| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/fragments/ |
| H A D | FragmentUtilsUnitTest.java | 69 Assert.assertEquals(read1.getBaseQualities()[i], HIGH_QUALITY); in testAdjustingTwoReads()
79 Assert.assertEquals(read2.getBaseQualities()[i], HIGH_QUALITY); in testAdjustingTwoReads()
115 Assert.assertEquals(read1.getBaseQualities()[i], HIGH_QUALITY); in testAdjustingTwoReadsWithSoftClipping()
125 Assert.assertEquals(read2.getBaseQualities()[i], HIGH_QUALITY); in testAdjustingTwoReadsWithSoftClipping()
163 Assert.assertEquals(read1.getBaseQualities()[i], HIGH_QUALITY); in testAdjustingTwoReadsWithSoftClippingOverlappingEachother()
171 Assert.assertEquals(read1.getBaseQualities()[i], HIGH_QUALITY); in testAdjustingTwoReadsWithSoftClippingOverlappingEachother()
177 Assert.assertEquals(read2.getBaseQualities()[i], HIGH_QUALITY); in testAdjustingTwoReadsWithSoftClippingOverlappingEachother()
212 Assert.assertEquals(read1.getBaseQualities(), read1Expected); in testLeadingIndelBehaviorForOverlappingReads()
213 Assert.assertEquals(read2.getBaseQualities(), read2Expected); in testLeadingIndelBehaviorForOverlappingReads()
242 Assert.assertEquals(read1.getBaseQualities(), read1Expected); in testIndelBehaviorForOverlappingReads()
[all …]
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/htsjdk/samtools/ |
| H A D | SAMRecordSparkCodec.java | 110 if (alignment.getReadLength() != alignment.getBaseQualities().length && in encode()
111 alignment.getBaseQualities().length != 0) { in encode()
114 "; quals length: " + alignment.getBaseQualities().length); in encode()
124 byte[] qualities = alignment.getBaseQualities(); in encode()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/ |
| H A D | GATKRead.java | 400 byte[] getBaseQualities();
414 return getBaseQualities(); in getBaseQualitiesNoCopy()
423 return getBaseQualities().length; in getBaseQualityCount()
436 return getBaseQualities()[i]; in getBaseQuality()
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| H A D | SAMRecordToGATKReadAdapter.java | 287 public byte[] getBaseQualities() { in getBaseQualities() method in SAMRecordToGATKReadAdapter
288 final byte[] baseQualities = samRecord.getBaseQualities(); in getBaseQualities()
296 final byte[] baseQualities = samRecord.getBaseQualities(); in getBaseQualitiesNoCopy()
302 final byte[] baseQualities = samRecord.getBaseQualities(); in getBaseQualityCount()
310 final byte[] baseQualities = samRecord.getBaseQualities(); in getBaseQuality()
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| H A D | ReadUtils.java | 124 if ( Arrays.equals(SAMRecord.NULL_QUALS, read.getBaseQualities()) ) { in getBaseQualityString()
127 return SAMUtils.phredToFastq(read.getBaseQualities()); in getBaseQualityString()
862 public static byte[] getBaseQualities( final GATKRead read, final EventType errorModel ) { in getBaseQualities() method in ReadUtils
865 return read.getBaseQualities(); in getBaseQualities()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/transformers/ |
| H A D | BaseQualityClipReadTransformer.java | 71 final byte[] quals = read.getBaseQualities(); in clipReadRightEnd()
83 final byte[] quals = read.getBaseQualities(); in clipReadLeftEnd()
|
| H A D | MisencodedBaseQualityReadTransformer.java | 18 final byte[] quals = read.getBaseQualities(); in apply()
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| H A D | BQSRReadTransformer.java | 139 read.setAttribute(SAMTag.OQ.name(), SAMUtils.phredToFastq(read.getBaseQualities())); in apply()
162 final byte[] quals = read.getBaseQualities(); in apply()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/metrics/ |
| H A D | QualityYieldMetrics.java | 79 tmp = read.getBaseQualities(); in addRead()
83 quals = read.getBaseQualities(); in addRead()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/baq/ |
| H A D | BAQ.java | 387 final byte[] baseQualities = read.getBaseQualities();
426 final byte[] rawQuals = read.getBaseQualities();
452 byte rawQual = read.getBaseQualities()[offset];
477 this(read.getBaseQualities(), read.getBases(), ref);
584 …BAQCalculationResult baqResult = calcBAQFromHMM(ref, read.getBases(), read.getBaseQualities(), que…
641 …byte[] BAQQuals = read.getBaseQualities(); // in general we are overwriting quals, so just ge…
655 …case OVERWRITE_QUALS: System.arraycopy(hmmResult.bq, 0, read.getBaseQualities(), 0, hmmResult.bq.l…
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/validation/ |
| H A D | CompareBaseQualities.java | 156 finalMatrix.add(read1.getBaseQualities(), read2.getBaseQualities()); in doWork()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/fragments/ |
| H A D | FragmentUtils.java | 68 final byte[] firstReadQuals = firstRead.getBaseQualities(); in adjustQualsOfOverlappingPairedFragments()
70 final byte[] secondReadQuals = secondRead.getBaseQualities(); in adjustQualsOfOverlappingPairedFragments()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/mergealignment/ |
| H A D | MultiHitAlignedReadIterator.java | 171 … System.arraycopy(rec.getBaseQualities(), 0, quals, startHardClip, rec.getBaseQualities().length); in replaceHardWithSoftClips()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/clipping/ |
| H A D | ClippingOp.java | 108 …final byte[] newQuals = readCopied.getBaseQualities(); //this makes a copy so we can modify in pla… in applyWriteQ0s()
202 System.arraycopy(read.getBaseQualities(), copyStart, newQuals, 0, newLength); in applyHardClipBases()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/read/ |
| H A D | ArtificialReadUtilsUnitTest.java | 110 Assert.assertEquals(unmappedRead.getBaseQualities(), new byte[]{30}); in testCreateArtificialUnmappedRead()
122 Assert.assertEquals(unmappedRead.getBaseQualities(), new byte[]{30}); in testCreateArtificialUnmappedReadWithAssignedPosition()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/testUtils/java/org/broadinstitute/hellbender/testutils/ |
| H A D | SamAssertionUtils.java | 309 if (!Arrays.equals(actualRead.getBaseQualities(), expectedRead.getBaseQualities())){ in readsEqualAllowAddingAttributes()
310 …e + " (" + Arrays.toString(actualRead.getBaseQualities()) + " vs " + Arrays.toString(expectedRead.… in readsEqualAllowAddingAttributes()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/ |
| H A D | ReadClassifier.java | 91 isHighQualityRegion(read.getBaseQualities(), clipStart); in hasInitialSoftClip()
104 … isHighQualityRegion(read.getBaseQualities(), read.getLength() - lastEle.getLength()); in hasFinalSoftClip()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/markduplicates/ |
| H A D | MarkDuplicatesScoringStrategy.java | 51 for ( final byte b : read.getBaseQualities() ) { in sumOfBaseQualities()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/transformers/ |
| H A D | BaseQualityClipReadTransformerTest.java | 49 Assert.assertEquals(readOut.getBaseQualities(),SAMUtils.fastqToPhred(qualsOut)); in testApply()
|
| H A D | MisencodedBaseQualityReadTransformerUnitTest.java | 48 Assert.assertEquals(fixedQuals, fixedRead.getBaseQualities()); in testFixBadQuals()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/ |
| H A D | RevertBaseQualityScoresIntegrationTest.java | 35 final byte[] baseQualities = read.getBaseQualities(); in hasOriginalQualScores()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/recalibration/ |
| H A D | ReadRecalibrationInfo.java | 41 this.baseQuals = read.getBaseQualities(); in ReadRecalibrationInfo()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/pathseq/ |
| H A D | PSBwaAligner.java | 42 … read.getBases(), read.getBaseQualities(), read.getReadGroup(), alignment, refNames, in applyAlignments()
|
| H A D | PSFilter.java | 81 newRead.setBaseQualities(read.getBaseQualities()); in clearReadAlignment()
84 SequenceUtil.reverseQualities(newRead.getBaseQualities()); in clearReadAlignment()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/clipping/ |
| H A D | ReadClipperUnitTest.java | 257 final byte[] quals = read.getBaseQualities(); in assertNoLowQualBases()
452 Assert.assertEquals(clippedRead.getBaseQualities().length, 0); in testHardClipSoftClippedBasesResultsInEmptyReadDontSetNegativeStartPosition()
470 Assert.assertEquals(clippedRead.getBaseQualities().length, 0); in testRevertSoftClippedBasesDoesntExplodeOnCompletelyClippedRead()
|