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Added some generic read tag/expression fliters for use on numeric tags (
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95 changes: 95 additions & 0 deletions
95
...n/java/org/broadinstitute/hellbender/engine/filters/JexlExpressionReadTagValueFilter.java
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package org.broadinstitute.hellbender.engine.filters; | ||
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import htsjdk.samtools.util.Lazy; | ||
import htsjdk.variant.variantcontext.VariantContextUtils; | ||
import org.apache.commons.jexl2.Expression; | ||
import org.apache.commons.jexl2.JexlContext; | ||
import org.apache.logging.log4j.LogManager; | ||
import org.apache.logging.log4j.Logger; | ||
import org.broadinstitute.barclay.argparser.Argument; | ||
import org.broadinstitute.barclay.help.DocumentedFeature; | ||
import org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions; | ||
import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine; | ||
import org.broadinstitute.hellbender.utils.help.HelpConstants; | ||
import org.broadinstitute.hellbender.utils.read.GATKRead; | ||
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import java.util.ArrayList; | ||
import java.util.Collections; | ||
import java.util.LinkedList; | ||
import java.util.List; | ||
import java.util.function.BiFunction; | ||
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/** | ||
* Keep only reads that the attributes of meet a given set of jexl expressions | ||
*/ | ||
@DocumentedFeature(groupName = HelpConstants.DOC_CAT_READFILTERS, groupSummary = HelpConstants.DOC_CAT_READFILTERS_SUMMARY, | ||
summary = "Keep only reads that meet all given jexl expressions (on their attributes)") | ||
public final class JexlExpressionReadTagValueFilter extends ReadFilter { | ||
private static final long serialVersionUID = 1L; | ||
private static final Logger logger = LogManager.getLogger(JexlExpressionReadTagValueFilter.class); | ||
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@Argument(fullName=ReadFilterArgumentDefinitions.READ_FILTER_EXPRESSION_LONG_NAME, doc="One or more JEXL expressions used to filter", optional=false) | ||
public List<String> filterExpressions = new ArrayList<>(); | ||
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private Lazy<List<Expression>> jexlExprs = new Lazy<>(() -> { | ||
List<Expression> l = new LinkedList<>(); | ||
for ( String expr : filterExpressions ) { | ||
final Expression jexl = VariantContextUtils.engine.get().createExpression(expr); | ||
logger.info("created jexl: " + jexl); | ||
l.add(jexl); | ||
} | ||
return l; | ||
}); | ||
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private static class GATKReadJexlContext implements JexlContext { | ||
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final private GATKRead read; | ||
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GATKReadJexlContext(final GATKRead read) { | ||
this.read = read; | ||
} | ||
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@Override | ||
public Object get(final String name) { | ||
return read.getAttributeAsString(name); | ||
} | ||
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@Override | ||
public void set(final String name, final Object value) { | ||
throw new IllegalArgumentException("setting attributes is not allowed"); | ||
} | ||
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@Override | ||
public boolean has(final String name) { | ||
return read.hasAttribute(name); | ||
} | ||
} | ||
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public JexlExpressionReadTagValueFilter() { | ||
} | ||
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// convenience constructor for using a single jexl expression | ||
public JexlExpressionReadTagValueFilter(final String jexlExpr) { | ||
this.filterExpressions = Collections.singletonList(jexlExpr); | ||
} | ||
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// convenience constructor for using a multiple jexl expressions | ||
public JexlExpressionReadTagValueFilter(final List<String> jexlExprs) { | ||
this.filterExpressions = jexlExprs; | ||
} | ||
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@Override | ||
public boolean test(final GATKRead read) { | ||
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// loop over expressions. At this point expressions are ANDed | ||
for ( Expression expr : jexlExprs.get() ) { | ||
Object v = expr.evaluate(new GATKReadJexlContext(read)); | ||
if (!v.equals(Boolean.TRUE)) { | ||
return false; | ||
} | ||
} | ||
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// if here, all expressions matched | ||
return true; | ||
} | ||
} |
78 changes: 78 additions & 0 deletions
78
src/main/java/org/broadinstitute/hellbender/engine/filters/ReadTagValueFilter.java
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package org.broadinstitute.hellbender.engine.filters; | ||
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import htsjdk.samtools.util.Lazy; | ||
import htsjdk.variant.variantcontext.VariantContextUtils; | ||
import org.apache.commons.jexl2.JexlContext; | ||
import org.apache.commons.jexl2.JexlEngine; | ||
import org.broadinstitute.barclay.argparser.Argument; | ||
import org.broadinstitute.barclay.help.DocumentedFeature; | ||
import org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions; | ||
import org.broadinstitute.hellbender.utils.help.HelpConstants; | ||
import org.broadinstitute.hellbender.utils.read.GATKRead; | ||
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import org.apache.commons.jexl2.Expression; | ||
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import java.util.ArrayList; | ||
import java.util.Collections; | ||
import java.util.LinkedList; | ||
import java.util.List; | ||
import java.util.function.BiFunction; | ||
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/** | ||
* Keep only reads that contain a tag with a value that agrees with parameters as specified. | ||
* | ||
*/ | ||
@DocumentedFeature(groupName = HelpConstants.DOC_CAT_READFILTERS, groupSummary = HelpConstants.DOC_CAT_READFILTERS_SUMMARY, | ||
summary = "Keep only reads that contains a tag with value that agrees with parameters") | ||
public final class ReadTagValueFilter extends ReadFilter { | ||
private static final long serialVersionUID = 1L; | ||
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@Argument(fullName = ReadFilterArgumentDefinitions.READ_FILTER_TAG, | ||
doc = "Look for this tag in read", optional=false) | ||
public String readFilterTagName = null; | ||
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@Argument(fullName = ReadFilterArgumentDefinitions.READ_FILTER_TAG_COMP, | ||
doc = "Compare value in tag to this value", optional=true) | ||
public Float readFilterTagComp = 0F; | ||
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public enum Operator { | ||
LESS((Float x, Float y) -> x < y), | ||
LESS_OR_EQUAL((Float x, Float y) -> x <= y), | ||
GREATER((Float x, Float y) -> x > y), | ||
GREATER_OR_EQUAL((Float x, Float y) -> x >= y), | ||
EQUAL(Float::equals), | ||
NOT_EQUAL((Float x, Float y) -> !x.equals(y)); | ||
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final BiFunction<Float, Float, Boolean> comp; | ||
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Operator(BiFunction<Float, Float, Boolean> comp) { | ||
this.comp = comp; | ||
} | ||
} | ||
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@Argument(fullName = ReadFilterArgumentDefinitions.READ_FILTER_TAG_OP, | ||
doc = "Compare value in tag to value with this operator. " + | ||
"If T is the value in the tag, OP is the operation provided, " + | ||
"and V is the value in read-filter-tag, then the " + | ||
"read will pass the filter iff T OP V is true.", optional = true) | ||
public Operator readFilterTagOp = Operator.EQUAL; | ||
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public ReadTagValueFilter() { | ||
} | ||
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// convenience constructor for using <tag operator value> form | ||
public ReadTagValueFilter(final String tagName, final float tagValue, final Operator operator) { | ||
this.readFilterTagName = tagName; | ||
this.readFilterTagComp = tagValue; | ||
this.readFilterTagOp = operator; | ||
} | ||
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@Override | ||
public boolean test(final GATKRead read) { | ||
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return read.hasAttribute(this.readFilterTagName) && | ||
this.readFilterTagComp != null && | ||
this.readFilterTagOp.comp.apply(read.getAttributeAsFloat(this.readFilterTagName), | ||
this.readFilterTagComp); | ||
} | ||
} |
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89 changes: 89 additions & 0 deletions
89
...rg/broadinstitute/hellbender/engine/filters/JexlExpressionReadTagValueFilterUnitTest.java
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package org.broadinstitute.hellbender.engine.filters; | ||
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import org.broadinstitute.hellbender.GATKBaseTest; | ||
import org.broadinstitute.hellbender.utils.read.GATKRead; | ||
import org.testng.Assert; | ||
import org.testng.annotations.DataProvider; | ||
import org.testng.annotations.Test; | ||
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import java.util.Arrays; | ||
import java.util.Iterator; | ||
import java.util.LinkedList; | ||
import java.util.List; | ||
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public class JexlExpressionReadTagValueFilterUnitTest extends GATKBaseTest { | ||
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@Test(dataProvider= "JexlExpressionReadTagValueFilterDataProvider") | ||
public void testJexlExpressionReadTagValueFilter(final String cigarString, | ||
final Object[] attrsNameAndValue, | ||
final String[] jexlExpr, | ||
final boolean expectedResult, | ||
final Class<? extends Throwable> expectedException) { | ||
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final JexlExpressionReadTagValueFilter filter; | ||
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// test different constructors here as well | ||
if ( jexlExpr.length == 1 ) { | ||
filter = new JexlExpressionReadTagValueFilter(jexlExpr[0]); | ||
} else { | ||
filter = new JexlExpressionReadTagValueFilter(Arrays.asList(jexlExpr)); | ||
} | ||
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final GATKRead read = ReadTagValueFilterUnitTest.buildSAMRead(cigarString, attrsNameAndValue); | ||
try { | ||
Assert.assertEquals(filter.test(read), expectedResult, cigarString); | ||
Assert.assertNull(expectedException); | ||
} catch (Throwable e) { | ||
if ( expectedException == null || !expectedException.isInstance(e) ) | ||
throw e; | ||
} | ||
} | ||
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@DataProvider(name = "JexlExpressionReadTagValueFilterDataProvider") | ||
public Iterator<Object[]> jexlExpressionReadTagValueFilterDataProvider() { | ||
final List<Object[]> result = new LinkedList<>(); | ||
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result.add(new Object[] { | ||
"100M", // cigar | ||
new Object[] {"TM", 1.0f}, // attributes | ||
new String[] {"TM == 1.0"}, // jexl expressions | ||
Boolean.TRUE, // expected | ||
null // expected exception | ||
}); | ||
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result.add(new Object[] { | ||
"100M", // cigar | ||
new Object[] {"TM", 1.0f}, // attributes | ||
new String[] {"TM < 1.0"}, // jexl expressions | ||
Boolean.FALSE, // expected | ||
null // expected exception | ||
}); | ||
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result.add(new Object[] { | ||
"100M", // cigar | ||
new Object[] {"TM", 1.0f}, // attributes | ||
new String[] {"NO_SUCH < 1.0"}, // jexl expressions | ||
Boolean.FALSE, // expected | ||
IllegalArgumentException.class // expected exception | ||
}); | ||
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result.add(new Object[] { | ||
"100M", // cigar | ||
new Object[] {"TM", 1.0f, "TA", 2.0f}, // attributes | ||
new String[] {"TM >= 1.0", "TA <= 2.0"}, // jexl expressions | ||
Boolean.TRUE, // expected | ||
null // expected exception | ||
}); | ||
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result.add(new Object[] { | ||
"100M", // cigar | ||
new Object[] {"TM", 1.0f, "TA", 2.0f}, // attributes | ||
new String[] {"TM >= 1.0", "TA < 2.0"}, // jexl expressions | ||
Boolean.FALSE, // expected | ||
null // expected exception | ||
}); | ||
return result.iterator(); | ||
} | ||
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} |
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