zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Vast improvements to AssessNA12878 code and functionality 

-- AssessNA12878 now breaks out multi-allelics into bi-allelic components.  This means that we can properly assess multi-allelic calls against the bi-allelic KB
-- Refactor AssessNA12878, moving into assess package in KB.  Split out previously private classes in the walker itself into separate classes.  Added real docs for all of the classes.
-- Vastly expand (from 0) unit tests for NA12878 assessments
-- Allow sites only VCs to be evaluated by Assessor
-- Move utility for creating simple VCs from a list of string alleles from GATKVariantContextUtilsUnitTest to GATKVariantContextUtils
-- Assessor bugfix for discordant records at a site.  Previous version didn't handle properly the case where one had a non-matching call in the callset w.r.t. the KB, so that the KB element was eaten during the analysis.  Fixed.  UnitTested
-- See GSA-781 -- Handle multi-allelic variants in KB for more information
-- Bugfix for missing site counting in AssessNA12878.  Previous version would count N misses for every missed value at a site.  Not that this has much impact but it's worth fixing
-- UnitTests for BadSitesWriter
-- UnitTests for filtered and filtering sites in the Assessor
-- Cleanup end report generation code (simply the code).  Note that instead of "indel" the new code will print out "INDELS"
-- Assessor DoC calculations now us LIBS and RBPs for the depth calculation.  The previous version was broken for reduced reads.  Added unit test that reads a complex reduced read example and matches the DoC of this BAM with the output of the GATK DoC tool here.
-- Added convenience constructor for LIBS using just SAMFileReader and an iterator.  It's now easy to create a LIBS from a BAM at a locus.  Added advanceToLocus function that moves the LIBS to a specific position.  UnitTested via the assessor (which isn't ideal, but is a proper test)
This commit is contained in:
Mark DePristo 2013-02-19 20:19:49 -05:00
parent 29319bf222
commit 8ac6d3521f
3 changed files with 82 additions and 16 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

52
public/java/src/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByState.java
View File

@ -28,13 +28,18 @@ package org.broadinstitute.sting.utils.locusiterator;
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import net.sf.samtools.CigarOperator;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMRecordIterator;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
import org.broadinstitute.sting.gatk.iterators.GATKSAMIterator;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.pileup.*;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
@ -136,6 +141,25 @@ public final class LocusIteratorByState extends LocusIterator {
readInformation.keepUniqueReadListInLIBS());
}
/**
* Create a new LocusIteratorByState based on a SAMFileReader using reads in an iterator it
*
* Simple constructor that uses the samples in the reader, doesn't do any downsampling,
* and makes a new GenomeLocParser using the reader. This constructor will be slow(ish)
* if you continually invoke this constructor, but it's easy to make.
*
* @param reader a non-null reader
* @param it an iterator from reader that has the reads we want to use to create ReadBackPileups
*/
public LocusIteratorByState(final SAMFileReader reader, final SAMRecordIterator it) {
this(new GATKSAMIterator(it),
new LIBSDownsamplingInfo(false, 0),
true,
new GenomeLocParser(reader.getFileHeader().getSequenceDictionary()),
SampleUtils.getSAMFileSamples(reader.getFileHeader()),
false);
}
/**
* Create a new LocusIteratorByState
*
@ -149,7 +173,8 @@ public final class LocusIteratorByState extends LocusIterator {
* be mapped to this null sample
* @param maintainUniqueReadsList if true, we will keep the unique reads from off the samIterator and make them
* available via the transferReadsFromAllPreviousPileups interface
*/ protected LocusIteratorByState(final Iterator<GATKSAMRecord> samIterator,
*/
protected LocusIteratorByState(final Iterator<GATKSAMRecord> samIterator,
final LIBSDownsamplingInfo downsamplingInfo,
final boolean includeReadsWithDeletionAtLoci,
final GenomeLocParser genomeLocParser,
@ -221,6 +246,29 @@ public final class LocusIteratorByState extends LocusIterator {
return currentAlignmentContext;
}
/**
* Move this LIBS until we are over position
*
* Will return null if cannot reach position (because we run out of data in the locus)
*
* @param position the start position of the AlignmentContext we want back
* @return a AlignmentContext at position, or null if this isn't possible
*/
public AlignmentContext advanceToLocus(final int position) {
while ( hasNext() ) {
final AlignmentContext context = next();
if ( context == null )
// we ran out of data
return null;
if ( context.getPosition() == position)
return context;
}
return null;
}
/**
* Creates the next alignment context from the given state. Note that this is implemented as a
* lazy load method. nextAlignmentContext MUST BE null in order for this method to advance to the

27
public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
View File

@ -589,6 +589,8 @@ public class GATKVariantContextUtils {
* simpleMerge does not verify any more unique sample names EVEN if genotypeMergeOptions == GenotypeMergeType.REQUIRE_UNIQUE. One should use
* SampleUtils.verifyUniqueSamplesNames to check that before using sempleMerge.
*
* For more information on this method see: http://www.thedistractionnetwork.com/programmer-problem/
*
* @param unsortedVCs collection of unsorted VCs
* @param priorityListOfVCs priority list detailing the order in which we should grab the VCs
* @param filteredRecordMergeType merge type for filtered records
@ -1292,4 +1294,29 @@ public class GATKVariantContextUtils {
return Integer.valueOf(getIndex(vc1)).compareTo(getIndex(vc2));
}
}
/**
* For testing purposes only. Create a site-only VariantContext at contig:start containing alleles
*
* @param name the name of the VC
* @param contig the contig for the VC
* @param start the start of the VC
* @param alleleStrings a non-null, non-empty list of strings for the alleles. The first will be the ref allele, and others the
* alt. Will compute the stop of the VC from the length of the reference allele
* @return a non-null VariantContext
*/
public static VariantContext makeFromAlleles(final String name, final String contig, final int start, final List<String> alleleStrings) {
if ( alleleStrings == null || alleleStrings.isEmpty() )
throw new IllegalArgumentException("alleleStrings must be non-empty, non-null list");
final List<Allele> alleles = new LinkedList<Allele>();
final int length = alleleStrings.get(0).length();
boolean first = true;
for ( final String alleleString : alleleStrings ) {
alleles.add(Allele.create(alleleString, first));
first = false;
}
return new VariantContextBuilder(name, contig, start, start+length-1, alleles).make();
}
}

19
public/java/test/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java
View File

@ -1,6 +1,6 @@
/*
* 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
@ -9,10 +9,10 @@
* 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
@ -966,21 +966,12 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
@Test(dataProvider = "ClipAlleleTest")
public void testClipAlleles(final List<String> alleleStrings, final List<String> expected, final int numLeftClipped) {
final List<Allele> alleles = new LinkedList<Allele>();
final int length = alleleStrings.get(0).length();
boolean first = true;
for ( final String alleleString : alleleStrings ) {
alleles.add(Allele.create(alleleString, first));
first = false;
}
final int start = 10;
final VariantContextBuilder builder = new VariantContextBuilder("test", "20", start, start+length-1, alleles);
final VariantContext unclipped = builder.make();
final VariantContext unclipped = GATKVariantContextUtils.makeFromAlleles("test", "20", start, alleleStrings);
final VariantContext clipped = GATKVariantContextUtils.trimAlleles(unclipped, true, true);
Assert.assertEquals(clipped.getStart(), unclipped.getStart() + numLeftClipped);
for ( int i = 0; i < alleles.size(); i++ ) {
for ( int i = 0; i < unclipped.getAlleles().size(); i++ ) {
final Allele trimmed = clipped.getAlleles().get(i);
Assert.assertEquals(trimmed.getBaseString(), expected.get(i));
}