| /dports/java/eclipse/eclipse.platform.releng.aggregator-R4_16/eclipse.jdt.core/org.eclipse.jdt.core.tests.model/workspace/JavaSearch15/src/g3/t/ref/ |
| H A D | R4.java | 8 import g3.t.def.NGS;
15 public NGS.Generic<NGM.Generic<?, ?, ?>> sgsm_wld;
16 …public NGS.Generic<NGM.Generic<NGM.Generic<?, ?, ?>,NGM.Generic<?, ?, ?>,NGM.Generic<?, ?, ?>>> sg…
17 public NGS.Generic<NGM.Generic<Object, Exception, RuntimeException>> sgsm_obj;
18 public NGM.Generic<NGS.Generic<?>, NGS.Generic<?>, NGS.Generic<?>> sgms_wld;
19 …public NGM.Generic<NGS.Generic<?>, NGS.Generic<NGS.Generic<?>>, NGS.Generic<NGS.Generic<NGS.Generi…
20 …public NGM.Generic<NGS.Generic<Object>, NGS.Generic<? extends Throwable>, NGS.Generic<? super Runt…
22 public g3.t.def.NGS.Generic<g3.t.def.NGM.Generic<?, ?, ?>> qgsm_wld;
25 …public g3.t.def.NGM.Generic<g3.t.def.NGS.Generic<?>, g3.t.def.NGS.Generic<?>, g3.t.def.NGS.Generic…
26 ….Generic<g3.t.def.NGS.Generic<?>, g3.t.def.NGS.Generic<g3.t.def.NGS.Generic<?>>, g3.t.def.NGS.Gene…
[all …]
|
| /dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-python/ngs/ |
| H A D | Alignment.py | 28 from . import NGS
63 return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetAlignmentId)
69 return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetReferenceSpec)
75 return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetReferenceBases)
81 return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetReadGroup)
84 return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetReadId)
87 return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetClippedFragmentBases)
99 return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetAlignedFragmentBases)
187 return bool(getNGSValue(self, NGS.lib_manager.PY_NGS_AlignmentHasMate, c_int))
190 return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetMateAlignmentId)
[all …]
|
| H A D | LibChecker.py | 32 from . import NGS
40 NGS.lib_manager.c_lib_engine = load_library(libname_engine, do_download=False, silent=True)
41 NGS.lib_manager.c_lib_sdk = load_library(libname_sdk, do_download=False, silent=True)
45 if NGS.lib_manager.c_lib_engine is None:
49 …NGS.lib_manager._bind(NGS.lib_manager.c_lib_engine, "PY_NGS_Engine_GetVersion", [POINTER(c_char_p)…
51 NGS.lib_manager.setattr("PY_NGS_Engine_GetVersion", None)
53 … if version_tuple( NGS.getVersion_impl() ) < get_library_version_tuple_remote(libname_engine):
56 if NGS.lib_manager.c_lib_sdk is None:
62 …NGS.lib_manager._bind(NGS.lib_manager.c_lib_sdk, "PY_NGS_RawStringRelease", [c_void_p, POINTER(c_v…
64 NGS.lib_manager.setattr("PY_NGS_PackageGetPackageVersion", None)
[all …]
|
| H A D | PileupEvent.py | 27 from . import NGS
44 return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetMappingQuality, c_int32)
50 return getNGSString(self, NGS.lib_manager.PY_NGS_PileupEventGetAlignmentId)
53 return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetAlignmentPosition, c_int64)
59 … return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetFirstAlignmentPosition, c_int64)
65 … return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetLastAlignmentPosition, c_int64)
96 return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetEventType, c_uint32)
116 return getNGSString(self, NGS.lib_manager.PY_NGS_PileupEventGetInsertionBases)
122 return getNGSString(self, NGS.lib_manager.PY_NGS_PileupEventGetInsertionQualities)
128 return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetEventRepeatCount, c_uint32)
[all …]
|
| H A D | __init__.py | 35 class NGS: class
40 NGS.lib_manager.initialize_ngs_bindings()
51 if NGS.lib_manager.PY_NGS_Engine_GetVersion is None:
59 res = NGS.lib_manager.PY_NGS_Engine_GetVersion(byref(ret), str_err, len(str_err))
72 NGS.lib_manager.initialize_ngs_bindings()
73 return NGS.getVersion_impl()
83 NGS.lib_manager.initialize_ngs_bindings()
90 NGS.lib_manager.initialize_ngs_bindings()
95 … res = NGS.lib_manager.PY_NGS_Engine_IsValid(spec.encode(), byref(ret), str_err, len(str_err))
104 NGS.lib_manager.initialize_ngs_bindings()
[all …]
|
| H A D | Reference.py | 28 from . import NGS
44 return getNGSString(self, NGS.lib_manager.PY_NGS_ReferenceGetCommonName)
50 return getNGSString(self, NGS.lib_manager.PY_NGS_ReferenceGetCanonicalName)
53 return bool(getNGSValue(self, NGS.lib_manager.PY_NGS_ReferenceGetIsCircular, c_int))
56 return bool(getNGSValue(self, NGS.lib_manager.PY_NGS_ReferenceGetIsLocal, c_int))
59 return getNGSValue(self, NGS.lib_manager.PY_NGS_ReferenceGetLength, c_uint64)
71 …res = NGS.lib_manager.PY_NGS_ReferenceGetReferenceBases(self.ref, offset, length, byref(ngs_str_re…
109 …res = NGS.lib_manager.PY_NGS_ReferenceGetAlignment(self.ref, alignmentId.encode("UTF-8"), byref(re…
122 …res = NGS.lib_manager.PY_NGS_ReferenceGetAlignments(self.ref, categories, byref(ret.ref), byref(ng…
172 …res = NGS.lib_manager.PY_NGS_ReferenceGetPileups(self.ref, categories, byref(ret.ref), byref(ngs_s…
[all …]
|
| H A D | ReadCollection.py | 29 from . import NGS
70 return getNGSString(self, NGS.lib_manager.PY_NGS_ReadCollectionGetName)
84 …ret.ref = getNGSValue(self, NGS.lib_manager.PY_NGS_ReadCollectionGetReadGroups, c_void_p) # TODO: …
96 …res = NGS.lib_manager.PY_NGS_ReadCollectionHasReadGroup(self.ref, spec.encode("UTF-8"), byref(ret)…
131 …ret.ref = getNGSValue(self, NGS.lib_manager.PY_NGS_ReadCollectionGetReferences, c_void_p) # TODO: …
143 …res = NGS.lib_manager.PY_NGS_ReadCollectionHasReference(self.ref, spec.encode("UTF-8"), byref(ret)…
185 …res = NGS.lib_manager.PY_NGS_ReadCollectionGetAlignments(self.ref, categories, byref(ret.ref), byr…
198 …res = NGS.lib_manager.PY_NGS_ReadCollectionGetAlignmentCount(self.ref, categories, byref(ret), byr…
245 …res = NGS.lib_manager.PY_NGS_ReadCollectionGetReads(self.ref, categories, byref(ret.ref), byref(ng…
258 …res = NGS.lib_manager.PY_NGS_ReadCollectionGetReadCount(self.ref, categories, byref(ret), byref(ng…
[all …]
|
| /dports/biology/ncbi-vdb/ngs-2.11.0/ngs-python/ngs/ |
| H A D | Alignment.py | 28 from . import NGS
63 return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetAlignmentId)
69 return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetReferenceSpec)
75 return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetReferenceBases)
81 return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetReadGroup)
84 return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetReadId)
87 return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetClippedFragmentBases)
99 return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetAlignedFragmentBases)
187 return bool(getNGSValue(self, NGS.lib_manager.PY_NGS_AlignmentHasMate, c_int))
190 return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetMateAlignmentId)
[all …]
|
| H A D | LibChecker.py | 32 from . import NGS
40 NGS.lib_manager.c_lib_engine = load_library(libname_engine, do_download=False, silent=True)
41 NGS.lib_manager.c_lib_sdk = load_library(libname_sdk, do_download=False, silent=True)
45 if NGS.lib_manager.c_lib_engine is None:
49 …NGS.lib_manager._bind(NGS.lib_manager.c_lib_engine, "PY_NGS_Engine_GetVersion", [POINTER(c_char_p)…
51 NGS.lib_manager.setattr("PY_NGS_Engine_GetVersion", None)
53 … if version_tuple( NGS.getVersion_impl() ) < get_library_version_tuple_remote(libname_engine):
56 if NGS.lib_manager.c_lib_sdk is None:
62 …NGS.lib_manager._bind(NGS.lib_manager.c_lib_sdk, "PY_NGS_RawStringRelease", [c_void_p, POINTER(c_v…
64 NGS.lib_manager.setattr("PY_NGS_PackageGetPackageVersion", None)
[all …]
|
| H A D | PileupEvent.py | 27 from . import NGS
44 return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetMappingQuality, c_int32)
50 return getNGSString(self, NGS.lib_manager.PY_NGS_PileupEventGetAlignmentId)
53 return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetAlignmentPosition, c_int64)
59 … return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetFirstAlignmentPosition, c_int64)
65 … return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetLastAlignmentPosition, c_int64)
96 return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetEventType, c_uint32)
116 return getNGSString(self, NGS.lib_manager.PY_NGS_PileupEventGetInsertionBases)
122 return getNGSString(self, NGS.lib_manager.PY_NGS_PileupEventGetInsertionQualities)
128 return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetEventRepeatCount, c_uint32)
[all …]
|
| H A D | __init__.py | 35 class NGS: class
40 NGS.lib_manager.initialize_ngs_bindings()
51 if NGS.lib_manager.PY_NGS_Engine_GetVersion is None:
59 res = NGS.lib_manager.PY_NGS_Engine_GetVersion(byref(ret), str_err, len(str_err))
72 NGS.lib_manager.initialize_ngs_bindings()
73 return NGS.getVersion_impl()
83 NGS.lib_manager.initialize_ngs_bindings()
90 NGS.lib_manager.initialize_ngs_bindings()
95 … res = NGS.lib_manager.PY_NGS_Engine_IsValid(spec.encode(), byref(ret), str_err, len(str_err))
104 NGS.lib_manager.initialize_ngs_bindings()
[all …]
|
| H A D | Reference.py | 28 from . import NGS
44 return getNGSString(self, NGS.lib_manager.PY_NGS_ReferenceGetCommonName)
50 return getNGSString(self, NGS.lib_manager.PY_NGS_ReferenceGetCanonicalName)
53 return bool(getNGSValue(self, NGS.lib_manager.PY_NGS_ReferenceGetIsCircular, c_int))
56 return bool(getNGSValue(self, NGS.lib_manager.PY_NGS_ReferenceGetIsLocal, c_int))
59 return getNGSValue(self, NGS.lib_manager.PY_NGS_ReferenceGetLength, c_uint64)
71 …res = NGS.lib_manager.PY_NGS_ReferenceGetReferenceBases(self.ref, offset, length, byref(ngs_str_re…
109 …res = NGS.lib_manager.PY_NGS_ReferenceGetAlignment(self.ref, alignmentId.encode("UTF-8"), byref(re…
122 …res = NGS.lib_manager.PY_NGS_ReferenceGetAlignments(self.ref, categories, byref(ret.ref), byref(ng…
172 …res = NGS.lib_manager.PY_NGS_ReferenceGetPileups(self.ref, categories, byref(ret.ref), byref(ngs_s…
[all …]
|
| H A D | ReadCollection.py | 29 from . import NGS
70 return getNGSString(self, NGS.lib_manager.PY_NGS_ReadCollectionGetName)
84 …ret.ref = getNGSValue(self, NGS.lib_manager.PY_NGS_ReadCollectionGetReadGroups, c_void_p) # TODO: …
96 …res = NGS.lib_manager.PY_NGS_ReadCollectionHasReadGroup(self.ref, spec.encode("UTF-8"), byref(ret)…
131 …ret.ref = getNGSValue(self, NGS.lib_manager.PY_NGS_ReadCollectionGetReferences, c_void_p) # TODO: …
143 …res = NGS.lib_manager.PY_NGS_ReadCollectionHasReference(self.ref, spec.encode("UTF-8"), byref(ret)…
185 …res = NGS.lib_manager.PY_NGS_ReadCollectionGetAlignments(self.ref, categories, byref(ret.ref), byr…
198 …res = NGS.lib_manager.PY_NGS_ReadCollectionGetAlignmentCount(self.ref, categories, byref(ret), byr…
245 …res = NGS.lib_manager.PY_NGS_ReadCollectionGetReads(self.ref, categories, byref(ret.ref), byref(ng…
258 …res = NGS.lib_manager.PY_NGS_ReadCollectionGetReadCount(self.ref, categories, byref(ret), byref(ng…
[all …]
|
| /dports/biology/ngs-sdk/ngs-2.11.1/ngs-python/ngs/ |
| H A D | Alignment.py | 28 from . import NGS
63 return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetAlignmentId)
69 return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetReferenceSpec)
75 return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetReferenceBases)
81 return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetReadGroup)
84 return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetReadId)
87 return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetClippedFragmentBases)
99 return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetAlignedFragmentBases)
187 return bool(getNGSValue(self, NGS.lib_manager.PY_NGS_AlignmentHasMate, c_int))
190 return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetMateAlignmentId)
[all …]
|
| H A D | LibChecker.py | 32 from . import NGS
40 NGS.lib_manager.c_lib_engine = load_library(libname_engine, do_download=False, silent=True)
41 NGS.lib_manager.c_lib_sdk = load_library(libname_sdk, do_download=False, silent=True)
45 if NGS.lib_manager.c_lib_engine is None:
49 …NGS.lib_manager._bind(NGS.lib_manager.c_lib_engine, "PY_NGS_Engine_GetVersion", [POINTER(c_char_p)…
51 NGS.lib_manager.setattr("PY_NGS_Engine_GetVersion", None)
53 … if version_tuple( NGS.getVersion_impl() ) < get_library_version_tuple_remote(libname_engine):
56 if NGS.lib_manager.c_lib_sdk is None:
62 …NGS.lib_manager._bind(NGS.lib_manager.c_lib_sdk, "PY_NGS_RawStringRelease", [c_void_p, POINTER(c_v…
64 NGS.lib_manager.setattr("PY_NGS_PackageGetPackageVersion", None)
[all …]
|
| H A D | PileupEvent.py | 27 from . import NGS
44 return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetMappingQuality, c_int32)
50 return getNGSString(self, NGS.lib_manager.PY_NGS_PileupEventGetAlignmentId)
53 return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetAlignmentPosition, c_int64)
59 … return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetFirstAlignmentPosition, c_int64)
65 … return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetLastAlignmentPosition, c_int64)
96 return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetEventType, c_uint32)
116 return getNGSString(self, NGS.lib_manager.PY_NGS_PileupEventGetInsertionBases)
122 return getNGSString(self, NGS.lib_manager.PY_NGS_PileupEventGetInsertionQualities)
128 return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetEventRepeatCount, c_uint32)
[all …]
|
| H A D | __init__.py | 35 class NGS: class
40 NGS.lib_manager.initialize_ngs_bindings()
51 if NGS.lib_manager.PY_NGS_Engine_GetVersion is None:
59 res = NGS.lib_manager.PY_NGS_Engine_GetVersion(byref(ret), str_err, len(str_err))
72 NGS.lib_manager.initialize_ngs_bindings()
73 return NGS.getVersion_impl()
83 NGS.lib_manager.initialize_ngs_bindings()
90 NGS.lib_manager.initialize_ngs_bindings()
95 … res = NGS.lib_manager.PY_NGS_Engine_IsValid(spec.encode(), byref(ret), str_err, len(str_err))
104 NGS.lib_manager.initialize_ngs_bindings()
[all …]
|
| H A D | Reference.py | 28 from . import NGS
44 return getNGSString(self, NGS.lib_manager.PY_NGS_ReferenceGetCommonName)
50 return getNGSString(self, NGS.lib_manager.PY_NGS_ReferenceGetCanonicalName)
53 return bool(getNGSValue(self, NGS.lib_manager.PY_NGS_ReferenceGetIsCircular, c_int))
56 return bool(getNGSValue(self, NGS.lib_manager.PY_NGS_ReferenceGetIsLocal, c_int))
59 return getNGSValue(self, NGS.lib_manager.PY_NGS_ReferenceGetLength, c_uint64)
71 …res = NGS.lib_manager.PY_NGS_ReferenceGetReferenceBases(self.ref, offset, length, byref(ngs_str_re…
109 …res = NGS.lib_manager.PY_NGS_ReferenceGetAlignment(self.ref, alignmentId.encode("UTF-8"), byref(re…
122 …res = NGS.lib_manager.PY_NGS_ReferenceGetAlignments(self.ref, categories, byref(ret.ref), byref(ng…
172 …res = NGS.lib_manager.PY_NGS_ReferenceGetPileups(self.ref, categories, byref(ret.ref), byref(ngs_s…
[all …]
|
| H A D | ReadCollection.py | 29 from . import NGS
70 return getNGSString(self, NGS.lib_manager.PY_NGS_ReadCollectionGetName)
84 …ret.ref = getNGSValue(self, NGS.lib_manager.PY_NGS_ReadCollectionGetReadGroups, c_void_p) # TODO: …
96 …res = NGS.lib_manager.PY_NGS_ReadCollectionHasReadGroup(self.ref, spec.encode("UTF-8"), byref(ret)…
131 …ret.ref = getNGSValue(self, NGS.lib_manager.PY_NGS_ReadCollectionGetReferences, c_void_p) # TODO: …
143 …res = NGS.lib_manager.PY_NGS_ReadCollectionHasReference(self.ref, spec.encode("UTF-8"), byref(ret)…
185 …res = NGS.lib_manager.PY_NGS_ReadCollectionGetAlignments(self.ref, categories, byref(ret.ref), byr…
198 …res = NGS.lib_manager.PY_NGS_ReadCollectionGetAlignmentCount(self.ref, categories, byref(ret), byr…
245 …res = NGS.lib_manager.PY_NGS_ReadCollectionGetReads(self.ref, categories, byref(ret.ref), byref(ng…
258 …res = NGS.lib_manager.PY_NGS_ReadCollectionGetReadCount(self.ref, categories, byref(ret), byref(ng…
[all …]
|
| /dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/test/ngs-python/ |
| H A D | tests.py | 2 from ngs import NGS
16 run = NGS.openReadCollection(PrimaryOnly)
20 run = NGS.openReadCollection(PrimaryOnly)
24 run = NGS.openReadCollection(WithSecondary)
31 return NGS.openReferenceSequence("NC_011752.1")
39 run = NGS.openReadCollection(PrimaryOnly)
43 run = NGS.openReadCollection("SRRsomejunk")
55 it = NGS.openReadCollection(PrimaryOnly).getReadGroups()
58 it = NGS.openReadCollection(PrimaryOnly).getReferences()
317 readCollection = NGS.openReadCollection(PrimaryOnly)
[all …]
|
| /dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/test/ngs-python/ |
| H A D | tests.py | 2 from ngs import NGS
16 run = NGS.openReadCollection(PrimaryOnly)
20 run = NGS.openReadCollection(PrimaryOnly)
24 run = NGS.openReadCollection(WithSecondary)
31 return NGS.openReferenceSequence("NC_011752.1")
39 run = NGS.openReadCollection(PrimaryOnly)
43 run = NGS.openReadCollection("SRRsomejunk")
55 it = NGS.openReadCollection(PrimaryOnly).getReadGroups()
58 it = NGS.openReadCollection(PrimaryOnly).getReferences()
317 readCollection = NGS.openReadCollection(PrimaryOnly)
[all …]
|
| /dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/test/ngs-java/ |
| H A D | ngs_test_CSRA1.java | 40 import gov.nih.nlm.ncbi.ngs.NGS;
571 return NGS . openReferenceSequence ( "NC_011752.1" ); in getReferenceSequence()
880 NGS.openReadCollection(null); in ReadCollection_openReadCollection_null()
889 NGS.setAppVersionString(null); in ReadCollection_setAppVersion_null()
897 NGS.openReferenceSequence(null); in ReadCollection_openReferenceSequence_null()
908 NGS.isValid(null); in ReadCollection_isValid_null()
919 ReadCollection run = NGS.openReadCollection(PrimaryOnly); in ReadCollection_hasReadGroup_null()
933 ReadCollection run = NGS.openReadCollection(PrimaryOnly); in ReadCollection_hasReference_null()
947 ReadCollection run = NGS.openReadCollection(PrimaryOnly); in ReadCollection_getReference_null()
959 ReadCollection run = NGS.openReadCollection(PrimaryOnly); in ReadCollection_getAlignment_null()
[all …]
|
| /dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/test/ngs-java/ |
| H A D | ngs_test_CSRA1.java | 40 import gov.nih.nlm.ncbi.ngs.NGS;
571 return NGS . openReferenceSequence ( "NC_011752.1" ); in getReferenceSequence()
880 NGS.openReadCollection(null); in ReadCollection_openReadCollection_null()
889 NGS.setAppVersionString(null); in ReadCollection_setAppVersion_null()
897 NGS.openReferenceSequence(null); in ReadCollection_openReferenceSequence_null()
908 NGS.isValid(null); in ReadCollection_isValid_null()
919 ReadCollection run = NGS.openReadCollection(PrimaryOnly); in ReadCollection_hasReadGroup_null()
933 ReadCollection run = NGS.openReadCollection(PrimaryOnly); in ReadCollection_hasReference_null()
947 ReadCollection run = NGS.openReadCollection(PrimaryOnly); in ReadCollection_getReference_null()
959 ReadCollection run = NGS.openReadCollection(PrimaryOnly); in ReadCollection_getAlignment_null()
[all …]
|
| /dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-java/examples/ |
| H A D | Makefile | 31 NGS-JavaTest.jar
54 NGS-JavaTest.jar: $(NGS_EXAMPLES_PATH)
72 run_frag: NGS-JavaTest.jar
75 run_align: NGS-JavaTest.jar
78 run_dump: NGS-JavaTest.jar
81 run_align_slice: NGS-JavaTest.jar
84 run_pileup: NGS-JavaTest.jar
87 run_ref: NGS-JavaTest.jar
90 run_read_group: NGS-JavaTest.jar
109 @ diff expected.txt actual.txt && rm actual.txt && echo NGS Java examples work as expected
|
| /dports/biology/ncbi-vdb/ngs-2.11.0/ngs-java/examples/ |
| H A D | Makefile | 31 NGS-JavaTest.jar
54 NGS-JavaTest.jar: $(NGS_EXAMPLES_PATH)
72 run_frag: NGS-JavaTest.jar
75 run_align: NGS-JavaTest.jar
78 run_dump: NGS-JavaTest.jar
81 run_align_slice: NGS-JavaTest.jar
84 run_pileup: NGS-JavaTest.jar
87 run_ref: NGS-JavaTest.jar
90 run_read_group: NGS-JavaTest.jar
109 @ diff expected.txt actual.txt && rm actual.txt && echo NGS Java examples work as expected
|