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Searched refs:SubstitutionTag (Results 1 – 17 of 17) sorted by relevance

/dports/biology/sra-tools/sra-tools-2.11.0/tools/pacbio-load/
H A Dpl-basecalls_cmn.c39 init_array_file( &tab->SubstitutionTag ); in init_BaseCalls_cmn()
52 free_array_file( &tab->SubstitutionTag ); in close_BaseCalls_cmn()
90 open_element( hdf5_dir, &tab->SubstitutionTag, path, "SubstitutionTag", in open_BaseCalls_cmn()
H A Dpl-consensus.c80 if ( tab->SubstitutionTag.extents != NULL ) in check_Consensus_totalcount()
81 res = check_table_count( &tab->SubstitutionTag, "SubstitutionTag", expected ); in check_Consensus_totalcount()
195 if ( tab->SubstitutionTag.extents != NULL ) in consensus_load_spot_bases()
197 &tab->SubstitutionTag, buffer, spot->offset, spot->NumEvent, in consensus_load_spot_bases()
H A Dpl-basecalls_cmn.h46 af_data SubstitutionTag; member
H A Dpl-sequence.c162 if ( res && tab->cmn.SubstitutionTag.rc == 0 ) in check_BaseCall_totalcount()
163 res = check_table_count( &tab->cmn.SubstitutionTag, "SubstitutionTag", expected ); in check_BaseCall_totalcount()
292 if ( tab->cmn.SubstitutionTag.rc == 0 ) in seq_load_spot_bases()
294 &tab->cmn.SubstitutionTag, buffer, spot->offset, spot->NumEvent, in seq_load_spot_bases()
/dports/biology/pbbam/pbbam-0.18.0/tests/src/cram/
H A Dpbmerge_dataset.t.in64 …tionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV…
65 …tionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV…
96 …tionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV…
97 …tionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV…
127 …tionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV…
128 …tionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV…
H A Dpbmerge_pacbio_ordering.t.in18 …tionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames…
28 …tionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames…
110 …tionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames…
111 …tionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames…
197 …tionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames…
198 …tionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames…
284 …tionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames…
285 …tionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames…
375 …tionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames…
376 …tionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames…
H A Dpbmerge_aligned_ordering.t.in19 …ERSION=2.3;InsertionQV=iq;DeletionQV=dq;SubstitutionQV=sq;MergeQV=mq;SubstitutionTag=st;DeletionTa…
37 …ERSION=2.3;InsertionQV=iq;DeletionQV=dq;SubstitutionQV=sq;MergeQV=mq;SubstitutionTag=st;DeletionTa…
59 …tionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;BINDINGKIT…
94 …tionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;BINDINGKIT…
129 …tionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;BINDINGKIT…
168 …tionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;BINDINGKIT…
H A Dpbmerge_mixed_ordering.t.in17 …tionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames…
28 …ERSION=2.3;InsertionQV=iq;DeletionQV=dq;SubstitutionQV=sq;MergeQV=mq;SubstitutionTag=st;DeletionTa…
H A Dpbmerge_fofn.t.in32 …RATEHZ=100;InsertionQV=iq;DeletionQV=dq;SubstitutionQV=sq;MergeQV=mq;SubstitutionTag=st;DeletionTa…
61 …tionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;BINDINGKIT…
99 …tionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;BINDINGKIT…
/dports/biology/pbbam/pbbam-0.18.0/tests/src/
H A Dtest_ZmwReadStitcher.cpp69 EXPECT_EQ(b1.SubstitutionTag(), b2.SubstitutionTag()); in Compare()
359 EXPECT_EQ(polyRecord.SubstitutionTag(), virtualRecord.SubstitutionTag()); in TEST()
395 EXPECT_EQ(polyRecord.SubstitutionTag(), virtualRecord.SubstitutionTag()); in TEST()
H A Dtest_WhitelistedZmwReadStitcher.cpp68 EXPECT_EQ(b1.SubstitutionTag(), b2.SubstitutionTag()); in Compare()
H A Dtest_BamRecord.cpp341 { return b.SubstitutionTag(orientation, aligned, exciseSoftClips); } in CheckBaseTagsClippedAndAligned()
689 EXPECT_THROW(bam.SubstitutionTag(), std::exception); in TEST()
/dports/biology/pbbam/pbbam-0.18.0/src/
H A DVirtualZmwBamRecord.cpp122 if (b.HasSubstitutionTag()) substitutionTag.append(std::move(b.SubstitutionTag())); in StitchSources()
207 if (!substitutionTag.empty()) this->SubstitutionTag(substitutionTag); in StitchSources()
H A DValidator.cpp290 if (b.SubstitutionTag().size() != expectedLength) in ValidateRecordTagLengths()
291 errors->AddTagLengthError(name, "SubstitutionTag", "st", b.SubstitutionTag().size(), in ValidateRecordTagLengths()
H A DBamRecord.cpp595 internal::Clip(SubstitutionTag(Orientation::NATIVE), clipFrom, clipLength); in ClipTags()
2095 std::string BamRecord::SubstitutionTag(Orientation orientation, bool aligned, in SubstitutionTag() function in PacBio::BAM::BamRecord
2101 BamRecord& BamRecord::SubstitutionTag(const std::string& tags) in SubstitutionTag() function in PacBio::BAM::BamRecord
/dports/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/
H A DBamRecordView.inl91 { return record_.SubstitutionTag(orientation_, aligned_, exciseSoftClips_); }
/dports/biology/pbbam/pbbam-0.18.0/include/pbbam/
H A DBamRecord.h433 std::string SubstitutionTag(Orientation orientation = Orientation::NATIVE, bool aligned = false,
879 BamRecord& SubstitutionTag(const std::string& tags);