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Searched refs:setIsDuplicate (Results 1 – 7 of 7) sorted by relevance

/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/transforms/markduplicates/
H A DMarkDuplicatesSpark.java228 .peek(read -> read.setIsDuplicate(false)) in mark()
235 read.setIsDuplicate(true); in mark()
240 read.setIsDuplicate(false); in mark()
250 read.setIsDuplicate(false); in mark()
254 read.setIsDuplicate(true); in mark()
259 read.setIsDuplicate(false); in mark()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/
H A DUnmarkDuplicates.java89 read.setIsDuplicate(false); in apply()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/
H A DGATKRead.java745 void setIsDuplicate( final boolean isDuplicate );
H A DSAMRecordToGATKReadAdapter.java600 public void setIsDuplicate( final boolean isDuplicate ) { in setIsDuplicate() method in SAMRecordToGATKReadAdapter
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/read/
H A DGATKReadAdaptersUnitTest.java800 read.setIsDuplicate(true); in testGetAndSetSimpleFlags()
803 read.setIsDuplicate(false); in testGetAndSetSimpleFlags()
1221 read.setIsDuplicate(true); in testSAMStringSimpleFlags()
1225 read.setIsDuplicate(false); in testSAMStringSimpleFlags()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/
H A DRevertSamSpark.java534 reads = reads.map(r -> {r.setIsDuplicate(false); return r;});
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/engine/filters/
H A DReadFilterLibraryUnitTest.java147 read.setIsDuplicate(true); in failsNOT_DUPLICATE()