| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/ |
| H A D | ReadsSparkSourceUnitTest.java | 64 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()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/engine/ |
| H A D | ReadsDataSourcePool.java | 18 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()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/read/ |
| H A D | ReadUtilsIntegrationTest.java | 62 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 D | HaplotypeCallerSpark.java | 147 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 D | VcfUtils.java | 65 final Path referencePath, in updateHeaderContigLines()
97 final Path referencePath) { in makeContigHeaderLines()
|
| /dports/devel/premake5/premake-5.0.0-alpha16-src/modules/vstudio/ |
| H A D | vs2005_csproj_user.lua | 75 function m.referencePath(prj) function
|
| H A D | vs2005_fsproj_user.lua | 75 function m.referencePath(prj) function
|
| /dports/games/0ad/0ad-0.0.23b-alpha/build/premake/premake5/modules/vstudio/ |
| H A D | vs2005_csproj_user.lua | 74 function m.referencePath(prj) function
|
| /dports/databases/hbase/hbase-1.2.1/hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/ |
| H A D | StoreFileInfo.java | 112 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 D | VcfUtilsUnitTest.java | 36 final Path referencePath, in testUpdateContigsReferenceNameOnly()
|
| /dports/www/firefox-esr/firefox-91.8.0/security/nss/lib/freebl/ |
| H A D | genload.c | 84 loader_LoadLibInReferenceDir(const char* referencePath, const char* name) in loader_LoadLibInReferenceDir()
|
| /dports/security/ca_root_nss/nss-3.71/nss/lib/freebl/ |
| H A D | genload.c | 84 loader_LoadLibInReferenceDir(const char* referencePath, const char* name) in loader_LoadLibInReferenceDir()
|
| /dports/www/firefox/firefox-99.0/security/nss/lib/freebl/ |
| H A D | genload.c | 84 loader_LoadLibInReferenceDir(const char* referencePath, const char* name) in loader_LoadLibInReferenceDir()
|
| /dports/lang/spidermonkey60/firefox-60.9.0/security/nss/lib/freebl/ |
| H A D | genload.c | 84 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 D | genload.c | 84 loader_LoadLibInReferenceDir(const char* referencePath, const char* name) in loader_LoadLibInReferenceDir()
|
| /dports/security/nss/nss-3.76.1/nss/lib/freebl/ |
| H A D | genload.c | 84 loader_LoadLibInReferenceDir(const char* referencePath, const char* name) in loader_LoadLibInReferenceDir()
|
| /dports/mail/thunderbird/thunderbird-91.8.0/security/nss/lib/freebl/ |
| H A D | genload.c | 84 loader_LoadLibInReferenceDir(const char* referencePath, const char* name) in loader_LoadLibInReferenceDir()
|
| /dports/lang/spidermonkey78/firefox-78.9.0/security/nss/lib/freebl/ |
| H A D | genload.c | 84 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 D | InsertSizeMetricsCollectorSparkUnitTest.java | 61 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 D | ReferenceFileSparkSource.java | 30 private transient Path referencePath; field in ReferenceFileSparkSource
|
| /dports/www/firefox-esr/firefox-91.8.0/security/nss/lib/util/ |
| H A D | secload.c | 64 loader_LoadLibInReferenceDir(const char* referencePath, const char* name) in loader_LoadLibInReferenceDir()
|
| /dports/security/ca_root_nss/nss-3.71/nss/lib/util/ |
| H A D | secload.c | 64 loader_LoadLibInReferenceDir(const char* referencePath, const char* name) in loader_LoadLibInReferenceDir()
|
| /dports/www/firefox/firefox-99.0/security/nss/lib/util/ |
| H A D | secload.c | 64 loader_LoadLibInReferenceDir(const char* referencePath, const char* name) in loader_LoadLibInReferenceDir()
|
| /dports/lang/spidermonkey60/firefox-60.9.0/security/nss/lib/util/ |
| H A D | secload.c | 64 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 D | secload.c | 64 loader_LoadLibInReferenceDir(const char* referencePath, const char* name) in loader_LoadLibInReferenceDir()
|