/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/ngs/ |
H A D | NGS_Reference.c | 185 int32_t map_qual ) in ITF_Reference_v1_get_filtered_alignments() 221 int32_t map_qual ) in ITF_Reference_v1_get_filtered_align_slice() 298 uint32_t flags, int32_t map_qual ) in ITF_Reference_v1_get_filtered_pileups() 316 int64_t start, uint64_t length, uint32_t flags, int32_t map_qual ) in ITF_Reference_v1_get_filtered_pileup_slice() 584 bool wants_primary, bool wants_secondary, uint32_t filters, int32_t map_qual ) in NGS_ReferenceGetFilteredAlignments() 643 …fset, uint64_t size, bool wants_primary, bool wants_secondary, uint32_t filters, int32_t map_qual ) in NGS_ReferenceGetFilteredAlignmentSlice() 678 …e * self, ctx_t ctx, bool wants_primary, bool wants_secondary, uint32_t filters, int32_t map_qual ) in NGS_ReferenceGetFilteredPileups() 724 int32_t map_qual ) in NGS_ReferenceGetFilteredPileupSlice() 870 bool wants_primary, bool wants_secondary, uint32_t filters, int32_t map_qual ) in Null_ReferenceGetAlignments() 891 int32_t map_qual) in Null_ReferenceGetAlignmentSlice() [all …]
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H A D | CSRA1_Reference.c | 462 …e * self, ctx_t ctx, bool wants_primary, bool wants_secondary, uint32_t filters, int32_t map_qual ) in CSRA1_ReferenceGetAlignments() 645 int32_t map_qual ) in CSRA1_ReferenceGetAlignmentSlice() 729 …e * self, ctx_t ctx, bool wants_primary, bool wants_secondary, uint32_t filters, int32_t map_qual ) in CSRA1_ReferenceGetPileups() 757 …fset, uint64_t size, bool wants_primary, bool wants_secondary, uint32_t filters, int32_t map_qual ) in CSRA1_ReferenceGetPileupSlice()
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H A D | CSRA1_ReferenceWindow.c | 93 int32_t map_qual; member 599 uint32_t map_qual; in ApplyFilters() local 712 uint32_t map_qual; in LoadAlignmentInfo() local 1014 int32_t map_qual, in CSRA1_ReferenceWindowInit() 1060 int32_t map_qual, in CSRA1_ReferenceWindowMake()
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H A D | CSRA1_Pileup.c | 871 int32_t map_qual; in CSRA1_PileupFilterAlignment() local 1654 uint32_t filters, int32_t map_qual ) in CSRA1_PileupInit() 1715 uint32_t filters, int32_t map_qual ) in CSRA1_PileupIteratorMake() 1783 uint32_t filters, int32_t map_qual ) in CSRA1_PileupIteratorMakeSlice()
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H A D | CSRA1_Pileup.h | 285 int32_t map_qual; member
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/ngs/ |
H A D | NGS_Reference.c | 185 int32_t map_qual ) in ITF_Reference_v1_get_filtered_alignments() 221 int32_t map_qual ) in ITF_Reference_v1_get_filtered_align_slice() 298 uint32_t flags, int32_t map_qual ) in ITF_Reference_v1_get_filtered_pileups() 316 int64_t start, uint64_t length, uint32_t flags, int32_t map_qual ) in ITF_Reference_v1_get_filtered_pileup_slice() 584 bool wants_primary, bool wants_secondary, uint32_t filters, int32_t map_qual ) in NGS_ReferenceGetFilteredAlignments() 643 …fset, uint64_t size, bool wants_primary, bool wants_secondary, uint32_t filters, int32_t map_qual ) in NGS_ReferenceGetFilteredAlignmentSlice() 678 …e * self, ctx_t ctx, bool wants_primary, bool wants_secondary, uint32_t filters, int32_t map_qual ) in NGS_ReferenceGetFilteredPileups() 724 int32_t map_qual ) in NGS_ReferenceGetFilteredPileupSlice() 870 bool wants_primary, bool wants_secondary, uint32_t filters, int32_t map_qual ) in Null_ReferenceGetAlignments() 891 int32_t map_qual) in Null_ReferenceGetAlignmentSlice() [all …]
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H A D | CSRA1_Reference.c | 462 …e * self, ctx_t ctx, bool wants_primary, bool wants_secondary, uint32_t filters, int32_t map_qual ) in CSRA1_ReferenceGetAlignments() 645 int32_t map_qual ) in CSRA1_ReferenceGetAlignmentSlice() 729 …e * self, ctx_t ctx, bool wants_primary, bool wants_secondary, uint32_t filters, int32_t map_qual ) in CSRA1_ReferenceGetPileups() 757 …fset, uint64_t size, bool wants_primary, bool wants_secondary, uint32_t filters, int32_t map_qual ) in CSRA1_ReferenceGetPileupSlice()
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H A D | CSRA1_ReferenceWindow.c | 93 int32_t map_qual; member 599 uint32_t map_qual; in ApplyFilters() local 712 uint32_t map_qual; in LoadAlignmentInfo() local 1014 int32_t map_qual, in CSRA1_ReferenceWindowInit() 1060 int32_t map_qual, in CSRA1_ReferenceWindowMake()
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H A D | CSRA1_Pileup.c | 871 int32_t map_qual; in CSRA1_PileupFilterAlignment() local 1654 uint32_t filters, int32_t map_qual ) in CSRA1_PileupInit() 1715 uint32_t filters, int32_t map_qual ) in CSRA1_PileupIteratorMake() 1783 uint32_t filters, int32_t map_qual ) in CSRA1_PileupIteratorMakeSlice()
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/dports/biology/stacks/stacks-2.4/src/ |
H A D | SamI.h | 135 int map_qual = is_integer(parts[4].c_str()); in next_seq() local
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H A D | Seq.cc | 138 AlnT aln_type, double pct_clipped, int map_qual in Seq()
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H A D | Seq.h | 98 int map_qual; variable
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/dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/adapter/ |
H A D | ReferenceItf.cpp | 227 … int64_t start, uint64_t length, uint32_t flags, int32_t map_qual ) in get_filtered_align_slice() 261 uint32_t flags, int32_t map_qual ) in get_filtered_pileups() 295 int64_t start, uint64_t length, uint32_t flags, int32_t map_qual ) in get_filtered_pileup_slice()
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/dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/adapter/ |
H A D | ReferenceItf.cpp | 227 … int64_t start, uint64_t length, uint32_t flags, int32_t map_qual ) in get_filtered_align_slice() 261 uint32_t flags, int32_t map_qual ) in get_filtered_pileups() 295 int64_t start, uint64_t length, uint32_t flags, int32_t map_qual ) in get_filtered_pileup_slice()
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/dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/adapter/ |
H A D | ReferenceItf.cpp | 227 … int64_t start, uint64_t length, uint32_t flags, int32_t map_qual ) in get_filtered_align_slice() 261 uint32_t flags, int32_t map_qual ) in get_filtered_pileups() 295 int64_t start, uint64_t length, uint32_t flags, int32_t map_qual ) in get_filtered_pileup_slice()
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/dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/language/python/ |
H A D | py_ReferenceItf.cpp | 292 …64_t start, uint64_t length, uint32_t categories, uint32_t filters, int32_t map_qual, void** pRet,… in PY_NGS_ReferenceGetFilteredAlignmentSlice() 344 …ilteredPileups ( void* pRef, uint32_t categories, uint32_t filters, int32_t map_qual, void** pRet,… in PY_NGS_ReferenceGetFilteredPileups() 396 …64_t start, uint64_t length, uint32_t categories, uint32_t filters, int32_t map_qual, void** pRet,… in PY_NGS_ReferenceGetFilteredPileupSlice()
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/dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/language/python/ |
H A D | py_ReferenceItf.cpp | 292 …64_t start, uint64_t length, uint32_t categories, uint32_t filters, int32_t map_qual, void** pRet,… in PY_NGS_ReferenceGetFilteredAlignmentSlice() 344 …ilteredPileups ( void* pRef, uint32_t categories, uint32_t filters, int32_t map_qual, void** pRet,… in PY_NGS_ReferenceGetFilteredPileups() 396 …64_t start, uint64_t length, uint32_t categories, uint32_t filters, int32_t map_qual, void** pRet,… in PY_NGS_ReferenceGetFilteredPileupSlice()
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/dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/language/python/ |
H A D | py_ReferenceItf.cpp | 292 …64_t start, uint64_t length, uint32_t categories, uint32_t filters, int32_t map_qual, void** pRet,… in PY_NGS_ReferenceGetFilteredAlignmentSlice() 344 …ilteredPileups ( void* pRef, uint32_t categories, uint32_t filters, int32_t map_qual, void** pRet,… in PY_NGS_ReferenceGetFilteredPileups() 396 …64_t start, uint64_t length, uint32_t categories, uint32_t filters, int32_t map_qual, void** pRet,… in PY_NGS_ReferenceGetFilteredPileupSlice()
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/dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/language/java/ |
H A D | jni_ReferenceItf.cpp | 450 ( JNIEnv * jenv, jobject jthis, jlong jself, jint categories, jint filters, jint map_qual ) in Java_ngs_itf_ReferenceItf_GetFilteredPileups() 508 …ject jthis, jlong jself, jlong offset, jlong length, jint categories, jint filters, jint map_qual ) in Java_ngs_itf_ReferenceItf_GetFilteredPileupSlice()
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/dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/language/java/ |
H A D | jni_ReferenceItf.cpp | 450 ( JNIEnv * jenv, jobject jthis, jlong jself, jint categories, jint filters, jint map_qual ) in Java_ngs_itf_ReferenceItf_GetFilteredPileups() 508 …ject jthis, jlong jself, jlong offset, jlong length, jint categories, jint filters, jint map_qual ) in Java_ngs_itf_ReferenceItf_GetFilteredPileupSlice()
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/dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/language/java/ |
H A D | jni_ReferenceItf.cpp | 450 ( JNIEnv * jenv, jobject jthis, jlong jself, jint categories, jint filters, jint map_qual ) in Java_ngs_itf_ReferenceItf_GetFilteredPileups() 508 …ject jthis, jlong jself, jlong offset, jlong length, jint categories, jint filters, jint map_qual ) in Java_ngs_itf_ReferenceItf_GetFilteredPileupSlice()
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/dports/biology/samtools/samtools-1.14/misc/ |
H A D | maq2sam.c | 59 uint8_t size, map_qual, info1, info2, c[2], flag, alt_qual; member
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/dports/biology/seqan1/seqan-1.3.1/lib/samtools/misc/ |
H A D | maq2sam.c | 34 uint8_t size, map_qual, info1, info2, c[2], flag, alt_qual; member
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/dports/biology/stringtie/stringtie-2.1.1/gclib/ |
H A D | GBam.cpp | 58 int pos, int map_qual, const char* cigar, int32_t mg_tid, int mate_pos, in GBamRecord()
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/dports/biology/gffread/gffread-0.12.7/gclib/ |
H A D | GBam.cpp | 61 int pos, int map_qual, const char* cigar, int32_t mg_tid, int mate_pos, in GBamRecord()
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