| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/ |
| H A D | ReadUtils.java | 920 boolean createOutputBamIndex, in createCommonSAMWriter() argument
928 createOutputBamIndex, in createCommonSAMWriter()
949 boolean createOutputBamIndex, in createCommonSAMWriter() argument
955 if (createOutputBamIndex && header.getSortOrder() != SAMFileHeader.SortOrder.coordinate) { in createCommonSAMWriter()
958 createOutputBamIndex = false; in createCommonSAMWriter()
961 …WriterFactory factory = new SAMFileWriterFactory().setCreateIndex(createOutputBamIndex).setCreateM… in createCommonSAMWriter()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/engine/spark/ |
| H A D | GATKSparkTool.java | 135 …public boolean createOutputBamIndex = ConfigFactory.getInstance().getGATKConfig().createOutputBamI… field in GATKSparkTool
139 …createOutputBamSplittingIndex = ConfigFactory.getInstance().getGATKConfig().createOutputBamIndex();
377 …getRecommendedNumReducers(), shardedPartsDir, createOutputBamIndex, createOutputBamSplittingIndex,… in writeReads()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/config/ |
| H A D | GATKConfig.java | 174 boolean createOutputBamIndex(); in createOutputBamIndex() method
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/ |
| H A D | print_reads_withPG.sam | 12 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --help…
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| H A D | test_no_pair_orientation_info.vcf | 38 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --crea…
39 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --crea…
52 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --crea…
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| H A D | test_no_pair_orientation_info_indels.vcf | 40 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --crea…
41 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --crea…
54 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --crea…
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/engine/ |
| H A D | GATKTool.java | 79 …public boolean createOutputBamIndex = ConfigFactory.getInstance().getGATKConfig().createOutputBamI… field in GATKTool
833 createOutputBamIndex, in createSAMWriter()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/resources/org/broadinstitute/hellbender/utils/config/ |
| H A D | GATKConfig.properties | 85 createOutputBamIndex = true key
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/ |
| H A D | Mutect2.java | 261 …m2Engine = new Mutect2Engine(MTAC, assemblyRegionArgs, createOutputBamIndex, createOutputBamMD5, g… in onTraversalStart()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/walkers/validation/basicshortmutpileup/ |
| H A D | synthetic.challenge.set1.tumor-vs-synthetic.challenge.set1.normal-filtered.vcf | 40 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --crea…
41 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --crea…
54 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --crea…
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| H A D | IS3.snv.indel.sv-vs-G15512.prenormal.sorted.vcf | 18 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --crea…
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ |
| H A D | HaplotypeCaller.java | 259 …hcEngine = new HaplotypeCallerEngine(hcArgs, assemblyRegionArgs, createOutputBamIndex, createOutpu… in onTraversalStart()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/ |
| H A D | expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.noMD.noBQSR.md.bqsr.vcf | 8 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --crea…
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| H A D | expected.MultiSite.reads.pipeline.vcf | 8 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --crea…
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/ |
| H A D | nonRefAD.g.vcf | 15 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --crea…
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| H A D | testNonRefADCorrection.expected.g.vcf | 15 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --crea…
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/walkers/ValidateVariants/ |
| H A D | NA12891.AS.chr20snippet.missingrefblock.g.vcf | 15 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --crea…
16 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --crea…
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| H A D | NA12891.AS.chr20snippet_BAD_INCOMPLETE_REGION.g.vcf | 15 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --crea…
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| H A D | NA12891.AS.chr20snippet.BAD_MISSING_NON_REF.g.vcf | 15 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --crea…
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/FixCallSetSampleOrdering/ |
| H A D | badlySorted1000-batch-size13.vcf | 6 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --crea…
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| H A D | badlySorted1000-batch-size50.vcf | 6 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --crea…
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| H A D | badlysorted1000-batchSize50-readerThreads5-samplesInHeaderAreDifferent-withDuplicateSample.vcf | 6 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --crea…
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| H A D | badlysorted1000-batchSize50-readerThreads5-samplesInHeaderAreDifferent.vcf | 6 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --crea…
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/ |
| H A D | NA12878.ob_filtered.vcf | 54 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --crea…
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/engine/ |
| H A D | CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10000000-10000020.with.unmapped.queryname.samtools.sam | 23 …rogressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --crea…
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