| /dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-java/ngs/itf/ |
| H A D | ReferenceItf.java | 230 …ilteredAlignmentSlice ( long offset, long length, int categories, int filters, int mappingQuality ) in getFilteredAlignmentSlice() argument
233 …f = this . GetFilteredAlignmentSlice ( self, offset, length, categories, filters, mappingQuality ); in getFilteredAlignmentSlice()
268 public PileupIterator getFilteredPileups ( int categories, int filters, int mappingQuality ) in getFilteredPileups() argument
271 long ref = this . GetFilteredPileups ( self, categories, filters, mappingQuality ); in getFilteredPileups()
310 …etFilteredPileupSlice ( long offset, long length, int categories, int filters, int mappingQuality ) in getFilteredPileupSlice() argument
313 … ref = this . GetFilteredPileupSlice ( self, offset, length, categories, filters, mappingQuality ); in getFilteredPileupSlice()
373 …nmentSlice ( long self, long offset, long length, int categories, int filters, int mappingQuality ) in GetFilteredAlignmentSlice() argument
377 …ivate native long GetFilteredPileups ( long self, int categories, int filters, int mappingQuality ) in GetFilteredPileups() argument
381 …PileupSlice ( long self, long offset, long count, int categories, int filters, int mappingQuality ) in GetFilteredPileupSlice() argument
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| /dports/biology/ncbi-vdb/ngs-2.11.0/ngs-java/ngs/itf/ |
| H A D | ReferenceItf.java | 230 …ilteredAlignmentSlice ( long offset, long length, int categories, int filters, int mappingQuality ) in getFilteredAlignmentSlice() argument
233 …f = this . GetFilteredAlignmentSlice ( self, offset, length, categories, filters, mappingQuality ); in getFilteredAlignmentSlice()
268 public PileupIterator getFilteredPileups ( int categories, int filters, int mappingQuality ) in getFilteredPileups() argument
271 long ref = this . GetFilteredPileups ( self, categories, filters, mappingQuality ); in getFilteredPileups()
310 …etFilteredPileupSlice ( long offset, long length, int categories, int filters, int mappingQuality ) in getFilteredPileupSlice() argument
313 … ref = this . GetFilteredPileupSlice ( self, offset, length, categories, filters, mappingQuality ); in getFilteredPileupSlice()
373 …nmentSlice ( long self, long offset, long length, int categories, int filters, int mappingQuality ) in GetFilteredAlignmentSlice() argument
377 …ivate native long GetFilteredPileups ( long self, int categories, int filters, int mappingQuality ) in GetFilteredPileups() argument
381 …PileupSlice ( long self, long offset, long count, int categories, int filters, int mappingQuality ) in GetFilteredPileupSlice() argument
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| /dports/biology/ngs-sdk/ngs-2.11.1/ngs-java/ngs/itf/ |
| H A D | ReferenceItf.java | 230 …ilteredAlignmentSlice ( long offset, long length, int categories, int filters, int mappingQuality ) in getFilteredAlignmentSlice() argument
233 …f = this . GetFilteredAlignmentSlice ( self, offset, length, categories, filters, mappingQuality ); in getFilteredAlignmentSlice()
268 public PileupIterator getFilteredPileups ( int categories, int filters, int mappingQuality ) in getFilteredPileups() argument
271 long ref = this . GetFilteredPileups ( self, categories, filters, mappingQuality ); in getFilteredPileups()
310 …etFilteredPileupSlice ( long offset, long length, int categories, int filters, int mappingQuality ) in getFilteredPileupSlice() argument
313 … ref = this . GetFilteredPileupSlice ( self, offset, length, categories, filters, mappingQuality ); in getFilteredPileupSlice()
373 …nmentSlice ( long self, long offset, long length, int categories, int filters, int mappingQuality ) in GetFilteredAlignmentSlice() argument
377 …ivate native long GetFilteredPileups ( long self, int categories, int filters, int mappingQuality ) in GetFilteredPileups() argument
381 …PileupSlice ( long self, long offset, long count, int categories, int filters, int mappingQuality ) in GetFilteredPileupSlice() argument
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/ |
| H A D | BreakpointEvidence.java | 252 private final int mappingQuality; field in BreakpointEvidence.ReadEvidence
266 this.mappingQuality = read.getMappingQuality(); in ReadEvidence()
283 this.mappingQuality = read.getMappingQuality(); in ReadEvidence()
301 this.mappingQuality = mappingQuality; in ReadEvidence()
317 this.mappingQuality = input.readInt(); in ReadEvidence()
329 output.writeInt(mappingQuality); in serialize()
371 + "\t" + mappingQuality; in stringRep()
381 mappingQuality == that.mappingQuality && in equals()
393 mappingQuality, templateSize, readGroup); in hashCode()
498 mappingQuality, templateSize, readGroup); in SplitRead()
[all …]
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| /dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/ngs/inl/ |
| H A D | Reference.hpp | 121 … AlignmentCategory categories, Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const in getFilteredAlignmentSlice()
123 …lignmentSlice ( start, length, ( uint32_t ) categories, ( uint32_t ) filters, mappingQuality ) ); } in getFilteredAlignmentSlice()
131 … AlignmentCategory categories, Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const in getFilteredPileups()
133 …) self -> getFilteredPileups ( ( uint32_t ) categories, ( uint32_t ) filters, mappingQuality ) ); } in getFilteredPileups()
146 … AlignmentCategory categories, Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const in getFilteredPileupSlice()
148 …edPileupSlice ( start, length, ( uint32_t ) categories, ( uint32_t ) filters, mappingQuality ) ); } in getFilteredPileupSlice()
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| /dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/ngs/inl/ |
| H A D | Reference.hpp | 121 … AlignmentCategory categories, Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const in getFilteredAlignmentSlice()
123 …lignmentSlice ( start, length, ( uint32_t ) categories, ( uint32_t ) filters, mappingQuality ) ); } in getFilteredAlignmentSlice()
131 … AlignmentCategory categories, Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const in getFilteredPileups()
133 …) self -> getFilteredPileups ( ( uint32_t ) categories, ( uint32_t ) filters, mappingQuality ) ); } in getFilteredPileups()
146 … AlignmentCategory categories, Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const in getFilteredPileupSlice()
148 …edPileupSlice ( start, length, ( uint32_t ) categories, ( uint32_t ) filters, mappingQuality ) ); } in getFilteredPileupSlice()
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| /dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/ngs/inl/ |
| H A D | Reference.hpp | 121 … AlignmentCategory categories, Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const in getFilteredAlignmentSlice()
123 …lignmentSlice ( start, length, ( uint32_t ) categories, ( uint32_t ) filters, mappingQuality ) ); } in getFilteredAlignmentSlice()
131 … AlignmentCategory categories, Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const in getFilteredPileups()
133 …) self -> getFilteredPileups ( ( uint32_t ) categories, ( uint32_t ) filters, mappingQuality ) ); } in getFilteredPileups()
146 … AlignmentCategory categories, Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const in getFilteredPileupSlice()
148 …edPileupSlice ( start, length, ( uint32_t ) categories, ( uint32_t ) filters, mappingQuality ) ); } in getFilteredPileupSlice()
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| /dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-python/ngs/ |
| H A D | Reference.py | 144 def getFilteredAlignmentSlice(self, start, length, categories, filters, mappingQuality): argument
156 …FilteredAlignmentSlice(self.ref, start, length, categories, filters, mappingQuality, byref(ret.ref…
178 def getFilteredPileups(self, categories, filters, mappingQuality): argument
185 …er.PY_NGS_ReferenceGetFilteredPileups(self.ref, categories, filters, mappingQuality, byref(ret.ref…
207 def getFilteredPileupSlice(self, start, length, categories, filters, mappingQuality): argument
219 …GetFilteredPileupSlice(self.ref, start, length, categories, filters, mappingQuality, byref(ret.ref…
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| /dports/biology/ncbi-vdb/ngs-2.11.0/ngs-python/ngs/ |
| H A D | Reference.py | 144 def getFilteredAlignmentSlice(self, start, length, categories, filters, mappingQuality): argument
156 …FilteredAlignmentSlice(self.ref, start, length, categories, filters, mappingQuality, byref(ret.ref…
178 def getFilteredPileups(self, categories, filters, mappingQuality): argument
185 …er.PY_NGS_ReferenceGetFilteredPileups(self.ref, categories, filters, mappingQuality, byref(ret.ref…
207 def getFilteredPileupSlice(self, start, length, categories, filters, mappingQuality): argument
219 …GetFilteredPileupSlice(self.ref, start, length, categories, filters, mappingQuality, byref(ret.ref…
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| /dports/biology/ngs-sdk/ngs-2.11.1/ngs-python/ngs/ |
| H A D | Reference.py | 144 def getFilteredAlignmentSlice(self, start, length, categories, filters, mappingQuality): argument
156 …FilteredAlignmentSlice(self.ref, start, length, categories, filters, mappingQuality, byref(ret.ref…
178 def getFilteredPileups(self, categories, filters, mappingQuality): argument
185 …er.PY_NGS_ReferenceGetFilteredPileups(self.ref, categories, filters, mappingQuality, byref(ret.ref…
207 def getFilteredPileupSlice(self, start, length, categories, filters, mappingQuality): argument
219 …GetFilteredPileupSlice(self.ref, start, length, categories, filters, mappingQuality, byref(ret.ref…
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| /dports/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/ |
| H A D | BamRecord.inl | 34 const uint8_t mappingQuality) argument
36 return input.Mapped(referenceId, refStart, strand, cigar, mappingQuality);
43 const uint8_t mappingQuality) const
46 result.Map(referenceId, refStart, strand, cigar, mappingQuality);
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| /dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-java/ngs/ |
| H A D | Reference.java | 206 …FilteredAlignmentSlice ( long start, long length, int categories, int filters, int mappingQuality ) in getFilteredAlignmentSlice() argument
232 PileupIterator getFilteredPileups ( int categories, int filters, int mappingQuality ) in getFilteredPileups() argument
271 int categories, int filters, int mappingQuality ) in getFilteredPileupSlice() argument
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| /dports/biology/ncbi-vdb/ngs-2.11.0/ngs-java/ngs/ |
| H A D | Reference.java | 206 …FilteredAlignmentSlice ( long start, long length, int categories, int filters, int mappingQuality ) in getFilteredAlignmentSlice() argument
232 PileupIterator getFilteredPileups ( int categories, int filters, int mappingQuality ) in getFilteredPileups() argument
271 int categories, int filters, int mappingQuality ) in getFilteredPileupSlice() argument
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| /dports/biology/ngs-sdk/ngs-2.11.1/ngs-java/ngs/ |
| H A D | Reference.java | 206 …FilteredAlignmentSlice ( long start, long length, int categories, int filters, int mappingQuality ) in getFilteredAlignmentSlice() argument
232 PileupIterator getFilteredPileups ( int categories, int filters, int mappingQuality ) in getFilteredPileups() argument
271 int categories, int filters, int mappingQuality ) in getFilteredPileupSlice() argument
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| /dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/ngs/itf/ |
| H A D | ReferenceItf.hpp | 83 …t64_t start, uint64_t length, uint32_t categories, uint32_t filters, int32_t mappingQuality ) const
87 …eupItf * getFilteredPileups ( uint32_t categories, uint32_t filters, int32_t mappingQuality ) const
93 …t64_t start, uint64_t length, uint32_t categories, uint32_t filters, int32_t mappingQuality ) const
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| /dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/ngs/itf/ |
| H A D | ReferenceItf.hpp | 83 …t64_t start, uint64_t length, uint32_t categories, uint32_t filters, int32_t mappingQuality ) const
87 …eupItf * getFilteredPileups ( uint32_t categories, uint32_t filters, int32_t mappingQuality ) const
93 …t64_t start, uint64_t length, uint32_t categories, uint32_t filters, int32_t mappingQuality ) const
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| /dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/ngs/itf/ |
| H A D | ReferenceItf.hpp | 83 …t64_t start, uint64_t length, uint32_t categories, uint32_t filters, int32_t mappingQuality ) const
87 …eupItf * getFilteredPileups ( uint32_t categories, uint32_t filters, int32_t mappingQuality ) const
93 …t64_t start, uint64_t length, uint32_t categories, uint32_t filters, int32_t mappingQuality ) const
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| /dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/ngs/ |
| H A D | Reference.hpp | 161 Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const
184 Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const
205 Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const
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| /dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/ngs/ |
| H A D | Reference.hpp | 161 Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const
184 Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const
205 Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const
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| /dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/ngs/ |
| H A D | Reference.hpp | 161 Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const
184 Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const
205 Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const
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| /dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/dispatch/ |
| H A D | ReferenceItf.cpp | 363 …t64_t start, uint64_t length, uint32_t categories, uint32_t filters, int32_t mappingQuality ) const in getFilteredAlignmentSlice()
390 … ret = ( * vt -> get_filtered_align_slice ) ( self, & err, start, length, flags, mappingQuality ); in getFilteredAlignmentSlice()
425 …ceItf :: getFilteredPileups ( uint32_t categories, uint32_t filters, int32_t mappingQuality ) const in getFilteredPileups()
452 … NGS_Pileup_v1 * ret = ( * vt -> get_filtered_pileups ) ( self, & err, flags, mappingQuality ); in getFilteredPileups()
493 …t64_t start, uint64_t length, uint32_t categories, uint32_t filters, int32_t mappingQuality ) const in getFilteredPileupSlice()
520 …ret = ( * vt -> get_filtered_pileup_slice ) ( self, & err, start, length, flags, mappingQuality ); in getFilteredPileupSlice()
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| /dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/dispatch/ |
| H A D | ReferenceItf.cpp | 363 …t64_t start, uint64_t length, uint32_t categories, uint32_t filters, int32_t mappingQuality ) const in getFilteredAlignmentSlice()
390 … ret = ( * vt -> get_filtered_align_slice ) ( self, & err, start, length, flags, mappingQuality ); in getFilteredAlignmentSlice()
425 …ceItf :: getFilteredPileups ( uint32_t categories, uint32_t filters, int32_t mappingQuality ) const in getFilteredPileups()
452 … NGS_Pileup_v1 * ret = ( * vt -> get_filtered_pileups ) ( self, & err, flags, mappingQuality ); in getFilteredPileups()
493 …t64_t start, uint64_t length, uint32_t categories, uint32_t filters, int32_t mappingQuality ) const in getFilteredPileupSlice()
520 …ret = ( * vt -> get_filtered_pileup_slice ) ( self, & err, start, length, flags, mappingQuality ); in getFilteredPileupSlice()
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| /dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/dispatch/ |
| H A D | ReferenceItf.cpp | 363 …t64_t start, uint64_t length, uint32_t categories, uint32_t filters, int32_t mappingQuality ) const in getFilteredAlignmentSlice()
390 … ret = ( * vt -> get_filtered_align_slice ) ( self, & err, start, length, flags, mappingQuality ); in getFilteredAlignmentSlice()
425 …ceItf :: getFilteredPileups ( uint32_t categories, uint32_t filters, int32_t mappingQuality ) const in getFilteredPileups()
452 … NGS_Pileup_v1 * ret = ( * vt -> get_filtered_pileups ) ( self, & err, flags, mappingQuality ); in getFilteredPileups()
493 …t64_t start, uint64_t length, uint32_t categories, uint32_t filters, int32_t mappingQuality ) const in getFilteredPileupSlice()
520 …ret = ( * vt -> get_filtered_pileup_slice ) ( self, & err, start, length, flags, mappingQuality ); in getFilteredPileupSlice()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/ |
| H A D | XGBoostEvidenceFilterUnitTest.java | 446 final int mappingQuality = Integer.parseInt(words[8]); in fromStringRep() local
476 forwardStrand, cigarString, mappingQuality, templateSize, readGroup, in fromStringRep()
482 … forwardStrand, cigarString, mappingQuality, templateSize, readGroup); in fromStringRep()
487 … forwardStrand, cigarString, mappingQuality, templateSize, readGroup); in fromStringRep()
492 … mappingQuality, templateSize, readGroup, target, targetForwardStrand, targetQuality in fromStringRep()
498 … mappingQuality, templateSize, readGroup, target, targetForwardStrand, targetQuality in fromStringRep()
504 … mappingQuality, templateSize, readGroup, target, targetForwardStrand, targetQuality in fromStringRep()
510 … mappingQuality, templateSize, readGroup, target, targetForwardStrand, targetQuality in fromStringRep()
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/datatype/ |
| H A D | U2Assembly.h | 173 packedViewRow(0), mappingQuality(255), flags(0), rnext("*"), pnext(0) { in U2AssemblyReadData()
207 quint8 mappingQuality; variable
|