Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Added some generic read tag/expression fliters for use on numeric tags #7746

Merged
merged 3 commits into from
May 10, 2022
Merged
Show file tree
Hide file tree
Changes from 2 commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Original file line number Diff line number Diff line change
Expand Up @@ -56,5 +56,11 @@ private ReadFilterArgumentDefinitions(){}

public static final String INVERT_SOFT_CLIP_RATIO_FILTER = "invert-soft-clip-ratio-filter";

public static final String READ_FILTER_TAG = "read-filter-tag";
public static final String READ_FILTER_TAG_COMP = "read-filter-tag-comp";
public static final String READ_FILTER_TAG_OP = "read-filter-tag-op";
public static final String READ_FILTER_EXPRESSION_LONG_NAME = "read-filter-expression";


public static final String MATE_TOO_DISTANT_LENGTH = "mate-too-distant-length";
}
Original file line number Diff line number Diff line change
@@ -0,0 +1,95 @@
package org.broadinstitute.hellbender.engine.filters;

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;

import java.util.ArrayList;
import java.util.Collections;
import java.util.LinkedList;
import java.util.List;
import java.util.function.BiFunction;

/**
* 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);

@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<>();

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;
});

private static class GATKReadJexlContext implements JexlContext {

final private GATKRead read;

GATKReadJexlContext(final GATKRead read) {
this.read = read;
}

@Override
public Object get(final String name) {
return read.getAttributeAsString(name);
}

@Override
public void set(final String name, final Object value) {
throw new IllegalArgumentException("setting attributes is not allowed");
}

@Override
public boolean has(final String name) {
return read.hasAttribute(name);
}
}

public JexlExpressionReadTagValueFilter() {
}

// convenience constructor for using a single jexl expression
public JexlExpressionReadTagValueFilter(final String jexlExpr) {
this.filterExpressions = Collections.singletonList(jexlExpr);
}

// convenience constructor for using a multiple jexl expressions
public JexlExpressionReadTagValueFilter(final List<String> jexlExprs) {
this.filterExpressions = jexlExprs;
}

@Override
public boolean test(final GATKRead read) {

// 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;
}
}

// if here, all expressions matched
return true;
}
}
Original file line number Diff line number Diff line change
@@ -0,0 +1,78 @@
package org.broadinstitute.hellbender.engine.filters;

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;

import org.apache.commons.jexl2.Expression;

import java.util.ArrayList;
import java.util.Collections;
import java.util.LinkedList;
import java.util.List;
import java.util.function.BiFunction;

/**
* 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;

@Argument(fullName = ReadFilterArgumentDefinitions.READ_FILTER_TAG,
doc = "Look for this tag in read", optional=false)
public String readFilterTagName = null;

@Argument(fullName = ReadFilterArgumentDefinitions.READ_FILTER_TAG_COMP,
doc = "Compare value in tag to this value", optional=true)
public Float readFilterTagComp = 0F;

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));

final BiFunction<Float, Float, Boolean> comp;

Operator(BiFunction<Float, Float, Boolean> comp) {
this.comp = comp;
}
}

@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;

public ReadTagValueFilter() {
}

// 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;
}

@Override
public boolean test(final GATKRead read) {

return read.hasAttribute(this.readFilterTagName) &&
this.readFilterTagComp != null &&
this.readFilterTagOp.comp.apply(read.getAttributeAsFloat(this.readFilterTagName),
this.readFilterTagComp);
}
}
Original file line number Diff line number Diff line change
Expand Up @@ -762,6 +762,16 @@ default Optional<SamPairUtil.PairOrientation> getPairOrientation() {
*/
Integer getAttributeAsInteger( final String attributeName );

/**
* Retrieve the value of a particular attribute typed as an floatingpoint value.
*
* @param attributeName name of the attribute to retrieve
* @return integer value of the requested attribute, or {@code null} if the attribute is not present
jamesemery marked this conversation as resolved.
Show resolved Hide resolved
* @throws GATKException.ReadAttributeTypeMismatch if the attribute
* value cannot be typed as a float
*/
Float getAttributeAsFloat( final String attributeName );

/**
* Retrieve the value of a particular attribute typed as a String.
*
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -630,6 +630,27 @@ else if ( attributeValue instanceof Integer ) {
}
}

@Override
public Float getAttributeAsFloat( final String attributeName ) {
ReadUtils.assertAttributeNameIsLegal(attributeName);
final Object attributeValue = samRecord.getAttribute(attributeName);

if ( attributeValue == null ) {
return null;
}
else if ( attributeValue instanceof Float ) {
return (Float)attributeValue;
}
else {
try {
return Float.parseFloat(attributeValue.toString());
}
catch ( NumberFormatException e ) {
throw new GATKException.ReadAttributeTypeMismatch(attributeName, "integer", e);
}
}
}

@Override
public String getAttributeAsString( final String attributeName ) {
ReadUtils.assertAttributeNameIsLegal(attributeName);
Expand Down
Original file line number Diff line number Diff line change
@@ -0,0 +1,89 @@
package org.broadinstitute.hellbender.engine.filters;

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;

import java.util.Arrays;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;

public class JexlExpressionReadTagValueFilterUnitTest extends GATKBaseTest {

@Test(dataProvider= "JexlExpressionReadTagValueFilterDataProvider")
public void testJexlExpressionReadTagValueFilter(final String cigarString,
final Object[] attrsNameAndValue,
final String[] jexlExpr,
final boolean expectedResult,
final Class<? extends Throwable> expectedException) {

final JexlExpressionReadTagValueFilter filter;

// test different constructors here as well
if ( jexlExpr.length == 1 ) {
filter = new JexlExpressionReadTagValueFilter(jexlExpr[0]);
} else {
filter = new JexlExpressionReadTagValueFilter(Arrays.asList(jexlExpr));
}

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;
}
}

@DataProvider(name = "JexlExpressionReadTagValueFilterDataProvider")
public Iterator<Object[]> jexlExpressionReadTagValueFilterDataProvider() {
final List<Object[]> result = new LinkedList<>();

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
});

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
});

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
});

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
});

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();
}


}
Loading