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Searched defs:map_qual (Results 1 – 25 of 27) sorted by relevance

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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/ngs/
H A DNGS_Reference.c185 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 …]
H A DCSRA1_Reference.c462 …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()
H A DCSRA1_ReferenceWindow.c93 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()
H A DCSRA1_Pileup.c871 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()
H A DCSRA1_Pileup.h285 int32_t map_qual; member
/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/ngs/
H A DNGS_Reference.c185 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 …]
H A DCSRA1_Reference.c462 …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()
H A DCSRA1_ReferenceWindow.c93 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()
H A DCSRA1_Pileup.c871 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()
/dports/biology/stacks/stacks-2.4/src/
H A DSamI.h135 int map_qual = is_integer(parts[4].c_str()); in next_seq() local
H A DSeq.cc138 AlnT aln_type, double pct_clipped, int map_qual in Seq()
H A DSeq.h98 int map_qual; variable
/dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/adapter/
H A DReferenceItf.cpp227 … 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()
/dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/adapter/
H A DReferenceItf.cpp227 … 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()
/dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/adapter/
H A DReferenceItf.cpp227 … 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()
/dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/language/python/
H A Dpy_ReferenceItf.cpp292 …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()
/dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/language/python/
H A Dpy_ReferenceItf.cpp292 …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()
/dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/language/python/
H A Dpy_ReferenceItf.cpp292 …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()
/dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/language/java/
H A Djni_ReferenceItf.cpp450 ( 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()
/dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/language/java/
H A Djni_ReferenceItf.cpp450 ( 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()
/dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/language/java/
H A Djni_ReferenceItf.cpp450 ( 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()
/dports/biology/samtools/samtools-1.14/misc/
H A Dmaq2sam.c59 uint8_t size, map_qual, info1, info2, c[2], flag, alt_qual; member
/dports/biology/seqan1/seqan-1.3.1/lib/samtools/misc/
H A Dmaq2sam.c34 uint8_t size, map_qual, info1, info2, c[2], flag, alt_qual; member
/dports/biology/stringtie/stringtie-2.1.1/gclib/
H A DGBam.cpp58 int pos, int map_qual, const char* cigar, int32_t mg_tid, int mate_pos, in GBamRecord()
/dports/biology/gffread/gffread-0.12.7/gclib/
H A DGBam.cpp61 int pos, int map_qual, const char* cigar, int32_t mg_tid, int mate_pos, in GBamRecord()

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