Searched refs:fastaRef (Results 1 – 13 of 13) sorted by relevance
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/ |
| H A D | ReferenceTwoBitSparkSourceUnitTest.java | 19 ReferenceSparkSource fastaRef = new ReferenceFileSparkSource(new GATKPath(fastaRefURL)); in goodIntervals() local
22 {fastaRef, twoBitRef, "20:2-10"}, in goodIntervals()
23 {fastaRef, twoBitRef, "20:4-5"}, in goodIntervals()
24 {fastaRef, twoBitRef, "20:4,000-5,000"}, in goodIntervals()
25 …{fastaRef, twoBitRef, "20:4,0,0,0-5,0,0,0"}, //this is OK too, we just remove commas wherever they… in goodIntervals()
30 …public void testIntervalConversion( ReferenceSparkSource fastaRef, ReferenceSparkSource twoBitRef,… in testIntervalConversion() argument
32 ReferenceBases expected = fastaRef.getReferenceBases(interval); in testIntervalConversion()
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| /dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/ |
| H A D | vcfcheck.cpp | 29 string fastaRef; in main() local
73 fastaRef = optarg; in main()
109 if (fastaRef.empty()) { in main()
115 ref.open(fastaRef); in main()
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| H A D | vcfprimers.cpp | 35 string fastaRef; in main() local
75 fastaRef = optarg; in main()
102 if (fastaRef.empty()) { in main()
108 ref.open(fastaRef); in main()
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| H A D | vcfentropy.cpp | 27 string fastaRef; in main() local
67 fastaRef = optarg; in main()
94 if (fastaRef.empty()) { in main()
100 ref.open(fastaRef); in main()
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| H A D | vcfevenregions.cpp | 43 string fastaRef; in main() local
93 fastaRef = optarg; in main()
132 if (fastaRef.empty()) { in main()
138 ref.open(fastaRef); in main()
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| /dports/biology/freebayes/freebayes-1.3.5/vcflib/src/ |
| H A D | vcfcheck.cpp | 29 string fastaRef; in main() local
73 fastaRef = optarg; in main()
109 if (fastaRef.empty()) { in main()
115 ref.open(fastaRef); in main()
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| H A D | vcfprimers.cpp | 35 string fastaRef; in main() local
75 fastaRef = optarg; in main()
102 if (fastaRef.empty()) { in main()
108 ref.open(fastaRef); in main()
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| H A D | vcfentropy.cpp | 27 string fastaRef; in main() local
67 fastaRef = optarg; in main()
94 if (fastaRef.empty()) { in main()
100 ref.open(fastaRef); in main()
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| H A D | vcfevenregions.cpp | 43 string fastaRef; in main() local
93 fastaRef = optarg; in main()
132 if (fastaRef.empty()) { in main()
138 ref.open(fastaRef); in main()
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| /dports/biology/vcflib/vcflib-1.0.2/src/ |
| H A D | vcfcheck.cpp | 38 string fastaRef; in main() local
82 fastaRef = optarg; in main()
118 if (fastaRef.empty()) { in main()
124 ref.open(fastaRef); in main()
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| H A D | vcfprimers.cpp | 46 string fastaRef; in main() local
86 fastaRef = optarg; in main()
113 if (fastaRef.empty()) { in main()
119 ref.open(fastaRef); in main()
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| H A D | vcfentropy.cpp | 39 string fastaRef; in main() local
79 fastaRef = optarg; in main()
106 if (fastaRef.empty()) { in main()
112 ref.open(fastaRef); in main()
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| H A D | vcfevenregions.cpp | 52 string fastaRef; in main() local
102 fastaRef = optarg; in main()
141 if (fastaRef.empty()) { in main()
147 ref.open(fastaRef); in main()
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