Had some free time, so I unplugged extended events from the walkers. Now they exist only in LocusIteratorByState, but ReadProperties.generateExtendedEvents() always returns false so that block is never actually executed anymore. I don't want to touch LIBS because I think David is in there right now.
This commit is contained in:
Eric Banks
parent
4075bc7d3d
commit
99d27ddcc4
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@ -356,10 +356,6 @@ public class GenomeAnalysisEngine {
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public BAQ.QualityMode getWalkerBAQQualityMode() { return WalkerManager.getBAQQualityMode(walker); }
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public BAQ.ApplicationTime getWalkerBAQApplicationTime() { return WalkerManager.getBAQApplicationTime(walker); }
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protected boolean generateExtendedEvents() {
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return walker.generateExtendedEvents();
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}
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protected boolean includeReadsWithDeletionAtLoci() {
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return walker.includeReadsWithDeletionAtLoci();
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}
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@ -766,7 +762,6 @@ public class GenomeAnalysisEngine {
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new ValidationExclusion(Arrays.asList(argCollection.unsafe)),
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filters,
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includeReadsWithDeletionAtLoci(),
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generateExtendedEvents(),
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getWalkerBAQApplicationTime() == BAQ.ApplicationTime.ON_INPUT ? argCollection.BAQMode : BAQ.CalculationMode.OFF,
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getWalkerBAQQualityMode(),
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refReader,
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@ -36,7 +36,6 @@ public class ReadProperties {
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private final Collection<ReadFilter> supplementalFilters;
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private final boolean includeReadsWithDeletionAtLoci;
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private final boolean useOriginalBaseQualities;
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private final boolean generateExtendedEvents;
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private final BAQ.CalculationMode cmode;
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private final BAQ.QualityMode qmode;
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private final IndexedFastaSequenceFile refReader; // read for BAQ, if desired
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@ -52,16 +51,9 @@ public class ReadProperties {
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return includeReadsWithDeletionAtLoci;
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}
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/**
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* Return true if the walker wants to see additional piles of "extended" events (indels). An indel is associated,
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* by convention, with the reference base immediately preceding the insertion/deletion, and if this flag is set
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* to 'true', any locus with an indel associated with it will cause exactly two subsequent calls to walker's map(): first call
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* will be made with a "conventional" base pileup, the next call will be made with a pileup of extended (indel/noevent)
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* events.
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* @return
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*/
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@Deprecated
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public boolean generateExtendedEvents() {
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return generateExtendedEvents;
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return false;
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}
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/**
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@ -144,9 +136,6 @@ public class ReadProperties {
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* @param downsamplingMethod Method for downsampling reads at a given locus.
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* @param exclusionList what safety checks we're willing to let slide
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* @param supplementalFilters additional filters to dynamically apply.
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* @param generateExtendedEvents if true, the engine will issue an extra call to walker's map() with
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* a pile of indel/noevent extended events at every locus with at least one indel associated with it
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* (in addition to a "regular" call to map() at this locus performed with base pileup)
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* @param includeReadsWithDeletionAtLoci if 'true', the base pileups sent to the walker's map() method
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* will explicitly list reads with deletion over the current reference base; otherwise, only observed
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* bases will be seen in the pileups, and the deletions will be skipped silently.
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@ -163,7 +152,6 @@ public class ReadProperties {
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ValidationExclusion exclusionList,
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Collection<ReadFilter> supplementalFilters,
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boolean includeReadsWithDeletionAtLoci,
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boolean generateExtendedEvents,
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BAQ.CalculationMode cmode,
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BAQ.QualityMode qmode,
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IndexedFastaSequenceFile refReader,
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@ -176,7 +164,6 @@ public class ReadProperties {
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this.exclusionList = exclusionList == null ? new ValidationExclusion() : exclusionList;
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this.supplementalFilters = supplementalFilters;
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this.includeReadsWithDeletionAtLoci = includeReadsWithDeletionAtLoci;
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this.generateExtendedEvents = generateExtendedEvents;
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this.useOriginalBaseQualities = useOriginalBaseQualities;
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this.cmode = cmode;
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this.qmode = qmode;
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@ -168,7 +168,6 @@ public class SAMDataSource {
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null,
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new ValidationExclusion(),
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new ArrayList<ReadFilter>(),
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false,
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false);
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}
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@ -186,8 +185,7 @@ public class SAMDataSource {
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DownsamplingMethod downsamplingMethod,
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ValidationExclusion exclusionList,
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Collection<ReadFilter> supplementalFilters,
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boolean includeReadsWithDeletionAtLoci,
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boolean generateExtendedEvents) {
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boolean includeReadsWithDeletionAtLoci) {
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this( samFiles,
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threadAllocation,
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numFileHandles,
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@ -199,7 +197,6 @@ public class SAMDataSource {
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exclusionList,
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supplementalFilters,
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includeReadsWithDeletionAtLoci,
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generateExtendedEvents,
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BAQ.CalculationMode.OFF,
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BAQ.QualityMode.DONT_MODIFY,
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null, // no BAQ
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@ -216,9 +213,6 @@ public class SAMDataSource {
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* @param downsamplingMethod Method for downsampling reads at a given locus.
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* @param exclusionList what safety checks we're willing to let slide
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* @param supplementalFilters additional filters to dynamically apply.
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* @param generateExtendedEvents if true, the engine will issue an extra call to walker's map() with
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* a pile of indel/noevent extended events at every locus with at least one indel associated with it
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* (in addition to a "regular" call to map() at this locus performed with base pileup)
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* @param includeReadsWithDeletionAtLoci if 'true', the base pileups sent to the walker's map() method
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* will explicitly list reads with deletion over the current reference base; otherwise, only observed
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* bases will be seen in the pileups, and the deletions will be skipped silently.
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@ -236,7 +230,6 @@ public class SAMDataSource {
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ValidationExclusion exclusionList,
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Collection<ReadFilter> supplementalFilters,
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boolean includeReadsWithDeletionAtLoci,
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boolean generateExtendedEvents,
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BAQ.CalculationMode cmode,
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BAQ.QualityMode qmode,
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IndexedFastaSequenceFile refReader,
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@ -309,7 +302,6 @@ public class SAMDataSource {
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exclusionList,
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supplementalFilters,
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includeReadsWithDeletionAtLoci,
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generateExtendedEvents,
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cmode,
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qmode,
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refReader,
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@ -66,9 +66,6 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
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@Output
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PrintStream out;
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@Argument(fullName="showIndelPileups",shortName="show_indels",doc="In addition to base pileups, generate pileups of extended indel events")
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public boolean SHOW_INDEL_PILEUPS = false;
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@Argument(fullName="showVerbose",shortName="verbose",doc="Add an extra verbose section to the pileup output")
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public boolean SHOW_VERBOSE = false;
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@ -78,8 +75,6 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
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public void initialize() {
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}
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public boolean generateExtendedEvents() { return SHOW_INDEL_PILEUPS; }
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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String rods = getReferenceOrderedData( tracker );
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@ -92,17 +87,6 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
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out.println();
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}
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if ( context.hasExtendedEventPileup() ) {
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ReadBackedExtendedEventPileup indelPileup = context.getExtendedEventPileup();
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List<Pair<String,Integer>> eventCounts = indelPileup.getEventStringsWithCounts(ref.getBases());
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out.printf("%s %s ", indelPileup.getShortPileupString(), rods);
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int i = 0;
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for ( ; i < eventCounts.size() - 1 ; i++ ) {
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out.printf("%s:%d,",eventCounts.get(i).first,eventCounts.get(i).second);
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}
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out.printf("%s:%d%n",eventCounts.get(i).first,eventCounts.get(i).second);
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}
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return 1;
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}
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@ -114,35 +114,6 @@ public abstract class Walker<MapType, ReduceType> {
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return false;
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}
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/**
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* This method states whether you want to see pileups of "extended events" (currently, indels only)
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* at every locus that has at least one indel associated with it. Consider the following situation:
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*
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* ref: AT--CTGA (note that we expanded the ref here with -- to accomodate insertion in read3)
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* read1: AT--CTGA (perfectly matches the ref)
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* read2: AT----GA (deletion -CT w.r.t. the ref)
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* read3: ATGGCTGA (insertion +GG w.r.t the ref)
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*
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* Normally, the locus iterator only returns read base pileups over reference bases, optionally with deleted bases
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* included (see #includeReadsWithDeletionAtLoci()). In other words, the pileup over the second reference base (T)
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* will be [T,T,T] (all reads count), for the next reference base (C) the pileup will be [C,C] (or [C,-,C] if
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* #includeReadsWithDeletionAtLoci() is true), next pileup generated over the next reference
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* 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
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* b) deletions are (optionally) seen only on a base-by-base basis (as the step-by-step traversal over the reference
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* bases is performed). In the extended event mode, however, if there is at least one indel associated with a reference
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* locus, the engine will generate an <i>additional</i> call to the walker's map() method, with a pileup of
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* full-length extended indel/noevent calls. This call will be made <i>after</i> the conventional base pileup call
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* at that locus. Thus, in the example above, a conventional call will be first made at the second reference base (T),
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* with the [T,T,T] pileup of read bases, then an extended event call will be made at the <i>same</i> locus with
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* pileup [no_event, -CT, +GG] (i.e. extended events associated with that reference base). After that, the traversal
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* engine will move to the next reference base.
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*
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* @return false if you do not want to receive extra pileups with extended events, or true if you do.
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*/
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public boolean generateExtendedEvents() {
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return false;
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}
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public void initialize() { }
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/**
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@ -74,10 +74,6 @@ public class GCContentByIntervalWalker extends LocusWalker<Long, Long> {
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public void initialize() {
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}
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public boolean generateExtendedEvents() {
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return false;
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}
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public Long reduceInit() {
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return 0L;
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}
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@ -227,10 +227,6 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
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}
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}
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public boolean generateExtendedEvents() {
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return false;
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}
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public PhasingStats reduceInit() {
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return new PhasingStats();
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}
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@ -1,56 +0,0 @@
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package org.broadinstitute.sting.gatk.walkers.qc;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.LocusWalker;
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import org.broadinstitute.sting.gatk.walkers.TreeReducible;
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import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
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import java.io.PrintStream;
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import java.util.Arrays;
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import java.util.List;
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/**
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* At each locus in the input data set, prints the reference base, genomic location, and
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* all aligning reads in a compact but human-readable form.
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*/
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public class PrintLocusContextWalker extends LocusWalker<AlignmentContext, Integer> implements TreeReducible<Integer> {
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@Output
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private PrintStream out;
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public AlignmentContext map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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out.printf( "In map: ref = %s, loc = %s %s, reads = %s%n", ref.getBaseAsChar(),
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context.getLocation(),
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context.hasExtendedEventPileup() ? "[extended]" : "",
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Arrays.deepToString( getReadNames(context.getReads()) ) );
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return context;
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}
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public Integer reduceInit() { return 0; }
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public Integer reduce(AlignmentContext context, Integer sum) {
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return sum + 1;
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}
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public Integer treeReduce(Integer lhs, Integer rhs) {
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return lhs + rhs;
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}
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private String[] getReadNames( List<GATKSAMRecord> reads ) {
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String[] readNames = new String[ reads.size() ];
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for( int i = 0; i < reads.size(); i++ ) {
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readNames[i] = String.format("%nname = %s, start = %d, end = %d", reads.get(i).getReadName(), reads.get(i).getAlignmentStart(), reads.get(i).getAlignmentEnd());
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}
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//Arrays.sort(readNames);
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return readNames;
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}
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@Override
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public boolean generateExtendedEvents() {
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return true;
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}
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}
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@ -76,7 +76,6 @@ public class DownsamplerBenchmark extends ReadProcessingBenchmark {
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new ValidationExclusion(Collections.singletonList(ValidationExclusion.TYPE.ALL)),
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Collections.<ReadFilter>emptyList(),
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false,
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false,
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BAQ.CalculationMode.OFF,
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BAQ.QualityMode.DONT_MODIFY,
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null, // no BAQ
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@ -109,7 +109,6 @@ public class SAMDataSourceUnitTest extends BaseTest {
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null,
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new ValidationExclusion(),
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new ArrayList<ReadFilter>(),
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false,
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false);
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Iterable<Shard> strat = data.createShardIteratorOverMappedReads(seq.getSequenceDictionary(),new LocusShardBalancer());
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@ -354,7 +354,6 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
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new ValidationExclusion(),
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Collections.<ReadFilter>emptyList(),
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false,
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false,
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BAQ.CalculationMode.OFF,
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BAQ.QualityMode.DONT_MODIFY,
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null, // no BAQ
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@ -23,16 +23,4 @@ public class PileupWalkerIntegrationTest extends WalkerTest {
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WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 1, Arrays.asList(expected_md5));
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executeTest("Testing the standard (no-indel) pileup on three merged FHS pools with 27 deletions in 969 bases", spec);
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}
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@Test
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public void testExtendedEventPileup() {
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String gatk_args = "-T Pileup -I " + validationDataLocation + "OV-0930.normal.chunk.bam "
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+ "-R " + hg18Reference
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+ " -show_indels -o %s";
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String expected_md5="06eedc2e7927650961d99d703f4301a4";
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WalkerTestSpec spec = new WalkerTestSpec(gatk_args,1,Arrays.asList(expected_md5));
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executeTest("Testing the extended pileup with indel records included on a small chunk of Ovarian dataset with 20 indels (1 D, 19 I)", spec);
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}
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}
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