| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/iterators/ |
| H A D | AllLocusIteratorUnitTest.java | 4 import org.broadinstitute.hellbender.engine.AlignmentContext;
21 final List<AlignmentContext> firstPileups = Arrays.asList( in testIteratorReturnsPileupsForAllLociData()
22 new AlignmentContext(new SimpleInterval("1", 5, 5), in testIteratorReturnsPileupsForAllLociData()
24 new AlignmentContext(new SimpleInterval("1", 15, 15), in testIteratorReturnsPileupsForAllLociData()
26 new AlignmentContext(new SimpleInterval("1", 19, 19), in testIteratorReturnsPileupsForAllLociData()
28 new AlignmentContext(new SimpleInterval("1", 22, 22), in testIteratorReturnsPileupsForAllLociData()
34 final List<AlignmentContext> secondPileups = Arrays.asList( in testIteratorReturnsPileupsForAllLociData()
35 new AlignmentContext(new SimpleInterval("1", 5, 5), in testIteratorReturnsPileupsForAllLociData()
66 AlignmentContext previousPileup = null; in testIteratorReturnsPileupsForAllLoci()
69 for ( final AlignmentContext pileup : returnedPileups ) { in testIteratorReturnsPileupsForAllLoci()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/iterators/ |
| H A D | AllLocusIterator.java | 4 import org.broadinstitute.hellbender.engine.AlignmentContext;
28 public class AllLocusIterator implements Iterator<AlignmentContext> {
29 private final PeekableIterator<AlignmentContext> nestedLocusIterator;
33 private AlignmentContext nextPileup;
62 public AlignmentContext next() { in next()
67 final AlignmentContext toReturn = nextPileup; in next()
72 private AlignmentContext advance() { in advance()
88 final AlignmentContext nextNestedPileup = nestedLocusIterator.peek(); in advance()
89 AlignmentContext toReturn; in advance()
109 private AlignmentContext createEmptyAlignmentContextForPosition(final int position) { in createEmptyAlignmentContextForPosition()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/engine/ |
| H A D | AlignmentContext.java | 18 public final class AlignmentContext implements Locatable, HasGenomeLocation { class
31 public AlignmentContext(final Locatable loc, final ReadPileup basePileup) { in AlignmentContext() method in AlignmentContext
35 …public AlignmentContext(final Locatable loc, final ReadPileup basePileup, final boolean hasPileupB… in AlignmentContext() method in AlignmentContext
86 public AlignmentContext stratify(final ReadOrientation type) { in stratify()
91 …return new AlignmentContext(loc, basePileup.makeFilteredPileup(pe -> !pe.getRead().isReverseStrand… in stratify()
93 …return new AlignmentContext(loc, basePileup.makeFilteredPileup(pe -> pe.getRead().isReverseStrand(… in stratify()
99 public Map<String, AlignmentContext> splitContextBySampleName(final SAMFileHeader header) { in splitContextBySampleName()
118 final Map<String, AlignmentContext> contexts = new LinkedHashMap<>(pileups.size()); in splitContextBySampleName()
124 contexts.put(entry.getKey(), new AlignmentContext(loc, entry.getValue())); in splitContextBySampleName()
129 …public static Map<String, AlignmentContext> splitContextBySampleName(final ReadPileup pileup, fina… in splitContextBySampleName()
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| H A D | LocusWalkerByInterval.java | 47 final Iterator<AlignmentContext> iterator = getAlignmentContextIterator(countedFilter); in traverse()
78 …public final void apply(AlignmentContext alignmentContext, ReferenceContext referenceContext, Feat… in apply()
110 …public abstract void apply(AlignmentContext alignmentContext, ReferenceContext referenceContext, F… in apply()
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| H A D | LocusWalker.java | 157 final Iterator<AlignmentContext> iterator = getAlignmentContextIterator(countedFilter); in traverse()
175 …final Iterator<AlignmentContext> getAlignmentContextIterator(final CountingReadFilter readFilterTo… in getAlignmentContextIterator()
210 …public abstract void apply(AlignmentContext alignmentContext, ReferenceContext referenceContext, F… in apply()
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| H A D | ActivityProfileStateIterator.java | 36 private final Iterator<AlignmentContext> locusIterator;
79 final AlignmentContext pileup = locusIterator.next(); in next()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/engine/ |
| H A D | AlignmentContextUnitTest.java | 51 final AlignmentContext ac = new AlignmentContext(loc, pileup); in test1Sample2Readgroups()
61 Assert.assertSame(ac.stratify(AlignmentContext.ReadOrientation.COMPLETE), ac, "Complete"); in test1Sample2Readgroups()
63 final AlignmentContext acFWD = ac.stratify(AlignmentContext.ReadOrientation.FORWARD); in test1Sample2Readgroups()
67 final AlignmentContext acREV = ac.stratify(AlignmentContext.ReadOrientation.REVERSE); in test1Sample2Readgroups()
68 AlignmentContext emptyAC= new AlignmentContext(loc, new ReadPileup(loc)); in test1Sample2Readgroups()
73 final Map<String, AlignmentContext> bySample = ac.splitContextBySampleName(header); in test1Sample2Readgroups()
76 final AlignmentContext firstAC = bySample.values().iterator().next(); in test1Sample2Readgroups()
80 …final Map<String, AlignmentContext> bySampleAssume1 = ac.splitContextBySampleName("sample1", heade… in test1Sample2Readgroups()
83 final AlignmentContext firstACAssume1 = bySampleAssume1.values().iterator().next(); in test1Sample2Readgroups()
87 …final Map<String, AlignmentContext> stringAlignmentContextMap = AlignmentContext.splitContextBySam… in test1Sample2Readgroups()
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| H A D | LocusWalkerUnitTest.java | 82 …public void apply(AlignmentContext alignmentContext, ReferenceContext referenceContext, FeatureCon…
115 …public void apply(AlignmentContext alignmentContext, ReferenceContext referenceContext, FeatureCon…
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/locusiterator/ |
| H A D | IntervalAlignmentContextIterator.java | 4 import org.broadinstitute.hellbender.engine.AlignmentContext;
21 public class IntervalAlignmentContextIterator implements Iterator<AlignmentContext> {
22 private Iterator<AlignmentContext> alignmentContextIterator;
25 private AlignmentContext currentAlignmentContext;
36 …public IntervalAlignmentContextIterator(Iterator<AlignmentContext> alignmentContextIterator, Inter… in IntervalAlignmentContextIterator()
57 public AlignmentContext next() { in next()
63 AlignmentContext result; in next()
89 private AlignmentContext createEmptyAlignmentContext(final SimpleInterval interval) { in createEmptyAlignmentContext()
90 return new AlignmentContext(interval, new ReadPileup(interval)); in createEmptyAlignmentContext()
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| H A D | LocusIteratorByState.java | 9 import org.broadinstitute.hellbender.engine.AlignmentContext;
45 public final class LocusIteratorByState implements Iterator<AlignmentContext> {
87 private AlignmentContext nextAlignmentContext;
263 public AlignmentContext next() { in next()
268 AlignmentContext currentAlignmentContext = nextAlignmentContext; in next()
287 …public AlignmentContext advanceToLocus(final int position, final boolean stopAtFirstNonEmptySiteAf… in advanceToLocus()
289 final AlignmentContext context = next(); in advanceToLocus()
351 …nextAlignmentContext = new AlignmentContext(location, new ReadPileup(location, allPileupElements)); in lazyLoadNextAlignmentContext()
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| H A D | AlignmentContextIteratorBuilder.java | 8 import org.broadinstitute.hellbender.engine.AlignmentContext;
73 …public Iterator<AlignmentContext> build(final Iterator<GATKRead> readIterator, final SAMFileHeader… in build()
99 …private static Iterator<AlignmentContext> createAlignmentContextIterator(final List<SimpleInterval… in createAlignmentContextIterator()
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| /dports/textproc/fop/fop-2.6/fop-core/src/main/java/org/apache/fop/layoutmgr/inline/ |
| H A D | AlignmentContext.java | 34 public class AlignmentContext implements Constants { class
56 private AlignmentContext parentAlignmentContext;
68 AlignmentContext(int height, in AlignmentContext() method in AlignmentContext
73 AlignmentContext parentAlignmentContext) { in AlignmentContext()
90 AlignmentContext(Font font, in AlignmentContext() method in AlignmentContext
96 AlignmentContext parentAlignmentContext) { in AlignmentContext()
114 private AlignmentContext(int altitude, in AlignmentContext() method in AlignmentContext
122 AlignmentContext parentAlignmentContext) { in AlignmentContext()
177 AlignmentContext(Font font, int lineHeight, WritingMode writingMode) { in AlignmentContext() method in AlignmentContext
344 public AlignmentContext getParentAlignmentContext() { in getParentAlignmentContext()
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| H A D | KnuthInlineBox.java | 33 private AlignmentContext alignmentContext;
46 int width, AlignmentContext alignmentContext, Position pos, boolean auxiliary) { in KnuthInlineBox()
54 public AlignmentContext getAlignmentContext() { in getAlignmentContext()
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| H A D | LeafNodeLayoutManager.java | 64 protected AlignmentContext alignmentContext;
82 protected AlignmentContext alignmentContext;
92 AlignmentContext alignmentContext) { in AreaInfo()
239 protected AlignmentContext makeAlignmentContext(LayoutContext context) { in makeAlignmentContext()
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| H A D | InlineContainerLayoutManager.java | 68 private AlignmentContext alignmentContext;
155 protected AlignmentContext makeAlignmentContext(LayoutContext context) { in makeAlignmentContext()
157 AlignmentContext ac = new AlignmentContext(contentAreaBPD, in makeAlignmentContext()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/engine/spark/ |
| H A D | LocusWalkerContext.java | 3 import org.broadinstitute.hellbender.engine.AlignmentContext;
11 private final AlignmentContext alignmentContext;
15 …public LocusWalkerContext(AlignmentContext alignmentContext, ReferenceContext referenceContext, Fe… in LocusWalkerContext()
21 public AlignmentContext getAlignmentContext() { in getAlignmentContext()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/locusiterator/ |
| H A D | IntervalAlignmentContextIteratorUnitTest.java | 5 import org.broadinstitute.hellbender.engine.AlignmentContext;
56 …final List<AlignmentContext> allAlignmentContexts = getAlignmentContexts(locusIntervals, BAM_FILE_… in testSimple()
84 …final List<AlignmentContext> allAlignmentContexts = getAlignmentContexts(locusIntervals, BAM_FILE_… in testCoveredOnly()
97 …final List<AlignmentContext> allAlignmentContexts = getAlignmentContexts(locusIntervals, BAM_FILE_… in testUnCoveredOnly()
112 …final List<AlignmentContext> allAlignmentContexts = getAlignmentContexts(locusIntervals, BAM_FILE_… in testPileupToNextPileup()
128 …final List<AlignmentContext> allAlignmentContexts = getAlignmentContexts(null, MINI_BAM.getAbsolut… in testNoIntervalsSpecified()
136 …final List<AlignmentContext> allAlignmentContexts = getAlignmentContexts(Collections.<SimpleInterv… in testIntervalIteratorIsEmpty()
140 …private List<AlignmentContext> getAlignmentContexts(final List<SimpleInterval> locusIntervals, fin… in getAlignmentContexts()
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| H A D | LocusIteratorByStateUnitTest.java | 6 import org.broadinstitute.hellbender.engine.AlignmentContext;
82 AlignmentContext context = li.next(); in testUnmappedAndAllIReadsPassThrough()
106 final AlignmentContext context = li.next(); in testAllIReadsPassThrough()
146 final AlignmentContext context = li.next(); in testXandEQOperators()
180 final AlignmentContext context = li.next(); in testIndelsInRegularPileup()
228 final AlignmentContext alignmentContext = li.next(); in testWholeIndelRead()
268 final AlignmentContext alignmentContext = li.next(); in testWholeIndelReadRepresentedTest()
288 final AlignmentContext alignmentContext = li.next(); in testWholeIndelReadRepresentedTest()
410 final AlignmentContext alignmentContext = li.next(); in testLIBS()
669 final AlignmentContext next = li.next(); in testLIBS_NotHoldingTooManyReads()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/ |
| H A D | ArtificialReadPileupTestProvider.java | 5 import org.broadinstitute.hellbender.engine.AlignmentContext;
78 …public Map<String,AlignmentContext> getAlignmentContextFromAlleles(int eventLength, String altBase… in getAlignmentContextFromAlleles()
81 public Map<String,AlignmentContext> getAlignmentContextFromAlleles(final int eventLength, in getAlignmentContextFromAlleles()
105 Map<String,AlignmentContext> contexts = new LinkedHashMap<>(); in getAlignmentContextFromAlleles()
108 …AlignmentContext context = new AlignmentContext(loc, generateRBPForVariant(loc, refAllele, altAlle… in getAlignmentContextFromAlleles()
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| /dports/textproc/fop/fop-2.6/fop-core/src/main/java/org/apache/fop/layoutmgr/ |
| H A D | LayoutContext.java | 26 import org.apache.fop.layoutmgr.inline.AlignmentContext;
108 private AlignmentContext alignmentContext;
464 public void setAlignmentContext(AlignmentContext alignmentContext) { in setAlignmentContext()
469 public AlignmentContext getAlignmentContext() { in getAlignmentContext()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ |
| H A D | PileupReadErrorCorrector.java | 6 import org.broadinstitute.hellbender.engine.AlignmentContext;
41 …final Iterator<AlignmentContext> locusIterator = new LocusIteratorByState(reads.iterator(), Downsa… in correctReads()
46 Utils.stream(locusIterator).map(AlignmentContext::getBasePileup).forEach(pileup -> { in correctReads()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/readorientation/ |
| H A D | CollectF1R2Counts.java | 8 import org.broadinstitute.hellbender.engine.AlignmentContext;
65 …public void apply(final AlignmentContext alignmentContext, final ReferenceContext referenceContext… in apply()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/ |
| H A D | MethylationTypeCaller.java | 90 …public void apply(AlignmentContext alignmentContext, ReferenceContext referenceContext, FeatureCon… in apply()
100 …final ReadPileup forwardBasePileup = alignmentContext.stratify(AlignmentContext.ReadOrientation.FO… in apply()
114 …final ReadPileup reverseBasePileup = alignmentContext.stratify(AlignmentContext.ReadOrientation.RE… in apply()
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| /dports/lang/spidermonkey78/firefox-78.9.0/layout/generic/ |
| H A D | nsIFrameInlines.h | 174 AlignmentContext aAlignmentContext) const { in BaselineBOffset()
180 if (aAlignmentContext == AlignmentContext::Inline) { in BaselineBOffset()
183 if (aAlignmentContext == AlignmentContext::Table) { in BaselineBOffset()
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| /dports/www/firefox-esr/firefox-91.8.0/layout/generic/ |
| H A D | nsIFrameInlines.h | 189 AlignmentContext aAlignmentContext) const { in BaselineBOffset()
195 if (aAlignmentContext == AlignmentContext::Inline) { in BaselineBOffset()
198 if (aAlignmentContext == AlignmentContext::Table) { in BaselineBOffset()
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