public int getPloidy() {
|
||||
|
|
|
|||
|
|
@ -83,7 +83,7 @@ public class VCFGenotypeWriterAdapter implements VCFGenotypeWriter {
|
|||
if ( mHeader == null )
|
||||
throw new IllegalStateException("The VCF Header must be written before records can be added");
|
||||
|
||||
VCFRecord call = VariantContextAdaptors.toVCF(vc, vc.getReference().toString().charAt(0), allowedGenotypeFormatStrings, false);
|
||||
VCFRecord call = VariantContextAdaptors.toVCF(vc, vc.getReference().toString().charAt(0), allowedGenotypeFormatStrings, false, false);
|
||||
|
||||
Set<Allele> altAlleles = vc.getAlternateAlleles();
|
||||
StringBuffer altAlleleCountString = new StringBuffer();
|
||||
|
|
|
|||
Loading…
Reference in New Issue