| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/readers/sra/ |
| H A D | sraread.cpp | 375 spotid_t spot_id = 0; in GetSpotInfo() local
389 return spot_id; in GetSpotInfo()
481 CSraStringValue name(m_Name, spot_id); in GetSpotEntry()
488 CSraValueFor<SRASpotDesc> sdesc(m_SDesc, spot_id); in GetSpotEntry()
493 CSraValueFor<SRAReadDesc> rdesc(m_RDesc, spot_id); in GetSpotEntry()
494 CSraStringValue read(m_Read, spot_id); in GetSpotEntry()
495 CSraBytesValue qual(m_Qual, spot_id); in GetSpotEntry()
585 CSraValueFor<SRASpotDesc> sdesc(m_SDesc, spot_id); in GetSequenceType()
593 TSeqPos CSraRun::GetSequenceLength(spotid_t spot_id, in GetSequenceLength() argument
596 CSraValueFor<SRASpotDesc> sdesc(m_SDesc, spot_id); in GetSequenceLength()
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| H A D | csraread.cpp | 1937 TVDBRowId spot_id, in CCSraShortReadIterator() argument
1941 Select(spot_id); in CCSraShortReadIterator()
1951 Select(spot_id, read_id); in CCSraShortReadIterator()
1981 bool CCSraShortReadIterator::Select(TVDBRowId spot_id) in Select() argument
1983 m_SpotId = spot_id; in Select()
1985 if ( spot_id < 1 || spot_id > m_MaxSpotId ) { in Select()
1995 bool CCSraShortReadIterator::Select(TVDBRowId spot_id, in Select() argument
1998 m_SpotId = spot_id; in Select()
2000 if ( spot_id < 1 || spot_id > m_MaxSpotId ) { in Select()
2021 void CCSraShortReadIterator::SetLastSpotId(TVDBRowId spot_id) in SetLastSpotId() argument
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| /dports/biology/sra-tools/sra-tools-2.11.0/tools/pacbio-load/ |
| H A D | pl-regions.c | 87 rgn->spot_id = 0; in rgn_init()
273 a_region->spot_id = block[ pacbio_idx_spot_id ]; in rgn_store_bio_or_adapter()
344 a_region->spot_id = spot_id; in rgn_generate()
373 rc = rgn_generate( stock, v, spot_id, 0, spot_len );
460 rc = rgn_generate( stock, to, spot_id, start, gap_len ); in rgn_correct()
515 rc = rgn_generate( stock, to, spot_id, start, gap_len ); in rgn_correct()
662 rc_t rgn_load( regions *rgn, const uint32_t spot_id, in rgn_load() argument
679 if ( !( rgn->spot_id == 0 || rgn->spot_id == ( spot_id - 1 ) ) ) in rgn_load()
691 if ( block[ pacbio_idx_spot_id ] == spot_id ) in rgn_load()
701 block[ pacbio_idx_spot_id ] == spot_id && in rgn_load()
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| H A D | pl-regions.h | 56 int32_t spot_id; member
92 uint32_t spot_id; member
121 rc_t rgn_load( regions *rgn, const uint32_t spot_id,
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/data_loaders/sra/ |
| H A D | sraloader.cpp | 94 CSRABlobId(const string& acc, unsigned spot_id);
106 CSRABlobId::CSRABlobId(const string& acc, unsigned spot_id) in CSRABlobId() argument
107 : m_Accession(acc), m_SpotId(spot_id) in CSRABlobId()
164 unsigned spot_id) in LoadSRAEntry() argument
170 return m_Run.GetSpotEntry(spot_id); in LoadSRAEntry()
175 unsigned spot_id, in GetSequenceType() argument
182 return m_Run.GetSequenceType(spot_id, read_id); in GetSequenceType()
187 unsigned spot_id, in GetSequenceLength() argument
194 return m_Run.GetSequenceLength(spot_id, read_id); in GetSequenceLength()
356 unsigned spot_id = in sx_GetReadId() local
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/data_loaders/csra/test/ |
| H A D | test_csra_loader_mt.cpp | 70 Int8 spot_id,
74 Int8 spot_id);
210 Int8 spot_id, in GetHandle() argument
214 str << "gnl|SRA|" << acc << '.' << spot_id << '.' << read_id; in GetHandle()
220 Int8 spot_id) in ExistsSpotId() argument
223 if ( !scope.GetIds(GetHandle(acc, spot_id, read_id)).empty() ) { in ExistsSpotId()
313 for ( Int8 spot_id = start_id; spot_id < stop_id; ++spot_id ) { in TestShortReads() local
315 CSeq_id_Handle id = GetHandle(acc, spot_id, read_id); in TestShortReads()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/sra/data_loaders/sra/impl/ |
| H A D | sraloader_impl.hpp | 54 unsigned spot_id,
57 unsigned spot_id,
61 unsigned spot_id);
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| /dports/biology/sra-tools/sra-tools-2.11.0/tools/qual-recalib-stat/ |
| H A D | spot_position.c | 73 const uint64_t spot_id, in query_spot_pos() argument
84 rc = read_cells( self->cursor, spot_id, self->columns, sidx_names, N_SIDX ); in query_spot_pos()
94 "read_nr=%u,n_read=%u,row_nr=%lu", seq_read_id, rd_start_len, spot_id ) ); in query_spot_pos()
108 "cannot read sequence row #$(row_nr)", "row_nr=%lu", spot_id ) ); in query_spot_pos()
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| H A D | spot_position.h | 59 const uint64_t spot_id,
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| H A D | reader.c | 187 row_data->spot_id = *( ( uint32_t * )self->rd_col[ RIDX_SEQ_SPOT_ID ].base ); in reader_get_data()
199 row_data->spot_id, &(row_data->base_pos_offset) ); in reader_get_data()
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| /dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/axf/ |
| H A D | project_read_from_sequence.c | 185 const int64_t *spot_id = argv [ 0 ] . u . data . base; in project_from_sequence_impl() local
195 spot_id += argv [ 0 ] . u . data . first_elem; in project_from_sequence_impl()
204 if ( spot_id[ 0 ] == 0 ) /*** valid case , the projection should be empty ***/ in project_from_sequence_impl()
212 SUB_DEBUG( ( "SUB.Rd in 'project_read_from_sequence.c' at #%lu\n", spot_id[ 0 ] ) ); in project_from_sequence_impl()
214 rc = VCursorCellDataDirect( self->curs, spot_id[ 0 ], self->read_len_idx, in project_from_sequence_impl()
219 rc = VCursorCellDataDirect( self->curs, spot_id[ 0 ], self->read_start_idx, in project_from_sequence_impl()
229 rc = VCursorCellDataDirect( self->curs, spot_id[ 0 ], self->col_idx, in project_from_sequence_impl()
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| /dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/axf/ |
| H A D | project_read_from_sequence.c | 185 const int64_t *spot_id = argv [ 0 ] . u . data . base; in project_from_sequence_impl() local
195 spot_id += argv [ 0 ] . u . data . first_elem; in project_from_sequence_impl()
204 if ( spot_id[ 0 ] == 0 ) /*** valid case , the projection should be empty ***/ in project_from_sequence_impl()
212 SUB_DEBUG( ( "SUB.Rd in 'project_read_from_sequence.c' at #%lu\n", spot_id[ 0 ] ) ); in project_from_sequence_impl()
214 rc = VCursorCellDataDirect( self->curs, spot_id[ 0 ], self->read_len_idx, in project_from_sequence_impl()
219 rc = VCursorCellDataDirect( self->curs, spot_id[ 0 ], self->read_start_idx, in project_from_sequence_impl()
229 rc = VCursorCellDataDirect( self->curs, spot_id[ 0 ], self->col_idx, in project_from_sequence_impl()
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| /dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/test/vdb/ |
| H A D | SYS-224064.cpp | 132 int64_t spot_id = 0; in LowLevelTest() local
145 spot_id = *static_cast<const int64_t*>(data); in LowLevelTest()
146 _ASSERT(spot_id); in LowLevelTest()
169 CALL(VCursorCellDataDirect(seq_cursor, spot_id, in LowLevelTest()
179 cout << " " << align_row << ":" << spot_id << "." << read_id in LowLevelTest()
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| /dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/test/vdb/ |
| H A D | SYS-224064.cpp | 132 int64_t spot_id = 0; in LowLevelTest() local
145 spot_id = *static_cast<const int64_t*>(data); in LowLevelTest()
146 _ASSERT(spot_id); in LowLevelTest()
169 CALL(VCursorCellDataDirect(seq_cursor, spot_id, in LowLevelTest()
179 cout << " " << align_row << ":" << spot_id << "." << read_id in LowLevelTest()
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| /dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/sraxf/ |
| H A D | stats.c | 399 spot_t const spot_id, in group_stats_update() argument
406 if (self->spot_max < spot_id) in group_stats_update()
407 self->spot_max = spot_id; in group_stats_update()
408 if (self->spot_min > spot_id) in group_stats_update()
409 self->spot_min = spot_id; in group_stats_update()
417 int64_t spot_id, in stats_data_update_table() argument
424 group_stats_update(&self->table, spot_id, spot_len, bio_spot_len, cmp_spot_len); in stats_data_update_table()
430 int64_t spot_id, in stats_data_update_group() argument
440 group_stats_update(&self->deflt, spot_id, spot_len, bio_spot_len, cmp_spot_len); in stats_data_update_group()
450 group_stats_update(fnd, spot_id, spot_len, bio_spot_len, cmp_spot_len); in stats_data_update_group()
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| /dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/sraxf/ |
| H A D | stats.c | 399 spot_t const spot_id, in group_stats_update() argument
406 if (self->spot_max < spot_id) in group_stats_update()
407 self->spot_max = spot_id; in group_stats_update()
408 if (self->spot_min > spot_id) in group_stats_update()
409 self->spot_min = spot_id; in group_stats_update()
417 int64_t spot_id, in stats_data_update_table() argument
424 group_stats_update(&self->table, spot_id, spot_len, bio_spot_len, cmp_spot_len); in stats_data_update_table()
430 int64_t spot_id, in stats_data_update_group() argument
440 group_stats_update(&self->deflt, spot_id, spot_len, bio_spot_len, cmp_spot_len); in stats_data_update_group()
450 group_stats_update(fnd, spot_id, spot_len, bio_spot_len, cmp_spot_len); in stats_data_update_group()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/sra/readers/sra/ |
| H A D | sraread.hpp | 174 CSeq_inst::TMol GetSequenceType(spotid_t spot_id, uint8_t read_id) const;
175 TSeqPos GetSequenceLength(spotid_t spot_id, uint8_t read_id) const;
176 CRef<CSeq_entry> GetSpotEntry(spotid_t spot_id) const;
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| H A D | csraread.hpp | 582 TVDBRowId spot_id,
585 TVDBRowId spot_id,
594 bool Select(TVDBRowId spot_id);
595 bool Select(TVDBRowId spot_id, uint32_t read_id);
596 void SetLastSpotId(TVDBRowId spot_id);
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| /dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/py_vdb/ |
| H A D | L2-table_read.py | 52 spot_id = cols[ "SPOT_ID" ].Read( row_id )
53 print( "SPOT_ID[1] = %s"%( spot_id ) )
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| /dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/py_vdb/ |
| H A D | L2-table_read.py | 52 spot_id = cols[ "SPOT_ID" ].Read( row_id )
53 print( "SPOT_ID[1] = %s"%( spot_id ) )
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/data_loaders/csra/ |
| H A D | csraloader_impl.cpp | 558 TVDBRowId spot_id; in GetReadsFileInfo() local
592 *spot_id_ptr = spot_id; in GetReadsFileInfo()
628 TVDBRowId spot_id; in GetBlobId() local
629 TFileLock info = GetReadsFileInfo(idh, &spot_id); in GetBlobId()
631 return GetReadsBlobId(info, spot_id); in GetBlobId()
730 TVDBRowId spot_id; in GetRecords() local
740 file = GetReadsFileInfo(idh, &spot_id); in GetRecords()
837 TVDBRowId spot_id; in GetShortReadIterator() local
839 TFileLock info = GetReadsFileInfo(idh, &spot_id, &read_id); in GetShortReadIterator()
1101 bool CCSRAFileInfo::IsValidReadId(TVDBRowId spot_id, Uint4 read_id, in IsValidReadId() argument
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| /dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/interfaces/align/ |
| H A D | writer-alignment.h | 169 …rc_t CC TableWriterAlgn_Write_SpotId(const TableWriterAlgn* cself, int64_t rowid, int64_t spot_id);
173 int64_t spot_id,
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| /dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/interfaces/align/ |
| H A D | writer-alignment.h | 169 …rc_t CC TableWriterAlgn_Write_SpotId(const TableWriterAlgn* cself, int64_t rowid, int64_t spot_id);
173 int64_t spot_id,
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| /dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/align/ |
| H A D | writer-alignment.c | 395 … rc_t CC TableWriterAlgn_Write_SpotId(const TableWriterAlgn* cself, int64_t rowid, int64_t spot_id) in TableWriterAlgn_Write_SpotId() argument
406 TW_COL_WRITE_VAR(cself->base, cself->cols_spotid[0], spot_id); in TableWriterAlgn_Write_SpotId()
416 int64_t spot_id, in TableWriterAlgn_Write_SpotInfo() argument
429 TW_COL_WRITE_VAR(cself->base, cself->cols_spotid[0], spot_id); in TableWriterAlgn_Write_SpotInfo()
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| /dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/align/ |
| H A D | writer-alignment.c | 395 … rc_t CC TableWriterAlgn_Write_SpotId(const TableWriterAlgn* cself, int64_t rowid, int64_t spot_id) in TableWriterAlgn_Write_SpotId() argument
406 TW_COL_WRITE_VAR(cself->base, cself->cols_spotid[0], spot_id); in TableWriterAlgn_Write_SpotId()
416 int64_t spot_id, in TableWriterAlgn_Write_SpotInfo() argument
429 TW_COL_WRITE_VAR(cself->base, cself->cols_spotid[0], spot_id); in TableWriterAlgn_Write_SpotInfo()
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