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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Ryan Poplin 2012-01-18 09:53:00 -05:00
parent 60024e0d7b ca11f68303
commit 0268da7560
4 changed files with 103 additions and 6 deletions
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16
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
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@ -18,6 +18,7 @@ import java.util.zip.GZIPInputStream;
public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
public final static int MAX_ALLELE_SIZE_BEFORE_WARNING = (int)Math.pow(2, 20);
protected final static Logger log = Logger.getLogger(VCFCodec.class);
protected final static int NUM_STANDARD_FIELDS = 8; // INFO is the 8th column
@ -252,7 +253,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
// if we have don't have a header, or we have a header with no genotyping data check that we have eight columns. Otherwise check that we have nine (normal colummns + genotyping data)
if (( (header == null || !header.hasGenotypingData()) && nParts != NUM_STANDARD_FIELDS) ||
(header != null && header.hasGenotypingData() && nParts != (NUM_STANDARD_FIELDS + 1)) )
(header != null && header.hasGenotypingData() && nParts != (NUM_STANDARD_FIELDS + 1)) )
throw new UserException.MalformedVCF("there aren't enough columns for line " + line + " (we expected " + (header == null ? NUM_STANDARD_FIELDS : NUM_STANDARD_FIELDS + 1) +
" tokens, and saw " + nParts + " )", lineNo);
@ -518,8 +519,11 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
* @param lineNo the line number for this record
*/
private static void checkAllele(String allele, boolean isRef, int lineNo) {
if ( allele == null || allele.length() == 0 )
generateException("Empty alleles are not permitted in VCF records", lineNo);
if ( allele == null || allele.length() == 0 )
generateException("Empty alleles are not permitted in VCF records", lineNo);
if ( MAX_ALLELE_SIZE_BEFORE_WARNING != -1 && allele.length() > MAX_ALLELE_SIZE_BEFORE_WARNING )
log.warn(String.format("Allele detected with length %d exceeding max size %d at approximately line %d, likely resulting in degraded VCF processing performance", allele.length(), MAX_ALLELE_SIZE_BEFORE_WARNING, lineNo));
if ( isSymbolicAllele(allele) ) {
if ( isRef ) {
@ -572,12 +576,13 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
public static int computeForwardClipping(List<Allele> unclippedAlleles, String ref) {
boolean clipping = true;
final byte ref0 = (byte)ref.charAt(0);
for ( Allele a : unclippedAlleles ) {
if ( a.isSymbolic() )
continue;
if ( a.length() < 1 || (a.getBases()[0] != ref.getBytes()[0]) ) {
if ( a.length() < 1 || (a.getBases()[0] != ref0) ) {
clipping = false;
break;
}
@ -604,7 +609,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
stillClipping = false;
else if ( ref.length() == clipping )
generateException("bad alleles encountered", lineNo);
else if ( a.getBases()[a.length()-clipping-1] != ref.getBytes()[ref.length()-clipping-1] )
else if ( a.getBases()[a.length()-clipping-1] != ((byte)ref.charAt(ref.length()-clipping-1)) )
stillClipping = false;
}
if ( stillClipping )
@ -613,6 +618,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
return clipping;
}
/**
* clip the alleles, based on the reference
*

91
public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFCodecUnitTest.java 100644
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@ -0,0 +1,91 @@
/*
* Copyright (c) 2012, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
// our package
package org.broadinstitute.sting.utils.codecs.vcf;
// the imports for unit testing.
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.testng.Assert;
import org.testng.annotations.BeforeSuite;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.util.*;
public class VCFCodecUnitTest extends BaseTest {
// --------------------------------------------------------------------------------
//
// Provider
//
// --------------------------------------------------------------------------------
private class AlleleClippingTestProvider extends TestDataProvider {
final String ref;
final List<Allele> alleles = new ArrayList<Allele>();
final int expectedClip;
private AlleleClippingTestProvider(final int expectedClip, final String ref, final String ... alleles) {
super(AlleleClippingTestProvider.class);
this.ref = ref;
for ( final String allele : alleles )
this.alleles.add(Allele.create(allele));
this.expectedClip = expectedClip;
}
@Override
public String toString() {
return String.format("ref=%s allele=%s reverse clip %d", ref, alleles, expectedClip);
}
}
@DataProvider(name = "AlleleClippingTestProvider")
public Object[][] MakeAlleleClippingTest() {
// pair clipping
new AlleleClippingTestProvider(0, "ATT", "CCG");
new AlleleClippingTestProvider(1, "ATT", "CCT");
new AlleleClippingTestProvider(2, "ATT", "CTT");
new AlleleClippingTestProvider(2, "ATT", "ATT"); // cannot completely clip allele
// triplets
new AlleleClippingTestProvider(0, "ATT", "CTT", "CGG");
new AlleleClippingTestProvider(1, "ATT", "CTT", "CGT"); // the T can go
new AlleleClippingTestProvider(2, "ATT", "CTT", "CTT"); // both Ts can go
return AlleleClippingTestProvider.getTests(AlleleClippingTestProvider.class);
}
@Test(dataProvider = "AlleleClippingTestProvider")
public void TestAlleleClipping(AlleleClippingTestProvider cfg) {
int result = AbstractVCFCodec.computeReverseClipping(cfg.alleles, cfg.ref, 0, 1);
Assert.assertEquals(result, cfg.expectedClip);
}
}

BIN
settings/repository/org.broad/tribble-46.jar → settings/repository/org.broad/tribble-53.jar
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2
settings/repository/org.broad/tribble-46.xml → settings/repository/org.broad/tribble-53.xml
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@ -1,3 +1,3 @@
<ivy-module version="1.0">
<info organisation="org.broad" module="tribble" revision="46" status="integration" />
<info organisation="org.broad" module="tribble" revision="53" status="integration" />
</ivy-module>