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NCBI C++ ToolKit: include/sra/readers/bam/bamindex.hpp Source File

1 #ifndef SRA__READER__BAM__BAMINDEX__HPP 2 #define SRA__READER__BAM__BAMINDEX__HPP 65 void Read

(

const string

& bam_file_name);

78 typedef

vector<SBamHeaderRefInfo>

TRefs

;

89 size_t

GetRefIndex(

const string

& name)

const

;

92 return

m_Refs[index].m_Name;

96 return

m_Refs[index].m_Length;

150 #define BAM_SUPPORT_CSI 154 #ifdef BAM_SUPPORT_CSI 171 static const bool is_CSI

false

;

233

constexpr

int

kAllowedLevels = 10;

234

constexpr

unsigned

kBaseBits =

306 if

( bin >= bin_start ) {

347 const char

Read

(

const char

* buffer_ptr,

const char

* buffer_end,

356 #ifdef BAM_SUPPORT_CSI 363 return

m_Chunks.front().first;

367 return

m_Chunks.back().second;

376 return

b1.

m_Bin

< b2;

380 return

b1 < b2.

m_Bin

;

386 const char

Read

(

const char

* buffer_ptr,

const char

* buffer_end,

399

vector<uint64_t> CollectEstimatedCoverage(

TIndexLevel

min_index_level,

404 return

CollectEstimatedCoverage(ToIndexLevel(min_index_level),

405

ToIndexLevel(max_index_level));

411

vector<TSeqPos> GetAlnOverStarts(

void

)

const

;

414

vector<TSeqPos> GetAlnOverEnds(

void

)

const

;

417 typedef

vector<SBamIndexBinInfo>

TBins

;

419

pair<TBinsIter, TBinsIter> GetLevelBins(

TIndexLevel

level)

const

;

422 return

GetLevelBins(ToIndexLevel(level));

427

pair<TBinsIter, TBinsIter> AddLevelFileRanges(vector<CBGZFRange>& ranges,

429

pair<TBin, TBin> bin_range)

const

;

430

pair<TBinsIter, TBinsIter> GetBinsIterRange(pair<TBin, TBin> bin_range)

const

;

432 void

SetLengthFromHeader(

TSeqPos

length);

451 CBamIndex

(

const string

& index_file_name);

459 void Read

(

const string

& index_file_name);

460 void Read

(

const char

* buffer_ptr,

size_t

buffer_size);

463 typedef

vector<SBamIndexRefIndex>

TRefs

;

470 return

m_Refs.size();

473 void

SetLengthFromHeader(

const CBamHeader

& header);

475 CBGZFRange

GetTotalFileRange(

size_t

ref_index)

const

;

478

MakeEstimatedCoverageAnnot(

const CBamHeader

& header,

479 const string

& ref_name,

480 const string

& seq_id,

481 const string

& annot_name,

482

TIndexLevel min_index_level,

483

TIndexLevel max_index_level)

const

;

486 const string

& ref_name,

487 const string

& seq_id,

488 const string

& annot_name,

492 return

MakeEstimatedCoverageAnnot(header, ref_name, seq_id, annot_name,

493

ToIndexLevel(min_index_level),

494

ToIndexLevel(max_index_level));

498 const string

& ref_name,

499 const string

& seq_id,

500 const string

& annot_name,

503 return

MakeEstimatedCoverageAnnot(header, ref_name, seq_id, annot_name,

504

min_index_level, GetMaxIndexLevel());

508 const string

& ref_name,

509 const string

& seq_id,

510 const string

& annot_name,

513 return

MakeEstimatedCoverageAnnot(header, ref_name, seq_id, annot_name,

514

ToIndexLevel(min_index_level));

517

MakeEstimatedCoverageAnnot(

const CBamHeader

& header,

518 const string

& ref_name,

520 const string

& annot_name,

521

TIndexLevel min_index_level,

522

TIndexLevel max_index_level)

const

;

525 const string

& ref_name,

527 const string

& annot_name,

531 return

MakeEstimatedCoverageAnnot(header, ref_name, seq_id, annot_name,

532

ToIndexLevel(min_index_level),

533

ToIndexLevel(max_index_level));

537 const string

& ref_name,

539 const string

& annot_name,

542 return

MakeEstimatedCoverageAnnot(header, ref_name, seq_id, annot_name,

543

min_index_level, GetMaxIndexLevel());

547 const string

& ref_name,

549 const string

& annot_name,

552 return

MakeEstimatedCoverageAnnot(header, ref_name, seq_id, annot_name,

553

ToIndexLevel(min_index_level));

558

MakeEstimatedCoverageAnnot(

size_t

ref_index,

559 const string

& seq_id,

560 const string

& annot_name,

561

TIndexLevel min_index_level,

562

TIndexLevel max_index_level)

const

;

565 const string

& seq_id,

566 const string

& annot_name,

570 return

MakeEstimatedCoverageAnnot(ref_index, seq_id, annot_name,

571

ToIndexLevel(min_index_level),

572

ToIndexLevel(max_index_level));

576 const string

& seq_id,

577 const string

& annot_name,

580 return

MakeEstimatedCoverageAnnot(ref_index, seq_id, annot_name,

581

min_index_level, GetMaxIndexLevel());

585 const string

& seq_id,

586 const string

& annot_name,

589 return

MakeEstimatedCoverageAnnot(ref_index, seq_id, annot_name,

590

ToIndexLevel(min_index_level));

593

MakeEstimatedCoverageAnnot(

size_t

ref_index,

595 const string

& annot_name,

596

TIndexLevel min_index_level,

597

TIndexLevel max_index_level)

const

;

601 const string

& annot_name,

605 return

MakeEstimatedCoverageAnnot(ref_index, seq_id, annot_name,

606

ToIndexLevel(min_index_level),

607

ToIndexLevel(max_index_level));

612 const string

& annot_name,

615 return

MakeEstimatedCoverageAnnot(ref_index, seq_id, annot_name,

616

min_index_level, GetMaxIndexLevel());

621 const string

& annot_name,

624 return

MakeEstimatedCoverageAnnot(ref_index, seq_id, annot_name,

625

ToIndexLevel(min_index_level));

629

MakeEstimatedCoverageAnnot(

size_t

ref_index,

630 const string

& seq_id,

631 const string

& annot_name,

633

TIndexLevel min_index_level,

634

TIndexLevel max_index_level)

const

;

637 const string

& seq_id,

638 const string

& annot_name,

643 return

MakeEstimatedCoverageAnnot(ref_index, seq_id, annot_name, ref_length,

644

ToIndexLevel(min_index_level),

645

ToIndexLevel(max_index_level));

649 const string

& seq_id,

650 const string

& annot_name,

654 return

MakeEstimatedCoverageAnnot(ref_index, seq_id, annot_name, ref_length,

655

min_index_level, GetMaxIndexLevel());

659 const string

& seq_id,

660 const string

& annot_name,

664 return

MakeEstimatedCoverageAnnot(ref_index, seq_id, annot_name, ref_length,

665

ToIndexLevel(min_index_level));

668

MakeEstimatedCoverageAnnot(

size_t

ref_index,

670 const string

& annot_name,

672

TIndexLevel min_index_level,

673

TIndexLevel max_index_level)

const

;

677 const string

& annot_name,

682 return

MakeEstimatedCoverageAnnot(ref_index, seq_id, annot_name, ref_length,

683

ToIndexLevel(min_index_level),

684

ToIndexLevel(max_index_level));

689 const string

& annot_name,

693 return

MakeEstimatedCoverageAnnot(ref_index, seq_id, annot_name, ref_length,

694

min_index_level, GetMaxIndexLevel());

699 const string

& annot_name,

703 return

MakeEstimatedCoverageAnnot(ref_index, seq_id, annot_name, ref_length,

704

ToIndexLevel(min_index_level));

710

CollectEstimatedCoverage(

size_t

ref_index,

711

TIndexLevel min_index_level,

712

TIndexLevel max_index_level)

const

;

718 return

CollectEstimatedCoverage(ref_index,

719

ToIndexLevel(min_index_level),

720

ToIndexLevel(max_index_level));

728 return

CollectEstimatedCoverage(ref_index, index_level, index_level);

734 return

CollectEstimatedCoverage(ref_index, ToIndexLevel(index_level));

741 return

CollectEstimatedCoverage(ref_index, 0, GetMaxIndexLevel());

748 return

GetRef(ref_index).EstimateDataSizeByAlnStartPos();

753 return

make_pair(m_TotalReadBytes, m_TotalReadSeconds);

765 template

class

Position>

772 typedef

pair<position_type, position_type>

TRange

;

796 if

( !(range.first < range.second) ) {

809

!((iter =

(

))->second < range.first) ) {

812 if

( !(iter->second < range.second) ) {

827

!(range.first < iter->first) &&

828

!(range.second < iter->second));

833

!(range.second <

->first) ) {

834 if

( range.second <

->second ) {

837

range.second =

->second;

843

iter->second = range.second;

878 const CBGZFPos

* file_pos =

nullptr

);

882 const CBGZFPos

* file_pos =

nullptr

);

887 const CBGZFPos

* file_pos =

nullptr

);

892 const CBGZFPos

* file_pos =

nullptr

)

894

SetRanges(index, ref_index, ref_range, index.

ToIndexLevel

(index_level), search_mode, file_pos);

898

TIndexLevel index_level,

899

ESearchMode search_mode = eSearchByOverlap,

900 const CBGZFPos

* file_pos =

nullptr

);

905 const CBGZFPos

* file_pos =

nullptr

)

907

AddRanges(index, ref_index, ref_range, index.

ToIndexLevel

(index_level), search_mode, file_pos);

911

TIndexLevel min_index_level, TIndexLevel max_index_level,

912

ESearchMode search_mode = eSearchByOverlap,

913 const CBGZFPos

* file_pos =

nullptr

);

918 const CBGZFPos

* file_pos =

nullptr

)

920

SetRanges(index, ref_index, ref_range,

923

search_mode, file_pos);

927

TIndexLevel min_index_level, TIndexLevel max_index_level,

928

ESearchMode search_mode = eSearchByOverlap,

929 const CBGZFPos

* file_pos =

nullptr

);

934 const CBGZFPos

* file_pos =

nullptr

)

936

AddRanges(index, ref_index, ref_range,

939

search_mode, file_pos);

957

AddFrom(header, file_pos);

969 return

m_Ranges.begin();

973 return

m_Ranges.end();

977 Uint8

GetFileSize()

const

;

980 void

AddSortedRanges(

const

vector<CBGZFRange>& ranges,

981 const CBGZFPos

* file_pos =

nullptr

);

999 CBamRawDb

(

const string

& bam_path,

const string

& index_path)

1001

Open(bam_path, index_path);

1006 void

Open(

const string

& bam_path);

1007 void

Open(

const string

& bam_path,

const string

& index_path);

1020 return

m_Index.GetFileName();

1028 return GetHeader

().GetRefIndex(ref_label);

1032 return GetHeader

().GetRefName(ref_index);

1036 return GetHeader

().GetRefLength(ref_index);

1047 size_t

ref_index = GetRefIndex(ref_label);

1048 return

GetIndex().GetRef(ref_index).EstimateDataSizeByAlnStartPos(GetRefSeqLength(ref_index));

1051 double

GetEstimatedSecondsPerByte()

const

;

1150 return

m_RecordSize;

1158 return

get_record_ptr() + get_record_size();

1172 return

get_record_ptr()[8];

1176 return

get_record_ptr()[9];

1182 static const char

kCIGARSymbols[];

1199

fAlign_WasPaired = 1 << 0,

1200

fAlign_IsMappedAsPair = 1 << 1,

1201

fAlign_SelfIsUnmapped = 1 << 2,

1202

fAlign_MateIsUnmapped = 1 << 3,

1203

fAlign_SelfIsReverse = 1 << 4,

1204

fAlign_MateIsReverse = 1 << 5,

1205

fAlign_IsFirst = 1 << 6,

1206

fAlign_IsSecond = 1 << 7,

1207

fAlign_IsNotPrimary = 1 << 8,

1208

fAlign_IsLowQuality = 1 << 9,

1209

fAlign_IsDuplicate = 1 << 10,

1210

fAlign_IsSupplementary = 1 << 11

1234 return

get_record_ptr()+32;

1242 return

get_read_name_end();

1254 size_t count

= get_cigar_ops_count();

1255

raw_cigar.resize(

count

);

1258 for

(

size_t i

= 0;

count

; ++

) {

1265 return

get_cigar_end();

1269 return

get_read_ptr() + (get_read_len()+1)/2;

1273 return

get_read_end();

1277 return

get_phred_quality_ptr() + get_read_len();

1281 return

get_phred_quality_end();

1285 return

get_record_end();

1290 return CTempString

(get_read_ptr(), (get_read_len()+1)/2);

1292 static const char

kBaseSymbols[];

1293 string

get_read()

const

;

1296 uint32_t

get_cigar_ref_size()

const

;

1297 uint32_t

get_cigar_read_size()

const

;

1299 string

get_cigar()

const

;

1300 bool

has_ambiguous_match()

const

;

1302 SBamAuxData

get_aux_data(

char

c1,

char

c2,

bool

allow_missing =

false

)

const

;

1318

: m_CurrentRangeEnd(0)

1323 const CBGZFPos

* file_pos =

nullptr

)

1324

: m_Reader(bam_db.GetFile())

1326

Select(bam_db, file_pos);

1329

: m_Reader(bam_db.GetFile())

1331

Select(bam_db, &file_pos);

1334 const string

& ref_label,

1337 const CBGZFPos

* file_pos =

nullptr

)

1338

: m_Reader(bam_db.GetFile())

1340

Select(bam_db, ref_label, ref_range, search_mode, file_pos);

1343 const string

& ref_label,

1347 const CBGZFPos

* file_pos =

nullptr

)

1348

: m_Reader(bam_db.GetFile())

1350

Select(bam_db, ref_label, ref_range, index_level, search_mode, file_pos);

1353 const string

& ref_label,

1357 const CBGZFPos

* file_pos =

nullptr

)

1358

: m_Reader(bam_db.GetFile())

1360

Select(bam_db, ref_label, ref_range, index_level, search_mode, file_pos);

1363 const string

& ref_label,

1368 const CBGZFPos

* file_pos =

nullptr

)

1369

: m_Reader(bam_db.GetFile())

1371

Select(bam_db, ref_label, ref_range, min_index_level, max_index_level, search_mode, file_pos);

1374 const string

& ref_label,

1379 const CBGZFPos

* file_pos =

nullptr

)

1380

: m_Reader(bam_db.GetFile())

1382

Select(bam_db, ref_label, ref_range, min_index_level, max_index_level, search_mode, file_pos);

1385 const string

& ref_label,

1388

ESearchMode search_mode = eSearchByOverlap,

1389 const CBGZFPos

* file_pos =

nullptr

);

1391 const string

& ref_label,

1394

TIndexLevel min_index_level,

1395

TIndexLevel max_index_level,

1396

ESearchMode search_mode = eSearchByOverlap,

1397 const CBGZFPos

* file_pos =

nullptr

);

1399 const string

& ref_label,

1402

EIndexLevel min_index_level,

1403

EIndexLevel max_index_level,

1404

ESearchMode search_mode,

1405 const CBGZFPos

* file_pos =

nullptr

);

1413 const CBGZFPos

* file_pos =

nullptr

)

1415

x_Select(bam_db.

GetHeader

(), file_pos);

1418 const string

& ref_label,

1421 const CBGZFPos

* file_pos =

nullptr

)

1425

search_mode, file_pos);

1428 const string

& ref_label,

1432 const CBGZFPos

* file_pos =

nullptr

)

1436

index_level, search_mode, file_pos);

1439 const string

& ref_label,

1443 const CBGZFPos

* file_pos =

nullptr

)

1447

index_level, search_mode, file_pos);

1450 const string

& ref_label,

1455 const CBGZFPos

* file_pos =

nullptr

)

1459

min_index_level, max_index_level, search_mode, file_pos);

1462 const string

& ref_label,

1467 const CBGZFPos

* file_pos =

nullptr

)

1471

min_index_level, max_index_level, search_mode, file_pos);

1477 const CBGZFPos

* file_pos =

nullptr

)

1479

x_Select(index, ref_index, ref_range,

1480

search_mode, file_pos);

1487 const CBGZFPos

* file_pos =

nullptr

)

1489

x_Select(index, ref_index, ref_range,

1490

index_level, search_mode, file_pos);

1497 const CBGZFPos

* file_pos =

nullptr

)

1499

x_Select(index, ref_index, ref_range,

1500

index_level, search_mode, file_pos);

1512 return

m_AlignInfo.get_file_pos();

1517 return

m_AlignInfo.get_ref_index();

1521 return

m_AlignRefRange.GetFrom();

1527 return

m_AlignInfo.get_next_ref_index();

1531 return

m_AlignInfo.get_next_ref_pos();

1536 return CTempString

(m_AlignInfo.get_read_name_ptr(),

1537

m_AlignInfo.get_read_name_len()-1);

1541 return

m_AlignInfo.get_short_seq_accession_id();

1545 return

m_AlignInfo.get_read_len();

1549 return

m_AlignInfo.get_read();

1553 return

m_AlignInfo.get_read_raw();

1557 return

m_AlignInfo.get_read(

str

);

1562 return

m_AlignInfo.get_cigar_ops_count();

1566 return

m_AlignInfo.get_cigar_op_data(index);

1570 return

m_AlignInfo.get_cigar(raw_cigar);

1574

m_AlignInfo.get_cigar(dst);

1578 return

m_AlignReadRange.GetFrom();

1582 return

m_AlignReadRange.GetLength();

1586 return

m_AlignRefRange.GetLength();

1590 return

make_pair(m_AlignRefRange, m_AlignReadRange);

1594 return

m_AlignInfo.has_ambiguous_match();

1599 return

m_AlignInfo.get_cigar();

1604 return

m_AlignInfo.get_bin();

1608 return

GetBAIIndexBin();

1612 return

GetRangeIndexLevel(m_AlignRefRange);

1616 return

RangeIsOnMinBinIndexLevel(m_AlignRefRange);

1621 return

m_AlignInfo.get_flag();

1636 return

(GetFlags() & m_AlignInfo.fAlign_SelfIsReverse)?

1642 return

(GetFlags() & m_AlignInfo.fAlign_SelfIsUnmapped) == 0;

1647 return

IsMapped()? m_AlignInfo.get_map_quality(): 0;

1652 return

(GetFlags() & m_AlignInfo.fAlign_IsMappedAsPair) != 0;

1656 return

(GetFlags() & m_AlignInfo.fAlign_IsFirst) != 0;

1660 return

(GetFlags() & m_AlignInfo.fAlign_IsSecond) != 0;

1664 return

(GetFlags() & m_AlignInfo.fAlign_IsNotPrimary) != 0;

1667 void

GetSegments(vector<int>& starts, vector<TSeqPos>& lens)

const

;

1671 return CBamAuxIterator

(m_AlignInfo.get_aux_data_ptr(), m_AlignInfo.get_aux_data_end());

1675 return

m_AlignInfo.get_aux_data(c1, c2, allow_missing);

1679 return

GetAuxData(c1, c2).GetInt(index);

1684 const CBGZFPos

* file_pos =

nullptr

);

1687

TIndexLevel min_index_level, TIndexLevel max_index_level,

1688

ESearchMode search_mode,

1689 const CBGZFPos

* file_pos =

nullptr

);

1694 const CBGZFPos

* file_pos =

nullptr

)

1696

x_Select(index, ref_index, ref_range,

1699

search_mode, file_pos);

1704 const CBGZFPos

* file_pos =

nullptr

)

1706

x_Select(index, ref_index, ref_range, 0, index.

GetMaxIndexLevel

(), search_mode, file_pos);

1712 const CBGZFPos

* file_pos =

nullptr

)

1714

x_Select(index, ref_index, ref_range, index_level, index_level, search_mode, file_pos);

1720 const CBGZFPos

* file_pos =

nullptr

)

1722

x_Select(index, ref_index, ref_range, index_level, index_level, search_mode, file_pos);

1724 bool

x_UpdateRange();

1728 return

m_Reader.HaveNextAvailableBytes() || x_UpdateRange();

1732

m_NextRange = m_Ranges.end();

1735 bool

x_NeedToSkip();

static bool operator<(const SBamIndexBinInfo &b1, const SBamIndexBinInfo &b2)

pair< CBGZFPos, CBGZFPos > CBGZFRange

CBamAuxIterator & operator++()

CBamAuxIterator(const char *aux_ptr, const char *aux_end)

const SBamAuxData & operator*() const

const SBamAuxData * operator->() const

DECLARE_OPERATOR_BOOL(m_AuxData)

void SetFrom(CBGZFPos file_pos)

CRangeUnion< CBGZFPos > TRanges

const_iterator end() const

void AddRanges(const CBamIndex &index, size_t ref_index, COpenRange< TSeqPos > ref_range, EIndexLevel min_index_level, EIndexLevel max_index_level, ESearchMode search_mode=eSearchByOverlap, const CBGZFPos *file_pos=nullptr)

const TRanges & GetRanges() const

void SetRanges(const CBamIndex &index, size_t ref_index, COpenRange< TSeqPos > ref_range, EIndexLevel index_level, ESearchMode search_mode=eSearchByOverlap, const CBGZFPos *file_pos=nullptr)

const_iterator begin() const

void SetRanges(const CBamIndex &index, size_t ref_index, COpenRange< TSeqPos > ref_range, EIndexLevel min_index_level, EIndexLevel max_index_level, ESearchMode search_mode=eSearchByOverlap, const CBGZFPos *file_pos=nullptr)

void SetFrom(const CBamHeader &header, const CBGZFPos *file_pos)

void SetWhole(const CBamHeader &header)

void AddRanges(const CBamIndex &index, size_t ref_index, COpenRange< TSeqPos > ref_range, EIndexLevel index_level, ESearchMode search_mode=eSearchByOverlap, const CBGZFPos *file_pos=nullptr)

TRanges::const_iterator const_iterator

const TRefs & GetRefs() const

double m_TotalReadSeconds

vector< uint64_t > CollectEstimatedCoverage(size_t ref_index) const

size_t GetRefCount() const

CRef< CSeq_annot > MakeEstimatedCoverageAnnot(size_t ref_index, const string &seq_id, const string &annot_name, EIndexLevel min_index_level, EIndexLevel max_index_level) const

vector< uint64_t > CollectEstimatedCoverage(size_t ref_index, EIndexLevel index_level) const

const string & GetFileName() const

CRef< CSeq_annot > MakeEstimatedCoverageAnnot(size_t ref_index, const string &seq_id, const string &annot_name, TSeqPos ref_length, EIndexLevel min_index_level) const

CRef< CSeq_annot > MakeEstimatedCoverageAnnot(size_t ref_index, const CSeq_id &seq_id, const string &annot_name, TSeqPos ref_length, EIndexLevel min_index_level, EIndexLevel max_index_level) const

CRef< CSeq_annot > MakeEstimatedCoverageAnnot(const CBamHeader &header, const string &ref_name, const CSeq_id &seq_id, const string &annot_name, EIndexLevel min_index_level) const

CRef< CSeq_annot > MakeEstimatedCoverageAnnot(size_t ref_index, const string &seq_id, const string &annot_name, EIndexLevel min_index_level) const

pair< Uint8, double > GetReadStatistics() const

CRef< CSeq_annot > MakeEstimatedCoverageAnnot(size_t ref_index, const CSeq_id &seq_id, const string &annot_name, EIndexLevel min_index_level) const

CRef< CSeq_annot > MakeEstimatedCoverageAnnot(size_t ref_index, const CSeq_id &seq_id, const string &annot_name, TSeqPos ref_length, TIndexLevel min_index_level=0) const

CRef< CSeq_annot > MakeEstimatedCoverageAnnot(const CBamHeader &header, const string &ref_name, const string &seq_id, const string &annot_name, EIndexLevel min_index_level) const

CRef< CSeq_annot > MakeEstimatedCoverageAnnot(const CBamHeader &header, const string &ref_name, const string &seq_id, const string &annot_name, TIndexLevel min_index_level=0) const

vector< uint64_t > EstimateDataSizeByAlnStartPos(size_t ref_index) const

vector< SBamIndexRefIndex > TRefs

CRef< CSeq_annot > MakeEstimatedCoverageAnnot(size_t ref_index, const CSeq_id &seq_id, const string &annot_name, TSeqPos ref_length, EIndexLevel min_index_level) const

CRef< CSeq_annot > MakeEstimatedCoverageAnnot(const CBamHeader &header, const string &ref_name, const string &seq_id, const string &annot_name, EIndexLevel min_index_level, EIndexLevel max_index_level) const

CRef< CSeq_annot > MakeEstimatedCoverageAnnot(size_t ref_index, const string &seq_id, const string &annot_name, TIndexLevel min_index_level=0) const

CRef< CSeq_annot > MakeEstimatedCoverageAnnot(size_t ref_index, const CSeq_id &seq_id, const string &annot_name, EIndexLevel min_index_level, EIndexLevel max_index_level) const

CRef< CSeq_annot > MakeEstimatedCoverageAnnot(const CBamHeader &header, const string &ref_name, const CSeq_id &seq_id, const string &annot_name, TIndexLevel min_index_level=0) const

CRef< CSeq_annot > MakeEstimatedCoverageAnnot(const CBamHeader &header, const string &ref_name, const CSeq_id &seq_id, const string &annot_name, EIndexLevel min_index_level, EIndexLevel max_index_level) const

CRef< CSeq_annot > MakeEstimatedCoverageAnnot(size_t ref_index, const string &seq_id, const string &annot_name, TSeqPos ref_length, TIndexLevel min_index_level=0) const

vector< uint64_t > CollectEstimatedCoverage(size_t ref_index, TIndexLevel index_level) const

CRef< CSeq_annot > MakeEstimatedCoverageAnnot(size_t ref_index, const string &seq_id, const string &annot_name, TSeqPos ref_length, EIndexLevel min_index_level, EIndexLevel max_index_level) const

CRef< CSeq_annot > MakeEstimatedCoverageAnnot(size_t ref_index, const CSeq_id &seq_id, const string &annot_name, TIndexLevel min_index_level=0) const

vector< uint64_t > CollectEstimatedCoverage(size_t ref_index, EIndexLevel min_index_level, EIndexLevel max_index_level) const

Uint2 GetCIGAROpsCount() const

TSeqPos GetRefSeqPos() const

Int8 GetAuxInt(char c1, char c2, size_t index=0) const

CBamRawAlignIterator(CBamRawDb &bam_db, const string &ref_label, CRange< TSeqPos > ref_range, TIndexLevel index_level, ESearchMode search_mode=eSearchByOverlap, const CBGZFPos *file_pos=nullptr)

Uint1 GetMapQuality() const

Uint2 GetIndexBin() const

CTempString GetShortSeqAcc() const

TSeqPos GetCIGARPos() const

TSeqPos GetNextRefSeqPos() const

Uint2 GetBAIIndexBin() const

CBamRawAlignIterator(CBamRawDb &bam_db, const CBGZFPos *file_pos=nullptr)

SBamAlignInfo m_AlignInfo

bool TryGetFlags(Uint2 &flags) const

void Select(CBamRawDb &bam_db, const string &ref_label, CRange< TSeqPos > ref_range, ESearchMode search_mode=eSearchByOverlap, const CBGZFPos *file_pos=nullptr)

int32_t GetNextRefSeqIndex() const

CBamRawAlignIterator(CBamRawDb &bam_db, const string &ref_label, CRange< TSeqPos > ref_range, EIndexLevel min_index_level, EIndexLevel max_index_level, ESearchMode search_mode, const CBGZFPos *file_pos=nullptr)

void GetCIGAR(CBamString &dst) const

CBamRawAlignIterator(CBamRawDb &bam_db, CBGZFPos file_pos)

pair< COpenRange< TSeqPos >, COpenRange< TSeqPos > > GetCIGARAlignment(void) const

CBamFileRangeSet::const_iterator m_NextRange

bool IsSecondInPair() const

void Select(CBamRawDb &bam_db, const string &ref_label, CRange< TSeqPos > ref_range, EIndexLevel min_index_level, EIndexLevel max_index_level, ESearchMode search_mode=eSearchByOverlap, const CBGZFPos *file_pos=nullptr)

void Select(CBamRawDb &bam_db, const string &ref_label, CRange< TSeqPos > ref_range, TIndexLevel min_index_level, TIndexLevel max_index_level, ESearchMode search_mode=eSearchByOverlap, const CBGZFPos *file_pos=nullptr)

TSeqPos GetShortSequenceLength(void) const

void Select(CBamRawDb &bam_db, const CBGZFPos *file_pos=nullptr)

TIndexLevel GetIndexLevel() const

SBamAuxData GetAuxData(char c1, char c2, bool allow_missing=false) const

TSeqPos GetCIGARRefSize() const

TSeqPos GetCIGARShortSize() const

void x_Select(const CBamIndex &index, size_t ref_index, CRange< TSeqPos > ref_range, EIndexLevel min_index_level, EIndexLevel max_index_level, ESearchMode search_mode, const CBGZFPos *file_pos=nullptr)

CTempString GetShortSeqId() const

CTempString GetShortSequenceRaw() const

void Select(const CBamIndex &index, size_t ref_index, CRange< TSeqPos > ref_range, TIndexLevel index_level, ESearchMode search_mode=eSearchByOverlap, const CBGZFPos *file_pos=nullptr)

CBamAuxIterator GetAuxIterator() const

void Select(CBamRawDb &bam_db, const string &ref_label, CRange< TSeqPos > ref_range, TIndexLevel index_level, ESearchMode search_mode=eSearchByOverlap, const CBGZFPos *file_pos=nullptr)

CBGZFPos GetFilePos() const

string GetShortSequence() const

CBamRawAlignIterator(CBamRawDb &bam_db, const string &ref_label, CRange< TSeqPos > ref_range, TIndexLevel min_index_level, TIndexLevel max_index_level, ESearchMode search_mode=eSearchByOverlap, const CBGZFPos *file_pos=nullptr)

CBamFileRangeSet m_Ranges

Uint4 GetCIGAROp(Uint2 index) const

void Select(const CBamIndex &index, size_t ref_index, CRange< TSeqPos > ref_range, EIndexLevel index_level, ESearchMode search_mode=eSearchByOverlap, const CBGZFPos *file_pos=nullptr)

bool HasAmbiguousMatch() const

TIndexLevel m_MinIndexLevel

void x_Select(const CBamIndex &index, size_t ref_index, CRange< TSeqPos > ref_range, EIndexLevel index_level, ESearchMode search_mode, const CBGZFPos *file_pos=nullptr)

CBamRawAlignIterator(CBamRawDb &bam_db, const string &ref_label, CRange< TSeqPos > ref_range, EIndexLevel index_level, ESearchMode search_mode, const CBGZFPos *file_pos=nullptr)

COpenRange< TSeqPos > m_QueryRefRange

bool IsFirstInPair() const

void Select(const CBamIndex &index, size_t ref_index, CRange< TSeqPos > ref_range, ESearchMode search_mode=eSearchByOverlap, const CBGZFPos *file_pos=nullptr)

void x_Select(const CBamIndex &index, size_t ref_index, CRange< TSeqPos > ref_range, TIndexLevel index_level, ESearchMode search_mode, const CBGZFPos *file_pos=nullptr)

ENa_strand GetStrand() const

void GetShortSequence(CBamString &str) const

DECLARE_OPERATOR_BOOL(m_CurrentRangeEnd)

COpenRange< TSeqPos > m_AlignRefRange

CBamRawAlignIterator & operator++()

CBGZFPos m_CurrentRangeEnd

void Select(CBamRawDb &bam_db, const string &ref_label, CRange< TSeqPos > ref_range, EIndexLevel index_level, ESearchMode search_mode, const CBGZFPos *file_pos=nullptr)

COpenRange< TSeqPos > m_AlignReadRange

void x_Select(const CBamIndex &index, size_t ref_index, CRange< TSeqPos > ref_range, ESearchMode search_mode, const CBGZFPos *file_pos=nullptr)

int32_t GetRefSeqIndex() const

bool IsOnMinBinIndexLevel() const

CBamRawAlignIterator(CBamRawDb &bam_db, const string &ref_label, CRange< TSeqPos > ref_range, ESearchMode search_mode=eSearchByOverlap, const CBGZFPos *file_pos=nullptr)

void GetCIGAR(vector< Uint4 > &raw_cigar) const

size_t GetRefIndex(const string &ref_label) const

CBamRawDb(const string &bam_path)

const string & GetIndexName() const

const string & GetRefName(size_t ref_index) const

size_t GetRefCount() const

const CBamHeader & GetHeader() const

const CBamIndex & GetIndex() const

TSeqPos GetRefSeqLength(size_t ref_index) const

vector< Uint8 > EstimateDataSizeByAlnStartPos(const string &ref_label) const

CBamRawDb(const string &bam_path, const string &index_path)

TRanges::const_iterator const_iterator

const_iterator end() const

map< position_type, position_type > TRanges

CRangeUnion< position_type > TThisType

TThisType & operator+=(const TRange &range)

void add_range(TRange range)

const_iterator begin() const

pair< position_type, position_type > TRange

TRanges::iterator iterator

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

iterator_bool insert(const value_type &val)

const_iterator upper_bound(const key_type &key) const

Include a standard set of the NCBI C++ Toolkit most basic headers.

static DLIST_TYPE *DLIST_NAME() prev(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

static DLIST_TYPE *DLIST_NAME() next(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

static const char * str(char *buf, int n)

unsigned int TSeqPos

Type for sequence locations and lengths.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

void Read(CObjectIStream &in, TObjectPtr object, const CTypeRef &type)

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

uint16_t Uint2

2-byte (16-bit) unsigned integer

int64_t Int8

8-byte (64-bit) signed integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

#define NCBI_BAMREAD_EXPORT

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

ENa_strand

strand of nucleic acid

std::istream & in(std::istream &in_, double &x_)

const char * get_phred_quality_end() const

const char * get_cigar_ptr() const

void get_cigar(vector< uint32_t > &raw_cigar) const

int32_t get_ref_pos() const

uint8_t get_map_quality() const

int32_t get_next_ref_pos() const

uint8_t get_read_name_len() const

CBGZFPos get_file_pos() const

const char * get_read_end() const

const char * get_read_ptr() const

uint32_t get_cigar_op_data(uint16_t index) const

const char * get_cigar_end() const

const char * get_aux_data_end() const

const char * get_read_name_ptr() const

const char * get_phred_quality_ptr() const

const char * get_read_name_end() const

const char * get_record_ptr() const

uint16_t get_flag() const

size_t get_record_size() const

const char * get_aux_data_ptr() const

uint16_t get_cigar_ops_count() const

const char * get_record_end() const

int32_t get_next_ref_index() const

CTempString get_read_raw() const

int32_t get_ref_index() const

uint32_t get_read_len() const

float GetFloat(size_t index=0) const

Int8 GetInt(size_t index=0) const

bool IsTag(char c1, char c2) const

CTempString GetTag() const

DECLARE_OPERATOR_BOOL(m_DataPtr)

CTempString GetString() const

CBGZFPos GetEndFilePos() const

vector< CBGZFRange > m_Chunks

CBGZFPos GetStartFilePos() const

COpenRange< TSeqPos > GetSeqRange(SBamIndexParams params) const

static const TShift kLevelStepBinShift

static const TShift kBAI_min_shift

static const TIndexLevel kMinBinIndexLevel

static const TIndexLevel kBAI_depth

static const TBin kMaxBinNumber

constexpr TShift GetMinBinShift() const

constexpr TSeqPos GetBinSize(TIndexLevel level) const

constexpr TBin GetPseudoBin() const

constexpr TBin GetBinNumberBase(int level) const

TIndexLevel Bin2IndexLevel(TBin bin) const

constexpr TBin GetBinNumberBaseReversed(int reversed_level) const

constexpr TBin GetMinBinNumberBase() const

bool RangeIsOnMinBinIndexLevel(CRange< TSeqPos > range) const

constexpr TBin GetFirstBin(TIndexLevel level) const

TBin GetBinNumber(TSeqPos pos, EIndexLevel level) const

TBin GetBinNumberOffset(TSeqPos pos, EIndexLevel level) const

constexpr TShift GetLevelBinShift(EIndexLevel level) const

constexpr TSeqPos GetPageSize() const

pair< TBin, TBin > GetBinRange(COpenRange< TSeqPos > ref_range, TIndexLevel index_level) const

COpenRange< TSeqPos > GetSeqRange(TBin bin) const

constexpr TSeqPos GetMaxBinSize() const

TBin GetBinNumber(TSeqPos pos, TIndexLevel level) const

bool IsOverflowPos(TSeqPos pos) const

TBin GetBinNumberOffset(TSeqPos pos, TIndexLevel level) const

TBin GetUpperBinNumber(TBin bin) const

constexpr TIndexLevel ToIndexLevel(EIndexLevel level) const

constexpr TSeqPos GetBinSize(EIndexLevel level) const

constexpr TBin GetFirstOverflowBin(TIndexLevel level=0) const

bool IsOverflowBin(TBin bin, TIndexLevel level=0) const

constexpr TBin GetBinNumberBase(EIndexLevel level) const

constexpr TShift GetPageShift() const

constexpr TShift GetMinLevelBinShift() const

TIndexLevel GetRangeIndexLevel(CRange< TSeqPos > range) const

constexpr TSeqPos GetMinBinSize() const

constexpr TShift GetLevelBinShift(TIndexLevel level) const

constexpr TIndexLevel GetMaxIndexLevel() const

constexpr TBin GetLastBin(TIndexLevel level) const

TSeqPos m_EstimatedLength

vector< uint64_t > CollectEstimatedCoverage(EIndexLevel min_index_level, EIndexLevel max_index_level) const

pair< TBinsIter, TBinsIter > GetLevelBins(EIndexLevel level) const

TBins::const_iterator TBinsIter

vector< SBamIndexBinInfo > TBins

CBGZFRange m_UnmappedChunk

vector< CBGZFPos > m_Overlaps

static Uint4 MakeUint4(const char *buf)

static Uint2 MakeUint2(const char *buf)

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