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Searched defs:referencePath (Results 1 – 25 of 50) sorted by relevance

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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/
H A DReadsSparkSourceUnitTest.java64 public void testGetHeader(final String bam, final String referencePath) { in testGetHeader()
75 private void doTestGetHeader(final String bam, final String referencePath) { in doTestGetHeader()
97 private void doLoadReadsTest(String bam, String referencePath) { in doLoadReadsTest()
124 public void readsSparkSourceTest(String bam, String referencePath) { in readsSparkSourceTest()
129 public void readsSparkSourceTestStrict(String bam, String referencePath) { in readsSparkSourceTestStrict()
134 public void readsSparkSourceTestLenient(String bam, String referencePath) { in readsSparkSourceTestLenient()
139 public void readsSparkSourceTestSilent(String bam, String referencePath) { in readsSparkSourceTestSilent()
144 …lic void shardedReadsSparkSourceTest(String expectedBam, String shardedBam, String referencePath) { in shardedReadsSparkSourceTest()
284 … getSerialReads(final JavaSparkContext ctx, final String bam, final GATKPath referencePath, final … in getSerialReads()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/engine/
H A DReadsDataSourcePool.java18 public ReadsDataSourcePool(final List<Path> readPaths, final Path referencePath) { in ReadsDataSourcePool()
61 private final Path referencePath; field in ReadsDataSourcePool.Factory
63 private Factory(final List<Path> paths, final Path referencePath) { in Factory()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/read/
H A DReadUtilsIntegrationTest.java62 final Path referencePath = referenceFile == null ? null : referenceFile.toPath(); in testCreatePathSAMWriter() local
65 … (outputPath, referencePath, samReader.getFileHeader(), preSorted, createIndex, createMD5)) { in testCreatePathSAMWriter() argument
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/
H A DHaplotypeCallerSpark.java147 final Path referencePath = IOUtils.getPath(reference); in processAssemblyRegions() local
197 final Path referencePath = IOUtils.getPath(referenceArguments.getReferenceFileName()); in assemblyRegionEvaluatorSupplierBroadcast() local
212 final Path referencePath = IOUtils.getPath(reference); in assemblyRegionEvaluatorSupplierBroadcast() local
271 final Path referencePath = IOUtils.getPath(reference); in callVariantsWithHaplotypeCallerAndWriteOutput() local
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/variant/
H A DVcfUtils.java65 final Path referencePath, in updateHeaderContigLines()
97 final Path referencePath) { in makeContigHeaderLines()
/dports/devel/premake5/premake-5.0.0-alpha16-src/modules/vstudio/
H A Dvs2005_csproj_user.lua75 function m.referencePath(prj) function
H A Dvs2005_fsproj_user.lua75 function m.referencePath(prj) function
/dports/games/0ad/0ad-0.0.23b-alpha/build/premake/premake5/modules/vstudio/
H A Dvs2005_csproj_user.lua74 function m.referencePath(prj) function
/dports/databases/hbase/hbase-1.2.1/hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/
H A DStoreFileInfo.java112 Path referencePath = getReferredToFile(p); in StoreFileInfo() local
232 Path referencePath = getReferredToFile(this.getPath()); in open() local
320 Path referencePath = getReferredToFile(this.getPath()); in getReferencedFileStatus() local
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/variant/
H A DVcfUtilsUnitTest.java36 final Path referencePath, in testUpdateContigsReferenceNameOnly()
/dports/www/firefox-esr/firefox-91.8.0/security/nss/lib/freebl/
H A Dgenload.c84 loader_LoadLibInReferenceDir(const char* referencePath, const char* name) in loader_LoadLibInReferenceDir()
/dports/security/ca_root_nss/nss-3.71/nss/lib/freebl/
H A Dgenload.c84 loader_LoadLibInReferenceDir(const char* referencePath, const char* name) in loader_LoadLibInReferenceDir()
/dports/www/firefox/firefox-99.0/security/nss/lib/freebl/
H A Dgenload.c84 loader_LoadLibInReferenceDir(const char* referencePath, const char* name) in loader_LoadLibInReferenceDir()
/dports/lang/spidermonkey60/firefox-60.9.0/security/nss/lib/freebl/
H A Dgenload.c84 loader_LoadLibInReferenceDir(const char* referencePath, const char* name) in loader_LoadLibInReferenceDir()
/dports/www/firefox-legacy/firefox-52.8.0esr/security/nss/lib/freebl/
H A Dgenload.c84 loader_LoadLibInReferenceDir(const char* referencePath, const char* name) in loader_LoadLibInReferenceDir()
/dports/security/nss/nss-3.76.1/nss/lib/freebl/
H A Dgenload.c84 loader_LoadLibInReferenceDir(const char* referencePath, const char* name) in loader_LoadLibInReferenceDir()
/dports/mail/thunderbird/thunderbird-91.8.0/security/nss/lib/freebl/
H A Dgenload.c84 loader_LoadLibInReferenceDir(const char* referencePath, const char* name) in loader_LoadLibInReferenceDir()
/dports/lang/spidermonkey78/firefox-78.9.0/security/nss/lib/freebl/
H A Dgenload.c84 loader_LoadLibInReferenceDir(const char* referencePath, const char* name) in loader_LoadLibInReferenceDir()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/
H A DInsertSizeMetricsCollectorSparkUnitTest.java61 final GATKPath referencePath = referenceName != null ? in test() local
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/engine/spark/datasources/
H A DReferenceFileSparkSource.java30 private transient Path referencePath; field in ReferenceFileSparkSource
/dports/www/firefox-esr/firefox-91.8.0/security/nss/lib/util/
H A Dsecload.c64 loader_LoadLibInReferenceDir(const char* referencePath, const char* name) in loader_LoadLibInReferenceDir()
/dports/security/ca_root_nss/nss-3.71/nss/lib/util/
H A Dsecload.c64 loader_LoadLibInReferenceDir(const char* referencePath, const char* name) in loader_LoadLibInReferenceDir()
/dports/www/firefox/firefox-99.0/security/nss/lib/util/
H A Dsecload.c64 loader_LoadLibInReferenceDir(const char* referencePath, const char* name) in loader_LoadLibInReferenceDir()
/dports/lang/spidermonkey60/firefox-60.9.0/security/nss/lib/util/
H A Dsecload.c64 loader_LoadLibInReferenceDir(const char* referencePath, const char* name) in loader_LoadLibInReferenceDir()
/dports/www/firefox-legacy/firefox-52.8.0esr/security/nss/lib/util/
H A Dsecload.c64 loader_LoadLibInReferenceDir(const char* referencePath, const char* name) in loader_LoadLibInReferenceDir()

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