Searched refs:indexImageFile (Results 1 – 7 of 7) sorted by relevance
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/bwa/ |
| H A D | BwaMemIndexCache.java | 21 public static synchronized BwaMemIndex getInstance( final String indexImageFile ) { in getInstance() argument
22 Utils.nonNull(indexImageFile, "the index image file name provided cannot be null"); in getInstance()
23 if (!instances.containsKey(indexImageFile)) { in getInstance()
24 instances.put(indexImageFile, new BwaMemIndex(indexImageFile)); in getInstance()
26 return instances.get(indexImageFile); in getInstance()
40 public static synchronized void closeInstance(final String indexImageFile) { in closeInstance() argument
41 Utils.nonNull(indexImageFile, "the input image file cannot be null"); in closeInstance()
42 if (instances.containsKey(indexImageFile)) { in closeInstance()
43 instances.get(indexImageFile).close(); in closeInstance()
44 instances.remove(indexImageFile); in closeInstance()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/bwa/ |
| H A D | BwaArgumentCollection.java | 28 public String indexImageFile; field in BwaArgumentCollection
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| H A D | BwaSpark.java | 66 …aSparkEngine(ctx, referenceArguments.getReferenceFileName(), bwaArgs.indexImageFile, getHeaderForR… in runTool() argument
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/ |
| H A D | BwaAndMarkDuplicatesPipelineSpark.java | 66 …aSparkEngine(ctx, referenceArguments.getReferenceFileName(), bwaArgs.indexImageFile, getHeaderForR… in runTool() argument
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| H A D | ReadsPipelineSpark.java | 174 …aSparkEngine(ctx, referenceArguments.getReferenceFileName(), bwaArgs.indexImageFile, getHeaderForR… in runTool()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/pathseq/ |
| H A D | PSFilter.java | 280 if (filterArgs.indexImageFile != null) {
281 reads = doBwaFilter(reads, filterArgs.indexImageFile, filterArgs.minSeedLength,
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| H A D | PSFilterArgumentCollection.java | 191 public String indexImageFile = null; field in PSFilterArgumentCollection
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