Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
This commit is contained in:
Ryan Poplin
commit
0b37c556f5
|
|
@ -356,10 +356,6 @@ public class GenomeAnalysisEngine {
|
|||
public BAQ.QualityMode getWalkerBAQQualityMode() { return WalkerManager.getBAQQualityMode(walker); }
|
||||
public BAQ.ApplicationTime getWalkerBAQApplicationTime() { return WalkerManager.getBAQApplicationTime(walker); }
|
||||
|
||||
protected boolean generateExtendedEvents() {
|
||||
return walker.generateExtendedEvents();
|
||||
}
|
||||
|
||||
protected boolean includeReadsWithDeletionAtLoci() {
|
||||
return walker.includeReadsWithDeletionAtLoci();
|
||||
}
|
||||
|
|
@ -766,7 +762,6 @@ public class GenomeAnalysisEngine {
|
|||
new ValidationExclusion(Arrays.asList(argCollection.unsafe)),
|
||||
filters,
|
||||
includeReadsWithDeletionAtLoci(),
|
||||
generateExtendedEvents(),
|
||||
getWalkerBAQApplicationTime() == BAQ.ApplicationTime.ON_INPUT ? argCollection.BAQMode : BAQ.CalculationMode.OFF,
|
||||
getWalkerBAQQualityMode(),
|
||||
refReader,
|
||||
|
|
|
|||
|
|
@ -36,7 +36,6 @@ public class ReadProperties {
|
|||
private final Collection<ReadFilter> supplementalFilters;
|
||||
private final boolean includeReadsWithDeletionAtLoci;
|
||||
private final boolean useOriginalBaseQualities;
|
||||
private final boolean generateExtendedEvents;
|
||||
private final BAQ.CalculationMode cmode;
|
||||
private final BAQ.QualityMode qmode;
|
||||
private final IndexedFastaSequenceFile refReader; // read for BAQ, if desired
|
||||
|
|
@ -52,16 +51,9 @@ public class ReadProperties {
|
|||
return includeReadsWithDeletionAtLoci;
|
||||
}
|
||||
|
||||
/**
|
||||
* Return true if the walker wants to see additional piles of "extended" events (indels). An indel is associated,
|
||||
* by convention, with the reference base immediately preceding the insertion/deletion, and if this flag is set
|
||||
* to 'true', any locus with an indel associated with it will cause exactly two subsequent calls to walker's map(): first call
|
||||
* will be made with a "conventional" base pileup, the next call will be made with a pileup of extended (indel/noevent)
|
||||
* events.
|
||||
* @return
|
||||
*/
|
||||
@Deprecated
|
||||
public boolean generateExtendedEvents() {
|
||||
return generateExtendedEvents;
|
||||
return false;
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -144,9 +136,6 @@ public class ReadProperties {
|
|||
* @param downsamplingMethod Method for downsampling reads at a given locus.
|
||||
* @param exclusionList what safety checks we're willing to let slide
|
||||
* @param supplementalFilters additional filters to dynamically apply.
|
||||
* @param generateExtendedEvents if true, the engine will issue an extra call to walker's map() with
|
||||
* a pile of indel/noevent extended events at every locus with at least one indel associated with it
|
||||
* (in addition to a "regular" call to map() at this locus performed with base pileup)
|
||||
* @param includeReadsWithDeletionAtLoci if 'true', the base pileups sent to the walker's map() method
|
||||
* will explicitly list reads with deletion over the current reference base; otherwise, only observed
|
||||
* bases will be seen in the pileups, and the deletions will be skipped silently.
|
||||
|
|
@ -163,7 +152,6 @@ public class ReadProperties {
|
|||
ValidationExclusion exclusionList,
|
||||
Collection<ReadFilter> supplementalFilters,
|
||||
boolean includeReadsWithDeletionAtLoci,
|
||||
boolean generateExtendedEvents,
|
||||
BAQ.CalculationMode cmode,
|
||||
BAQ.QualityMode qmode,
|
||||
IndexedFastaSequenceFile refReader,
|
||||
|
|
@ -176,7 +164,6 @@ public class ReadProperties {
|
|||
this.exclusionList = exclusionList == null ? new ValidationExclusion() : exclusionList;
|
||||
this.supplementalFilters = supplementalFilters;
|
||||
this.includeReadsWithDeletionAtLoci = includeReadsWithDeletionAtLoci;
|
||||
this.generateExtendedEvents = generateExtendedEvents;
|
||||
this.useOriginalBaseQualities = useOriginalBaseQualities;
|
||||
this.cmode = cmode;
|
||||
this.qmode = qmode;
|
||||
|
|
|
|||
|
|
@ -168,7 +168,6 @@ public class SAMDataSource {
|
|||
null,
|
||||
new ValidationExclusion(),
|
||||
new ArrayList<ReadFilter>(),
|
||||
false,
|
||||
false);
|
||||
}
|
||||
|
||||
|
|
@ -186,8 +185,7 @@ public class SAMDataSource {
|
|||
DownsamplingMethod downsamplingMethod,
|
||||
ValidationExclusion exclusionList,
|
||||
Collection<ReadFilter> supplementalFilters,
|
||||
boolean includeReadsWithDeletionAtLoci,
|
||||
boolean generateExtendedEvents) {
|
||||
boolean includeReadsWithDeletionAtLoci) {
|
||||
this( samFiles,
|
||||
threadAllocation,
|
||||
numFileHandles,
|
||||
|
|
@ -199,7 +197,6 @@ public class SAMDataSource {
|
|||
exclusionList,
|
||||
supplementalFilters,
|
||||
includeReadsWithDeletionAtLoci,
|
||||
generateExtendedEvents,
|
||||
BAQ.CalculationMode.OFF,
|
||||
BAQ.QualityMode.DONT_MODIFY,
|
||||
null, // no BAQ
|
||||
|
|
@ -216,9 +213,6 @@ public class SAMDataSource {
|
|||
* @param downsamplingMethod Method for downsampling reads at a given locus.
|
||||
* @param exclusionList what safety checks we're willing to let slide
|
||||
* @param supplementalFilters additional filters to dynamically apply.
|
||||
* @param generateExtendedEvents if true, the engine will issue an extra call to walker's map() with
|
||||
* a pile of indel/noevent extended events at every locus with at least one indel associated with it
|
||||
* (in addition to a "regular" call to map() at this locus performed with base pileup)
|
||||
* @param includeReadsWithDeletionAtLoci if 'true', the base pileups sent to the walker's map() method
|
||||
* will explicitly list reads with deletion over the current reference base; otherwise, only observed
|
||||
* bases will be seen in the pileups, and the deletions will be skipped silently.
|
||||
|
|
@ -236,7 +230,6 @@ public class SAMDataSource {
|
|||
ValidationExclusion exclusionList,
|
||||
Collection<ReadFilter> supplementalFilters,
|
||||
boolean includeReadsWithDeletionAtLoci,
|
||||
boolean generateExtendedEvents,
|
||||
BAQ.CalculationMode cmode,
|
||||
BAQ.QualityMode qmode,
|
||||
IndexedFastaSequenceFile refReader,
|
||||
|
|
@ -309,7 +302,6 @@ public class SAMDataSource {
|
|||
exclusionList,
|
||||
supplementalFilters,
|
||||
includeReadsWithDeletionAtLoci,
|
||||
generateExtendedEvents,
|
||||
cmode,
|
||||
qmode,
|
||||
refReader,
|
||||
|
|
|
|||
|
|
@ -66,9 +66,6 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
|
|||
@Output
|
||||
PrintStream out;
|
||||
|
||||
@Argument(fullName="showIndelPileups",shortName="show_indels",doc="In addition to base pileups, generate pileups of extended indel events")
|
||||
public boolean SHOW_INDEL_PILEUPS = false;
|
||||
|
||||
@Argument(fullName="showVerbose",shortName="verbose",doc="Add an extra verbose section to the pileup output")
|
||||
public boolean SHOW_VERBOSE = false;
|
||||
|
||||
|
|
@ -78,8 +75,6 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
|
|||
public void initialize() {
|
||||
}
|
||||
|
||||
public boolean generateExtendedEvents() { return SHOW_INDEL_PILEUPS; }
|
||||
|
||||
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
|
||||
|
||||
String rods = getReferenceOrderedData( tracker );
|
||||
|
|
@ -92,17 +87,6 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
|
|||
out.println();
|
||||
}
|
||||
|
||||
if ( context.hasExtendedEventPileup() ) {
|
||||
ReadBackedExtendedEventPileup indelPileup = context.getExtendedEventPileup();
|
||||
List<Pair<String,Integer>> eventCounts = indelPileup.getEventStringsWithCounts(ref.getBases());
|
||||
|
||||
out.printf("%s %s ", indelPileup.getShortPileupString(), rods);
|
||||
int i = 0;
|
||||
for ( ; i < eventCounts.size() - 1 ; i++ ) {
|
||||
out.printf("%s:%d,",eventCounts.get(i).first,eventCounts.get(i).second);
|
||||
}
|
||||
out.printf("%s:%d%n",eventCounts.get(i).first,eventCounts.get(i).second);
|
||||
}
|
||||
return 1;
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -114,35 +114,6 @@ public abstract class Walker<MapType, ReduceType> {
|
|||
return false;
|
||||
}
|
||||
|
||||
/**
|
||||
* This method states whether you want to see pileups of "extended events" (currently, indels only)
|
||||
* at every locus that has at least one indel associated with it. Consider the following situation:
|
||||
*
|
||||
* ref: AT--CTGA (note that we expanded the ref here with -- to accomodate insertion in read3)
|
||||
* read1: AT--CTGA (perfectly matches the ref)
|
||||
* read2: AT----GA (deletion -CT w.r.t. the ref)
|
||||
* read3: ATGGCTGA (insertion +GG w.r.t the ref)
|
||||
*
|
||||
* Normally, the locus iterator only returns read base pileups over reference bases, optionally with deleted bases
|
||||
* included (see #includeReadsWithDeletionAtLoci()). In other words, the pileup over the second reference base (T)
|
||||
* will be [T,T,T] (all reads count), for the next reference base (C) the pileup will be [C,C] (or [C,-,C] if
|
||||
* #includeReadsWithDeletionAtLoci() is true), next pileup generated over the next reference
|
||||
* base (T) will be either [T,T], or [T,'-',T], etc. In this default mode, a) insertions are not seen by a walker at all, and
|
||||
* b) deletions are (optionally) seen only on a base-by-base basis (as the step-by-step traversal over the reference
|
||||
* bases is performed). In the extended event mode, however, if there is at least one indel associated with a reference
|
||||
* locus, the engine will generate an <i>additional</i> call to the walker's map() method, with a pileup of
|
||||
* full-length extended indel/noevent calls. This call will be made <i>after</i> the conventional base pileup call
|
||||
* at that locus. Thus, in the example above, a conventional call will be first made at the second reference base (T),
|
||||
* with the [T,T,T] pileup of read bases, then an extended event call will be made at the <i>same</i> locus with
|
||||
* pileup [no_event, -CT, +GG] (i.e. extended events associated with that reference base). After that, the traversal
|
||||
* engine will move to the next reference base.
|
||||
*
|
||||
* @return false if you do not want to receive extra pileups with extended events, or true if you do.
|
||||
*/
|
||||
public boolean generateExtendedEvents() {
|
||||
return false;
|
||||
}
|
||||
|
||||
public void initialize() { }
|
||||
|
||||
/**
|
||||
|
|
|
|||
|
|
@ -74,10 +74,6 @@ public class GCContentByIntervalWalker extends LocusWalker<Long, Long> {
|
|||
public void initialize() {
|
||||
}
|
||||
|
||||
public boolean generateExtendedEvents() {
|
||||
return false;
|
||||
}
|
||||
|
||||
public Long reduceInit() {
|
||||
return 0L;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -227,10 +227,6 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
|
|||
}
|
||||
}
|
||||
|
||||
public boolean generateExtendedEvents() {
|
||||
return false;
|
||||
}
|
||||
|
||||
public PhasingStats reduceInit() {
|
||||
return new PhasingStats();
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,56 +0,0 @@
|
|||
package org.broadinstitute.sting.gatk.walkers.qc;
|
||||
|
||||
import org.broadinstitute.sting.commandline.Output;
|
||||
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
||||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
|
||||
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
|
||||
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
|
||||
|
||||
import java.io.PrintStream;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
||||
/**
|
||||
* At each locus in the input data set, prints the reference base, genomic location, and
|
||||
* all aligning reads in a compact but human-readable form.
|
||||
*/
|
||||
public class PrintLocusContextWalker extends LocusWalker<AlignmentContext, Integer> implements TreeReducible<Integer> {
|
||||
@Output
|
||||
private PrintStream out;
|
||||
|
||||
public AlignmentContext map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
|
||||
out.printf( "In map: ref = %s, loc = %s %s, reads = %s%n", ref.getBaseAsChar(),
|
||||
context.getLocation(),
|
||||
context.hasExtendedEventPileup() ? "[extended]" : "",
|
||||
Arrays.deepToString( getReadNames(context.getReads()) ) );
|
||||
return context;
|
||||
}
|
||||
|
||||
|
||||
|
||||
public Integer reduceInit() { return 0; }
|
||||
|
||||
public Integer reduce(AlignmentContext context, Integer sum) {
|
||||
return sum + 1;
|
||||
}
|
||||
|
||||
public Integer treeReduce(Integer lhs, Integer rhs) {
|
||||
return lhs + rhs;
|
||||
}
|
||||
|
||||
private String[] getReadNames( List<GATKSAMRecord> reads ) {
|
||||
String[] readNames = new String[ reads.size() ];
|
||||
for( int i = 0; i < reads.size(); i++ ) {
|
||||
readNames[i] = String.format("%nname = %s, start = %d, end = %d", reads.get(i).getReadName(), reads.get(i).getAlignmentStart(), reads.get(i).getAlignmentEnd());
|
||||
}
|
||||
//Arrays.sort(readNames);
|
||||
return readNames;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean generateExtendedEvents() {
|
||||
return true;
|
||||
}
|
||||
}
|
||||
|
|
@ -76,7 +76,6 @@ public class DownsamplerBenchmark extends ReadProcessingBenchmark {
|
|||
new ValidationExclusion(Collections.singletonList(ValidationExclusion.TYPE.ALL)),
|
||||
Collections.<ReadFilter>emptyList(),
|
||||
false,
|
||||
false,
|
||||
BAQ.CalculationMode.OFF,
|
||||
BAQ.QualityMode.DONT_MODIFY,
|
||||
null, // no BAQ
|
||||
|
|
|
|||
|
|
@ -109,7 +109,6 @@ public class SAMDataSourceUnitTest extends BaseTest {
|
|||
null,
|
||||
new ValidationExclusion(),
|
||||
new ArrayList<ReadFilter>(),
|
||||
false,
|
||||
false);
|
||||
|
||||
Iterable<Shard> strat = data.createShardIteratorOverMappedReads(seq.getSequenceDictionary(),new LocusShardBalancer());
|
||||
|
|
|
|||
|
|
@ -43,49 +43,6 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
|
|||
return new LocusIteratorByState(new FakeCloseableIterator<SAMRecord>(reads.iterator()), readAttributes, genomeLocParser, LocusIteratorByState.sampleListForSAMWithoutReadGroups());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testIndelBaseQualityFiltering() {
|
||||
final byte[] bases = new byte[] {'A','A','A','A','A','A','A','A','A','A'};
|
||||
|
||||
// create a test version of the Reads object
|
||||
ReadProperties readAttributes = createTestReadProperties();
|
||||
JVMUtils.setFieldValue(JVMUtils.findField(ReadProperties.class,"generateExtendedEvents"),readAttributes,true);
|
||||
|
||||
SAMRecord before = ArtificialSAMUtils.createArtificialRead(header,"before",0,1,10);
|
||||
before.setReadBases(bases);
|
||||
before.setBaseQualities(new byte[] {20,20,20,20,0,20,20,20,20,20});
|
||||
before.setCigarString("10M");
|
||||
|
||||
SAMRecord during = ArtificialSAMUtils.createArtificialRead(header,"during",0,2,10);
|
||||
during.setReadBases(bases);
|
||||
during.setBaseQualities(new byte[] {20,20,20,20,20,20,20,20,20,20,20});
|
||||
during.setCigarString("4M1I6M");
|
||||
|
||||
SAMRecord after = ArtificialSAMUtils.createArtificialRead(header,"after",0,3,10);
|
||||
after.setReadBases(bases);
|
||||
after.setBaseQualities(new byte[] {20,20,0,20,20,20,20,20,20,20});
|
||||
after.setCigarString("10M");
|
||||
|
||||
List<SAMRecord> reads = Arrays.asList(before,during,after);
|
||||
|
||||
// create the iterator by state with the fake reads and fake records
|
||||
li = makeLTBS(reads,readAttributes);
|
||||
|
||||
boolean foundExtendedEventPileup = false;
|
||||
while (li.hasNext()) {
|
||||
AlignmentContext context = li.next();
|
||||
if(!context.hasExtendedEventPileup())
|
||||
continue;
|
||||
|
||||
ReadBackedExtendedEventPileup pileup = context.getExtendedEventPileup().getBaseFilteredPileup(10);
|
||||
Assert.assertEquals(pileup.getLocation().getStart(), 5, "Extended event pileup at wrong location");
|
||||
Assert.assertEquals(pileup.getNumberOfElements(), 3, "Pileup size is incorrect");
|
||||
|
||||
foundExtendedEventPileup = true;
|
||||
}
|
||||
|
||||
Assert.assertTrue(foundExtendedEventPileup,"Extended event pileup not found");
|
||||
}
|
||||
@Test
|
||||
public void testIndelsInRegularPileup() {
|
||||
final byte[] bases = new byte[] {'A','A','A','A','A','A','A','A','A','A'};
|
||||
|
|
@ -93,7 +50,6 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
|
|||
|
||||
// create a test version of the Reads object
|
||||
ReadProperties readAttributes = createTestReadProperties();
|
||||
JVMUtils.setFieldValue(JVMUtils.findField(ReadProperties.class,"generateExtendedEvents"),readAttributes,true);
|
||||
|
||||
SAMRecord before = ArtificialSAMUtils.createArtificialRead(header,"before",0,1,10);
|
||||
before.setReadBases(bases);
|
||||
|
|
@ -136,59 +92,6 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
|
|||
Assert.assertTrue(foundIndel,"Indel in pileup not found");
|
||||
}
|
||||
|
||||
/**
|
||||
* Right now, the GATK's extended event pileup DOES NOT include reads which stop immediately before an insertion
|
||||
* but DOES include reads which stop immediately after an insertion. This is almost certainly WRONG. Eric is
|
||||
* figuring out the right way to handle this; in the meantime, adding this test to monitor that:
|
||||
* A) the behavior is consistent
|
||||
* B) so that we do end up with an automated test for this case when the model is fixed.
|
||||
*/
|
||||
@Test
|
||||
public void testIndelPileupContainsAbuttingReads() {
|
||||
final byte[] bases = new byte[] {'A','A','A','A','A','A','A','A','A','A'};
|
||||
final byte[] quals = new byte[] { 20, 20, 20, 20, 20, 20, 20, 20, 20, 20};
|
||||
|
||||
// create a test version of the Reads object
|
||||
ReadProperties readAttributes = createTestReadProperties();
|
||||
JVMUtils.setFieldValue(JVMUtils.findField(ReadProperties.class,"generateExtendedEvents"),readAttributes,true);
|
||||
|
||||
SAMRecord before = ArtificialSAMUtils.createArtificialRead(header,"before",0,1,10);
|
||||
before.setReadBases(bases);
|
||||
before.setBaseQualities(quals);
|
||||
before.setCigarString("10M");
|
||||
|
||||
SAMRecord during = ArtificialSAMUtils.createArtificialRead(header,"during",0,6,10);
|
||||
during.setReadBases(bases);
|
||||
during.setBaseQualities(quals);
|
||||
during.setCigarString("5M1I5M");
|
||||
|
||||
SAMRecord after = ArtificialSAMUtils.createArtificialRead(header,"after",0,11,10);
|
||||
after.setReadBases(bases);
|
||||
after.setBaseQualities(quals);
|
||||
after.setCigarString("10M");
|
||||
|
||||
List<SAMRecord> reads = Arrays.asList(before,during,after);
|
||||
|
||||
// create the iterator by state with the fake reads and fake records
|
||||
li = makeLTBS(reads,readAttributes);
|
||||
|
||||
boolean foundExtendedEventPileup = false;
|
||||
while (li.hasNext()) {
|
||||
AlignmentContext context = li.next();
|
||||
if(!context.hasExtendedEventPileup())
|
||||
continue;
|
||||
|
||||
Assert.assertEquals(context.getLocation().getStart(), 10, "Extended event pileup at wrong location");
|
||||
Assert.assertEquals(context.size(), 2, "Pileup size is incorrect");
|
||||
Assert.assertEquals(context.getExtendedEventPileup().getReads().get(0), during, "Read in pileup is incorrect");
|
||||
Assert.assertEquals(context.getExtendedEventPileup().getReads().get(1), after, "Read in pileup is incorrect");
|
||||
|
||||
foundExtendedEventPileup = true;
|
||||
}
|
||||
|
||||
Assert.assertTrue(foundExtendedEventPileup,"Extended event pileup not found");
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testWholeIndelReadInIsolation() {
|
||||
final int firstLocus = 44367789;
|
||||
|
|
@ -214,17 +117,6 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
|
|||
ReadBackedPileup basePileup = alignmentContext.getBasePileup();
|
||||
Assert.assertEquals(basePileup.getReads().size(),1,"Pileup is of incorrect size");
|
||||
Assert.assertSame(basePileup.getReads().get(0),indelOnlyRead,"Read in pileup is incorrect");
|
||||
|
||||
// Turn on extended events, and make sure the event is found.
|
||||
JVMUtils.setFieldValue(JVMUtils.findField(ReadProperties.class,"generateExtendedEvents"),readAttributes,true);
|
||||
li = makeLTBS(reads, readAttributes);
|
||||
|
||||
Assert.assertTrue(li.hasNext(),"LocusIteratorByState with extended events should contain exactly one pileup");
|
||||
alignmentContext = li.next();
|
||||
Assert.assertEquals(alignmentContext.getLocation().getStart(),firstLocus-1,"Extended event pileup is at incorrect location.");
|
||||
ReadBackedExtendedEventPileup extendedEventPileup = alignmentContext.getExtendedEventPileup();
|
||||
Assert.assertEquals(extendedEventPileup.getReads().size(),1,"Pileup is of incorrect size");
|
||||
Assert.assertSame(extendedEventPileup.getReads().get(0),indelOnlyRead,"Read in pileup is incorrect");
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -232,7 +124,7 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
|
|||
* not negatively influence the ordering of the pileup.
|
||||
*/
|
||||
@Test
|
||||
public void testWholeIndelReadWithoutExtendedEvents() {
|
||||
public void testWholeIndelRead() {
|
||||
final int firstLocus = 44367788, secondLocus = firstLocus + 1;
|
||||
|
||||
SAMRecord leadingRead = ArtificialSAMUtils.createArtificialRead(header,"leading",0,firstLocus,76);
|
||||
|
|
@ -280,70 +172,6 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
|
|||
Assert.assertEquals(numAlignmentContextsFound,2,"Found incorrect number of alignment contexts");
|
||||
}
|
||||
|
||||
/**
|
||||
* Test to make sure that reads supporting only an indel (example cigar string: 76I) do
|
||||
* not negatively influence the ordering of the pileup.
|
||||
*/
|
||||
@Test
|
||||
public void testWholeIndelReadWithExtendedEvents() {
|
||||
final int firstLocus = 44367788, secondLocus = firstLocus + 1;
|
||||
|
||||
// create a test version of the Reads object
|
||||
ReadProperties readAttributes = createTestReadProperties();
|
||||
JVMUtils.setFieldValue(JVMUtils.findField(ReadProperties.class,"generateExtendedEvents"),readAttributes,true);
|
||||
|
||||
SAMRecord leadingRead = ArtificialSAMUtils.createArtificialRead(header,"leading",0,firstLocus,76);
|
||||
leadingRead.setReadBases(Utils.dupBytes((byte)'A',76));
|
||||
leadingRead.setBaseQualities(Utils.dupBytes((byte)'@',76));
|
||||
leadingRead.setCigarString("1M75I");
|
||||
|
||||
SAMRecord indelOnlyRead = ArtificialSAMUtils.createArtificialRead(header,"indelOnly",0,secondLocus,76);
|
||||
indelOnlyRead.setReadBases(Utils.dupBytes((byte)'A',76));
|
||||
indelOnlyRead.setBaseQualities(Utils.dupBytes((byte)'@',76));
|
||||
indelOnlyRead.setCigarString("76I");
|
||||
|
||||
SAMRecord fullMatchAfterIndel = ArtificialSAMUtils.createArtificialRead(header,"fullMatch",0,secondLocus,1);
|
||||
fullMatchAfterIndel.setReadBases(Utils.dupBytes((byte)'A',1));
|
||||
fullMatchAfterIndel.setBaseQualities(Utils.dupBytes((byte)'@',1));
|
||||
fullMatchAfterIndel.setCigarString("1M");
|
||||
|
||||
List<SAMRecord> reads = Arrays.asList(leadingRead,indelOnlyRead,fullMatchAfterIndel);
|
||||
|
||||
// create the iterator by state with the fake reads and fake records
|
||||
li = makeLTBS(reads,readAttributes);
|
||||
|
||||
Assert.assertTrue(li.hasNext(),"Missing first locus at " + firstLocus);
|
||||
AlignmentContext alignmentContext = li.next();
|
||||
Assert.assertEquals(alignmentContext.getLocation().getStart(),firstLocus,"Incorrect locus at this position; should be " + firstLocus);
|
||||
List<GATKSAMRecord> readsAtLocus = alignmentContext.getBasePileup().getReads();
|
||||
Assert.assertEquals(readsAtLocus.size(),1,"Wrong number of reads at locus " + firstLocus);
|
||||
Assert.assertSame(readsAtLocus.get(0),leadingRead,"leadingRead absent from pileup at locus " + firstLocus);
|
||||
|
||||
Assert.assertTrue(li.hasNext(),"Missing extended event at " + firstLocus);
|
||||
alignmentContext = li.next();
|
||||
Assert.assertEquals(alignmentContext.getLocation().getStart(),firstLocus,"Incorrect extended event locus at this position; should be " + firstLocus);
|
||||
readsAtLocus = alignmentContext.getExtendedEventPileup().getReads();
|
||||
Assert.assertEquals(readsAtLocus.size(),3,"Wrong number of reads at extended event locus " + firstLocus);
|
||||
Assert.assertSame(readsAtLocus.get(0),leadingRead,"leadingRead absent from pileup at extended event locus " + firstLocus);
|
||||
Assert.assertSame(readsAtLocus.get(1),indelOnlyRead,"indelOnlyRead absent from pileup at extended event locus " + firstLocus);
|
||||
// Weird, but as above, reads immediately after the indel are included in the extended event pileup
|
||||
Assert.assertSame(readsAtLocus.get(2),fullMatchAfterIndel,"fullMatchAfterIndel absent from pileup at extended event locus " + firstLocus);
|
||||
|
||||
// Traditionally, reads that end with indels bleed into the pileup at the following locus. Verify that the next pileup contains this read
|
||||
// and considers it to be an indel-containing read.
|
||||
Assert.assertTrue(li.hasNext(),"Missing base pileup at " + secondLocus);
|
||||
alignmentContext = li.next();
|
||||
Assert.assertEquals(alignmentContext.getLocation().getStart(),secondLocus,"Incorrect extended event locus at this position; should be " + secondLocus);
|
||||
readsAtLocus = alignmentContext.getBasePileup().getReads();
|
||||
Assert.assertEquals(readsAtLocus.size(),3,"Wrong number of reads at extended event locus " + secondLocus);
|
||||
Assert.assertSame(readsAtLocus.get(0),leadingRead,"leadingRead absent from pileup at extended event locus " + secondLocus);
|
||||
Assert.assertSame(readsAtLocus.get(1),indelOnlyRead,"indelOnlyRead absent from pileup at extended event locus " + secondLocus);
|
||||
// Weird, but as above, reads immediately after the indel are included in the extended event pileup
|
||||
Assert.assertSame(readsAtLocus.get(2),fullMatchAfterIndel,"fullMatchAfterIndel absent from pileup at extended event locus " + secondLocus);
|
||||
|
||||
Assert.assertFalse(li.hasNext(),"Too many alignment contexts");
|
||||
}
|
||||
|
||||
private static ReadProperties createTestReadProperties() {
|
||||
return new ReadProperties(
|
||||
Collections.<SAMReaderID>emptyList(),
|
||||
|
|
@ -354,7 +182,6 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
|
|||
new ValidationExclusion(),
|
||||
Collections.<ReadFilter>emptyList(),
|
||||
false,
|
||||
false,
|
||||
BAQ.CalculationMode.OFF,
|
||||
BAQ.QualityMode.DONT_MODIFY,
|
||||
null, // no BAQ
|
||||
|
|
|
|||
|
|
@ -23,16 +23,4 @@ public class PileupWalkerIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 1, Arrays.asList(expected_md5));
|
||||
executeTest("Testing the standard (no-indel) pileup on three merged FHS pools with 27 deletions in 969 bases", spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExtendedEventPileup() {
|
||||
String gatk_args = "-T Pileup -I " + validationDataLocation + "OV-0930.normal.chunk.bam "
|
||||
+ "-R " + hg18Reference
|
||||
+ " -show_indels -o %s";
|
||||
String expected_md5="06eedc2e7927650961d99d703f4301a4";
|
||||
WalkerTestSpec spec = new WalkerTestSpec(gatk_args,1,Arrays.asList(expected_md5));
|
||||
executeTest("Testing the extended pileup with indel records included on a small chunk of Ovarian dataset with 20 indels (1 D, 19 I)", spec);
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue