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NCBI C++ ToolKit: src/sra/data_loaders/bam/bamloader_impl.cpp Source File

(BAM_LOADER, SKIP_EMPTY_PILEUP_GRAPHS)::GetDefault();

(BAM_LOADER, SKIP_EMPTY_PILEUP_GRAPHS)::SetDefault(param);

(BAM_LOADER, ESTIMATED_COVERAGE_GRAPH)::GetDefault();

(BAM_LOADER, ESTIMATED_COVERAGE_GRAPH)::SetDefault(param);

(BAM_LOADER, PREFER_RAW_INDEX_OVER_COVERAGE_GRAPH)::GetDefault();

(BAM_LOADER, SPLIT_BIN_DATA_SIZE)::GetDefault();

(BAM_LOADER, SPLIT_BIN_MIN_LENGTH)::GetDefault();

<

Call>

( retry_count == 0 ) {

(

= 1;

< retry_count; ++

) {

( exception& exc ) {

(

<<name<<

<<wait_sec<<

);

: m_BamName(bam_name), m_SeqId(seq_id)

: m_IdMapper(params.m_IdMapper)

( !mapper_file_name.empty() ) {

+def_name);

vector<string> tokens;

( getline(

, line) ) {

( tokens.size() < 4 ) {

+line+

);

.m_BamSeqLabel = tokens[0];

.m_Label = tokens[1];

( tokens[2].

() ) {

.m_BamFileName = tokens[3];

( tokens.size() >= 4 ) {

.m_CovFileName = tokens[4];

.m_BamSeqLabel,

.m_SeqId);

bam_info = iter->second;

( !

.m_CovFileName.empty() ) {

.m_BamFileName = bam;

it->second->GetShortSeqBlobId(ret, idh);

it->second->GetRefSeqBlobId(ret, idh);

& name = it->m_AnnotName;

( name.empty() ) {

& refseq_label,

refseq_label = rit.GetRefSeqId();

(

.m_IdMapper.get() ) {

( !include_tags.empty() ) {

(

&

: tags ) {

<<refseq_label<<

<<refseq_id);

<<refseq_id<<

<<refseq_label<<

<<

());

it->second->GetShortSeqBlobId(ret, idh);

->SetBlobId(ret, idh);

it->second.GetNCPointer();

(

.spot1.empty() ) {

(

.spot1 == seq ) {

(

.spot2.empty() ) {

(

.spot2 == seq ) {

& refseqid,

m_RefSeqId(refseqid),

m_LoadedRanges(

)

<<idh<<

<<ret->ToString()<<

<<id->ToString());

Collect(

& bam_db,

& ref_id,

GetStatCount(

)

{

GetStatLen(

)

{

m_RefPosLast - m_RefPosFirst + .5;

SRefStat::Collect(

& bam_db,

& ref_id,

m_RefPosQuery = ref_pos;

( ; ait; ++ait ) {

( pos < ref_pos ) {

( min_quality > 0 && ait.

() < min_quality ) {

(

> ref_len ) {

(

> m_RefLenMax ) {

(

> m_RefPosMax ) {

( m_Count == 0 ) {

( ++m_Count ==

) {

<<m_RefPosQuery<<

<<m_Count<<

<<

m_RefPosFirst<<

<<m_RefPosLast<<

<<m_RefPosMax-m_RefPosLast<<

<<

<<m_RefLenMax<<

<<skipped);

<<

);

( alist.size() != 1 ) {

<<

annot = alist.front();

( glist.size() != 1 ) {

<<

graph = glist.front();

( (*it)->IsUser() &&

(*it)->GetUser().GetType().GetStr() ==

) {

params = &(*it)->GetUser();

vmul = graph->

();

vadd = graph->

();

outliers_mul = 1./slot;

non_zero_count = 0;

vector<double> cov(

);

vmin =

.GetMin();

vmax =

.GetMax();

vg =

(vv[

]);

vmin =

.GetMin();

vmax =

.GetMax();

total_cov = avg_cov*non_zero_count*slot;

avg_align_len = total_cov/align_cnt;

max_align_len =

(avg_align_len*2+50);

cov_to_align_cnt = (align_cnt*slot)/total_cov;

next_cnt =

==

? 0: cov[

] * cov_to_align_cnt;

<<cur_first<<

<<cur_last<<

<<cur_cnt);

end = cur_last*slot+slot;

(

)

;

cur_cnt +=

(next_cnt, 1e-9);

<<

<<

<<exc);

< over_ends.size()? over_ends[

]:

*bin_size+bin_size-1;

vector<Uint4> over_ends = refseq.GetAlnOverEnds();

<<bin_size<<

<<data_sizes.size()<<

<<(bin_size*data_sizes.size()));

<<accumulate(data_sizes.begin(), data_sizes.end(),

(0)));

kZeroBlocks = 8;

kMaxChunkLength = 300*1024*1024;

cur_data_size = 0;

( split_bin_data_size == 0 || split_bin_min_length == 0 ) {

(

= 0;

<= bin_count; ++

) {

(

< bin_count && !data_sizes[

] ) {

(

== bin_count || zero_count >= kZeroBlocks ) {

( cur_data_size ) {

(last_pos < pos-zero_count*bin_size);

non_zero_end = pos - zero_count*bin_size;

.m_DataSize = cur_data_size;

.m_RefSeqRange.SetFrom(last_pos);

.m_RefSeqRange.SetTo(

(over_ends,

-zero_count-1, bin_size));

.m_MaxRefSeqFrom = non_zero_end-1;

<<

.m_RefSeqRange.GetFrom()<<

<<

.m_MaxRefSeqFrom<<

<<

.m_RefSeqRange.GetTo()<<

<<

.m_DataSize);

last_pos = non_zero_end;

( zero_count > 0 ) {

(last_pos == pos-zero_count*bin_size);

.m_DataSize = 0;

.m_RefSeqRange.SetFrom(last_pos);

.m_RefSeqRange.SetTo(

(over_ends,

-zero_count, bin_size));

.m_MaxRefSeqFrom = last_pos;

<<

.m_RefSeqRange.GetFrom()<<

<<

.m_MaxRefSeqFrom<<

<<

.m_RefSeqRange.GetTo()<<

<<

.m_DataSize);

(

== bin_count ) {

cur_data_size += data_sizes[

];

pos+bin_size-last_pos >= kMaxChunkLength ||

(

+1 < bin_count && data_sizes[

+1] > split_bin_data_size) ) {

data_sizes[

] > split_bin_data_size &&

bin_size > split_bin_min_length ) {

(cur_data_size == data_sizes[

]);

split_shift = 0;

( (cur_data_size >> split_shift) > split_bin_data_size &&

(bin_size >> split_shift) > split_bin_min_length ) {

sub_chunk_count = 1 << split_shift;

sub_chunk_data_size = cur_data_size >> split_shift;

sub_chunk_len = bin_size >> split_shift;

<<

.size()<<

<<last_pos<<

<<(pos+bin_size)<<

<<ref_end<<

<<

<<cur_data_size);

(

= 0;

< sub_chunk_count; ++

) {

.m_DataSize = sub_chunk_data_size;

.m_RefSeqRange.SetFrom(last_pos+

*sub_chunk_len);

.m_MaxRefSeqFrom = pos+(

+1)*sub_chunk_len-1;

.m_RefSeqRange.SetTo(

==0? ref_end:

.m_MaxRefSeqFrom);

.m_PileupChunkCount =

==0? sub_chunk_count: 0;

<<

.size()<<

<<

.m_RefSeqRange.GetFrom()<<

<<

.m_MaxRefSeqFrom<<

<<

.m_RefSeqRange.GetTo()<<

<<

.m_DataSize);

last_pos = pos+bin_size;

.m_DataSize = cur_data_size;

.m_RefSeqRange.SetFrom(last_pos);

.m_RefSeqRange.SetTo(

(over_ends,

, bin_size));

.m_MaxRefSeqFrom = pos+bin_size-1;

<<

.m_RefSeqRange.GetFrom()<<

<<

.m_MaxRefSeqFrom<<

<<

.m_RefSeqRange.GetTo()<<

<<

.m_DataSize);

last_pos = pos+bin_size;

kStatCount = 1000;

ref_begin = 0, ref_end_min = 0, ref_end = 0, max_len = 0;

stat_len = 0, stat_cnt = 0;

scan_first = 1;

( stat[0].m_Count != kStatCount ) {

( stat[0].m_Count > 0 ) {

ref_begin = stat[0].m_RefPosFirst;

ref_end_min = stat[0].m_RefPosLast;

max_len = stat[0].m_RefLenMax;

stat_len = stat[0].GetStatLen();

stat_cnt = stat[0].GetStatCount();

(

>

+max_len+1 ) {

(

<<

<<

<<

<<

<<mid);

(

k = scan_first; k <

; ++k ) {

( k && ref_pos < stat[k-1].m_RefPosLast ) {

ref_pos = stat[k-1].m_RefPosLast;

(

<<k<<

<<ref_pos);

stat_len += stat[k].GetStatLen();

stat_cnt += stat[k].GetStatCount();

( stat[k].m_RefLenMax > max_len ) {

max_len = stat[k].m_RefLenMax;

density = stat_cnt / stat_len;

exp_count = (ref_end-ref_begin)*density;

chunks = unsigned(exp_count/

+1);

chunks =

(chunks,

(sqrt(exp_count)+1));

<<ref_begin<<

<<ref_end-1<<

<<exp_count<<

<<chunks);

vector<TSeqPos> pp(chunks+1);

(

k = 1; k < chunks; ++k ) {

(

(ref_end-ref_begin)*k/chunks);

pp[chunks] = ref_end;

(

k = 0; k < chunks; ++k ) {

( k+1 < chunks ) {

end2 =

(end2, pp[k+2]);

( min_quality > 0 && ait.

() < min_quality ) {

( ref_end > ref_len ) {

rr.push_back(

(ref_pos, ref_end));

( !rr.empty() ) {

(rr.begin(), rr.end());

(

p = 0; p < rr.size(); ) {

min_from = rr[p].GetFrom();

max_from = rr[e++].GetFrom();

( e < rr.size() && rr[e].GetFrom() == max_from ) {

max_to_open = max_from;

(

= p;

< e; ++

) {

max_to_open =

(max_to_open, rr[

].GetToOpen());

<<

(min_from, max_from)<<

<<max_to_open-1);

rr[0].GetFrom()<<

<<rr.back().GetTo()<<

<<rr.size()<<

<<

.size());

& chunk =

[range_id];

last_range_id = range_id;

( chunk_count ) {

last_range_id += chunk_count-1;

( last_range_id+1 <

.size() ) {

refseq_index = size_t(-1);

(

range_id = 0; range_id <

.size(); ++range_id ) {

align_count =

[range_id].GetAlignCount();

data_size =

[range_id].m_DataSize;

( align_count == 0 && data_size != 0 ) {

( data_size == 0 && align_count != 0 ) {

( has_pileup &&

[range_id].m_PileupChunkCount ) {

bytes = data_size*

[range_id].m_PileupChunkCount;

<<chunk->

()<<

<<pileup_range<<

<<bytes<<

);

(

[range_id].m_PileupChunkCount > 1 ) {

<<chunk->

()<<

<<pileup_range);

(

[range_id].m_PileupChunkCount > 1 ) {

<<chunk->

()<<

<<wide_range<<

<<bytes<<

);

( align_count ) {

(

[range_id].m_PileupChunkCount != 1 ) {

<<chunk->

()<<

<<start_range<<

<<data_size<<

);

<<chunk->

()<<

<<start_range<<

<<bytes<<

);

<<chunk->

()<<

<<wide_range<<

<<bytes<<

);

<<chunk->

()<<

<<wide_range<<

<<data_size<<

);

<<chunk->

()<<

<<wide_range<<

<<align_count<<

);

start_range =

[range_id].GetAlignStartRange();

start_range.GetFrom(), start_range.GetLength(),

&

[range_id].m_FilePosFirstStarting);

max_end_pos =

(max_end_pos, start_range.GetToOpen());

start_range.GetFrom(), start_range.GetLength(),

start_range =

[range_id].GetAlignStartRange();

start_range.GetFrom(), start_range.GetLength(),

vector<CSeq_id_Handle>& short_ids)

vector<CSeq_id_Handle> new_short_ids;

(

&

: short_ids ) {

new_short_ids.push_back(

);

( new_short_ids.empty() ) {

(

&

: new_short_ids ) {

sw_attach.

();

time = sw_attach.

();

<<

range_id<<

<<(seq_chunk_id-range_id*

)<<

<<

[range_id].GetRefSeqRange()<<

<<time);

skipped = 0,

= 0, repl_count = 0, fail_count = 0;

vector<CSeq_id_Handle> short_ids;

( ; ait; ++ait ) {

(align_pos >=

[range_id].GetRefSeqRange().GetFrom());

( min_quality > 0 && ait.

() < min_quality ) {

( align_end > max_end_pos ) {

( !align_list ) {

align_list = &annot->

().SetAlign();

sw_create.

();

time = sw_create.

();

<<

[range_id].GetRefSeqRange()<<

<<

<<

<<repl_count<<

<<fail_count<<

<<skipped<<

<<time);

time = sw_attach.

();

<<

[range_id].GetRefSeqRange()<<

<<time);

<<

[range_id].GetRefSeqRange()<<

<<

<<

<<repl_count<<

<<fail_count<<

<<skipped<<

<<

.

());

= 0, skipped = 0, dups = 0, far_refs = 0;

list< CRef<CBioseq> > bioseqs;

(

= 1;

< sub_chunk_count; ++

) {

start_range.GetFrom(), split_pos-start_range.GetFrom(),

&

[range_id].m_FilePosFirstCrossing);

( ; ait; ++ait ) {

(align_pos<split_pos);

( min_quality > 0 && ait.

() < min_quality ) {

( align_end <= split_pos ) {

( iter ==

.

() || iter->second != chunk_id ) {

( !loaded.

(seq_id).second ) {

( ; ait; ++ait ){

( align_pos < start_range.GetFrom() ) {

( min_quality > 0 && ait.

() < min_quality ) {

( align_end > max_end_pos ) {

( iter ==

.

() || iter->second != chunk_id ) {

( !loaded.

(seq_id).second ) {

<<

<<skipped<<

<<dups<<

<<far_refs<<

<<

.

());

total_pileup_range;

total_pileup_aligns;

total_pileup_time_collect;

total_pileup_time_max;

total_pileup_time_make;

STimePrinter {

( total_pileup_range ) {

<<total_pileup_range<<

<<total_pileup_aligns<<

<<total_pileup_time_collect<<

<<total_pileup_time_max<<

<<total_pileup_time_make);

file_pos_first_crossing(),

file_pos_first_starting()

vector<SSplit> TSplits;

TSplits::iterator cur_split;

vector<CSeq_id_Handle> short_ids;

TSeq2Chunk* seq2chunk = 0;

seq_chunk_id = 0;

seq_skipped = 0;

seq_dups = 0;

seq_count = 0;

list<CRef<CBioseq>> bioseqs;

SPileupGraphCreator(

& annot_name,

: annot_name(annot_name),

ref_range(ref_range),

min_quality(min_quality),

cur_split(splits.begin())

( min_quality > 0 && ait.

() < min_quality ) {

( cur_split != splits.end() ) {

( !cur_split->file_pos_first_starting ) {

( pos >= cur_split->seq_pos ) {

( end > cur_split->seq_pos ) {

( !cur_split->file_pos_first_crossing ) {

( !align_list ) {

align_list = &annot->

().SetAlign();

short_ids.push_back(seq_id);

iter = seq2chunk->insert(make_pair(seq_id, seq_chunk_id)).first;

( iter->second != seq_chunk_id ) {

( !loaded.

(seq_id).second ) {

x_CreateGraph(SGraph&

)

*

titles[

] = {

,

,

,

,

,

,

graph->SetTitle(titles[&

-graphs]);

loc.

(*ref_id);

graph->SetNumval(length);

x_FinalizeGraph(SGraph&

)

(

.max_value < 256 ) {

(

.graph->GetGraph().IsByte());

(

.graph->GetGraph().GetByte().GetValues().size() == ref_range.

());

.SetMax(

.max_value);

(

.graph->GetGraph().IsInt());

(

.graph->GetGraph().GetInt().GetValues().size() == ref_range.

());

.SetMax(

.max_value);

x_AdjustACGT(

ref_offset)

have_acgt =

;

(

k = 0; k < kNumStat_ACGT; ++k ) {

( graphs[k].graph ) {

(

k = 0; k < kNumStat_ACGT; ++k ) {

SGraph&

= graphs[k];

.bytes = &

.graph->SetGraph().SetByte().SetValues();

(

k = 0; k <

; ++k ) {

SGraph&

= graphs[k];

.bytes = &

.graph->SetGraph().SetByte().SetValues();

.bytes->reserve(

);

(

k = 0; k <

; ++k ) {

x_FinalizeGraph(graphs[k]);

AddZerosBy16(

)

(

k = 0; k <

; ++k ) {

SGraph&

= graphs[k];

x_UpdateMaxIsInt(SGraph&

, TCount max_added,

ref_offset)

.max_value = max_added;

( max_added >= 256 ) {

.ints = &

.graph->SetGraph().SetInt().SetValues();

.bytes = &

.graph->SetGraph().SetByte().SetValues();

( max_added >= 256 ) {

.max_value =

(

.max_value, max_added);

.ints = &int_graph->SetValues();

=

.bytes->size();

.graph->SetGraph().SetInt(*int_graph);

(

.ints ) {

.max_value =

(

.max_value, max_added);

x_AddValuesBy16(SGraph&

,

,

TCount* src)

(

.ints ) {

x_AddValues(SGraph&

,

,

TCount* src)

(

.ints ) {

( make_intron ) {

dst_byte = 0, dst_int = 0;

(

k = 0; k < kNumStat_ACGT; ++k ) {

SGraph&

= graphs[k];

(

.ints ) {

( dst_byte == kNumStat_ACGT ) {

( dst_int == kNumStat_ACGT ) {

(

k = 0; k < kNumStat_ACGT; ++k ) {

SGraph&

= graphs[k];

x_AddValues(graphs[kStat_Gap],

, values.

.

());

( make_intron ) {

(

k = 0; k < kNumStat_ACGT; ++k ) {

SGraph&

= graphs[k];

(

k = 0; k <

; ++k ) {

SGraph&

= graphs[k];

( max_added != 0 ||

.graph ) {

x_UpdateMaxIsInt(

, max_added, ref_offset);

x_AdjustACGT(ref_offset);

x_AddValuesBy16(

, values);

(

k = 0; k <

; ++k ) {

SGraph&

= graphs[k];

( max_added != 0 ||

.graph ) {

x_UpdateMaxIsInt(

, max_added, ref_offset);

x_AdjustACGT(ref_offset);

x_AddValues(

, values);

gg.splits.push_back(

[range_id+

].GetRefSeqRange().GetFrom());

gg.cur_split = gg.splits.begin();

intron_mode, gap_to_intron_threshold);

seq2chunk_guard.Release();

[range_id+

].m_FilePosFirstCrossing = gg.splits[

-1].file_pos_first_crossing;

[range_id+

].m_FilePosFirstStarting = gg.splits[

-1].file_pos_first_starting;

desc->SetName(name);

annot->

().Set().push_back(desc);

total_bytes = 0;

(

k = 0; k < ss.

; ++k ) {

SPileupGraphCreator::SGraph&

= gg.graphs[k];

annot->

().SetGraph().push_back(

.graph);

total_bytes +=

.bytes->size()*

(

.bytes->front())+10000;

total_bytes +=

.ints->size()*

(

.ints->front())+10000;

align_count = 0;

align_count = gg.annot->GetData().GetAlign().size();

<<

<<align_count<<

<<

.

());

(

k = 0; k <

; ++k ) {

[k].resize(

);

:

[

][pos] += 1;

;

:

[

][pos] += 1;

;

:

[

][pos] += 1;

;

:

[

][pos] += 1;

;

1:

[

][pos] += 1;

;

2:

[

][pos] += 1;

;

4:

[

][pos] += 1;

;

8:

[

][pos] += 1;

;

( gap_pos < 0 ) {

gap_end = gap_pos + gap_len;

( gap_end >

) {

[stat][gap_pos] += 1;

( gap_end <

) {

[stat][gap_end] -= 1;

+=

[stat][

];

[stat][

] =

;

[

].empty()? 0: *max_element(

[

].begin(),

[

].end());

(

k = 0; k <

; ++k ) {

b2 = read_raw[pos/2];

pos%2? b2&0xf: b2>>4;

= 0, skipped = 0;

( ; ait; ++ait ) {

( !ss.AcceptAlign(ait) ) {

align_pos = rit->GetRefSeqPos();

( align_end > ref_len ) {

ss_pos = align_pos - graph_range.GetFrom();

read_raw = rit->GetShortSequenceRaw();

op = rit->GetCIGAROp(

);

seglen = op >> 4;

( op & 0xf ) {

( ; ait; ++ait ) {

( !ss.AcceptAlign(ait) ) {

( align_end > ref_len ) {

* ptr = cigar.

();

* end = ptr + cigar.

();

( ptr != end ) {

( ; ++ptr != end; ) {

( c >=

&& c <=

) {

seglen = seglen*10+(c-

);

( seglen == 0 ) {

(4,

<<

<<

<<cigar);

(

==

) {

(

==

||

==

) {

ss.

(ss_pos, read[read_pos]);

(

==

||

==

) {

(

==

) {

(

==

) {

(

==

) {

(

!=

) {

(14,

<<

<<

<<cigar);

annot->

().Set().push_back(desc);

total_bytes = 0;

,

,

,

,

,

,

loc.

(*ref_id);

loc.

(graph_range.GetFrom());

loc.

(graph_range.GetTo());

graph->

(graph_range.GetLength());

.SetValues().assign(ss.

[k].begin(), ss.

[k].end());

total_bytes += graph_range.GetLength()*

(

.GetValues()[0])+10000;

.SetValues().assign(ss.

[k].begin(), ss.

[k].end());

total_bytes += graph_range.GetLength()*

(

.GetValues()[0])+10000;

annot->

().SetGraph().push_back(graph);

bool IsReverse(ENa_strand s)

static const size_t kChunkSize

static bool GetMinMapQualityParam(void)

static const Uint8 kDefaultSplitBinDataSize

NCBI_DEFINE_ERR_SUBCODE_X(30)

static double s_CreateTime

static string GetMapperContext(void)

static const size_t kChunkDataSize

static const double k_make_align_seconds

static const TSeqPos kDefaultSplitBinMinLength

static string GetIncludeAlignTagsParam(void)

std::invoke_result< Call >::type CallWithRetry(Call &&call, const char *name, int retry_count=0)

static const CUser_field & GetIdField(const CUser_field &field, int id)

static TSeqPos s_GetGapToIntronThreshold(void)

static int GetDebugLevel(void)

NCBI_PARAM_DEF(bool, BAM_LOADER, PILEUP_GRAPHS, true)

static const double k_make_graph_seconds

static const Uint8 kSingleAlignBytes

static const double k_make_read_seconds

static Uint8 GetSplitBinDataSize(void)

static bool GetPreferRawIndexOverCoverageGraphParam(void)

static string GetMapperFileName(void)

static bool GetSkipEmptyPileupGraphsParam(void)

static TSeqPos s_GetEnd(const vector< TSeqPos > &over_ends, TSeqPos i, TSeqPos bin_size)

static bool s_GetMakeIntronGraph(void)

static const size_t kSplitLevelsChunkDataSize

static bool GetEstimatedCoverageGraphParam(void)

static bool GetPileupGraphsParam(void)

NCBI_PARAM_DEF_EX(int, BAM_LOADER, DEBUG, 0, eParam_NoThread, BAM_LOADER_DEBUG)

static TSeqPos GetSplitBinMinLength(void)

static const int kMainChunkId

static double s_AttachTime

static Uint1 sx_GetBaseRaw(CTempString read_raw, TSeqPos pos)

NCBI_PARAM_DECL(int, BAM_LOADER, DEBUG)

#define PILEUP_NAME_SUFFIX

@ eChunk_short_seq_pileup

bool operator==(const CBlobId &id) const

bool operator<(const CBlobId &id) const

CBAMBlobId(const CTempString &str)

string ToString(void) const

Get string representation of blob id.

CDataSource::SGiFound GetGi(const CSeq_id_Handle &idh)

CRef< CBAMBlobId > GetRefSeqBlobId(const CSeq_id_Handle &idh)

CBamRefSeqInfo * GetRefSeqInfo(const CBAMBlobId &blob_id)

CBAMDataLoader::TAnnotNames GetPossibleAnnotNames(void) const

bool IsShortSeq(const CSeq_id_Handle &idh)

void LoadChunk(const CBAMBlobId &blob_id, CTSE_Chunk_Info &chunk)

double EstimateLoadSeconds(const CBAMBlobId &blob_id, const CTSE_Chunk_Info &chunk, Uint4 bytes)

CDataSource::SAccVerFound GetAccVer(const CSeq_id_Handle &idh)

string GetLabel(const CSeq_id_Handle &idh)

CBAMDataLoader_Impl(const CBAMDataLoader::SLoaderParams &params)

void GetIds(const CSeq_id_Handle &idh, TIds &ids)

TTaxId GetTaxId(const CSeq_id_Handle &idh)

vector< CSeq_id_Handle > TIds

bool BAMFilesOpened() const

friend class CBamFileInfo

void AddBamFile(const CBAMDataLoader::SBamFileName &bam)

~CBAMDataLoader_Impl(void)

void LoadBAMEntry(const CBAMBlobId &blob_id, CTSE_LoadLock &load_lock)

AutoPtr< IIdMapper > m_IdMapper

CRef< CBAMBlobId > GetShortSeqBlobId(const CSeq_id_Handle &idh)

vector< SDirSeqInfo > TSeqInfos

static void SetMinMapQualityParamDefault(int param)

static void SetIncludeAlignTagsParamDefault(const string &param)

static void SetPileupGraphsParamDefault(bool param)

static string GetIncludeAlignTagsParamDefault(void)

static bool GetPreOpenParam(void)

static void SetEstimatedCoverageGraphParamDefault(bool param)

static void SetSkipEmptyPileupGraphsParamDefault(bool param)

static bool GetPileupGraphsParamDefault(void)

static bool GetEstimatedCoverageGraphParamDefault(void)

vector< CAnnotName > TAnnotNames

static int GetMinMapQualityParamDefault(void)

static void SetPreOpenParam(bool param)

static bool GetSkipEmptyPileupGraphsParamDefault(void)

void SetEstimated(bool estimated=true)

void SetAnnotName(const string &name)

CRef< CSeq_annot > MakeSeq_annot(CBamMgr &mgr, const string &bam_file, const string &bam_index)

Generate Seq-annot for BAM file using BAM file index.

void SetRefLabel(const string &ref_label)

void SetRefId(const CSeq_id &ref_id)

void SetMinMapQuality(int qual)

ISpotIdDetector interface is used to detect spot id in case of incorrect flag combination.

CRef< CSeq_align > GetMatchAlign(void) const

CRef< CBioseq > GetShortBioseq(void) const

CTempString GetShortSequence(void) const

TSeqPos GetShortSequenceLength(void) const

CRef< CSeq_id > GetShortSeq_id(void) const

CRef< CSeq_annot > GetSeq_annot(void) const

TSeqPos GetRefSeqPos(void) const

CTempString GetCIGAR(void) const

TSeqPos GetCIGARRefSize(void) const

CBamRawAlignIterator * GetRawIndexIteratorPtr() const

Uint1 GetMapQuality(void) const

void SetSpotIdDetector(ISpotIdDetector *spot_id_detector)

TSeqPos GetCIGARPos(void) const

bool IsSetStrand(void) const

ENa_strand GetStrand(void) const

size_t CollectPileup(SPileupValues &values, const string &ref_id, CRange< TSeqPos > graph_range, ICollectPileupCallback *callback=0, SPileupValues::EIntronMode intron_mode=SPileupValues::eNoCountIntron, TSeqPos gap_to_intron_threshold=kInvalidSeqPos) const

bool UsesRawIndex() const

bool IncludeAlignTag(CTempString tag)

void SetIdMapper(IIdMapper *idmapper, EOwnership ownership)

TSeqPos GetRefSeqLength(const string &str) const

const string & GetBamName(void) const

void GetRefSeqBlobId(CRef< CBAMBlobId > &ret, const CSeq_id_Handle &idh) const

const string & GetAnnotName(void) const

void GetShortSeqBlobId(CRef< CBAMBlobId > &ret, const CSeq_id_Handle &idh) const

void x_Initialize(const CBAMDataLoader_Impl &impl, const CBAMDataLoader::SBamFileName &bam)

CBamRefSeqInfo * GetRefSeqInfo(const CSeq_id_Handle &seq_id) const

void AddRefSeq(const string &refseq_label, const CSeq_id_Handle &refseq_id)

CBamFileInfo(const CBAMDataLoader_Impl &impl, const CBAMDataLoader::SBamFileName &bam, const string &refseq_label=kEmptyStr, const CSeq_id_Handle &seq_id=CSeq_id_Handle())

TSeqPos GetRefSeqLength(const string &id) const

static Uint8 GetFileSize(CBGZFRange range)

const SBamIndexRefIndex & GetRef(size_t ref_index) const

CBGZFPos GetFilePos() const

bool IsOnMinBinIndexLevel() const

size_t GetRefIndex(const string &ref_label) const

double GetEstimatedSecondsPerByte() const

const CBamIndex & GetIndex() const

TSeqPos GetRefSeqLength(size_t ref_index) const

void AddRefSeqRange(const TRange &range)

TRange GetAlignStartRange() const

const TRange & GetRefSeqRange(void) const

void LoadMainChunk(CTSE_Chunk_Info &chunk_info)

void SetBlobId(CRef< CBAMBlobId > &ret, const CSeq_id_Handle &idh) const

void x_LoadRangesScan(void)

CBamRefSeqInfo(CBamFileInfo *bam_file, const string &refseqid, const CSeq_id_Handle &seq_id)

void x_AddSeqChunk(CTSE_Chunk_Info &chunk_info, const vector< CSeq_id_Handle > &short_ids)

void x_LoadRangesStat(void)

void LoadSeqChunk(CTSE_Chunk_Info &chunk_info)

void LoadPileupChunk(CTSE_Chunk_Info &chunk_info)

const string & GetRefSeqId(void) const

void GetShortSeqBlobId(CRef< CBAMBlobId > &ret, const CSeq_id_Handle &idh) const

CRef< CSeq_entry > m_CovEntry

double EstimatePileupLoadSeconds(const CTSE_Chunk_Info &chunk, Uint4 bytes) const

void LoadMainSplit(CTSE_LoadLock &load_lock)

void LoadAlignChunk(CTSE_Chunk_Info &chunk_info)

double EstimateLoadSeconds(const CTSE_Chunk_Info &chunk, Uint4 bytes) const

const CSeq_id_Handle & GetRefSeq_id(void) const

double EstimateSeqLoadSeconds(const CTSE_Chunk_Info &chunk, Uint4 bytes) const

void CreateChunks(CTSE_Split_Info &split_info)

CRange< TSeqPos > GetChunkGraphRange(size_t range_id)

void LoadMainEntry(CTSE_LoadLock &load_lock)

bool x_LoadRangesEstimated(void)

double EstimateAlignLoadSeconds(const CTSE_Chunk_Info &chunk, Uint4 bytes) const

void LoadChunk(CTSE_Chunk_Info &chunk_info)

CIRef< CBamAlignIterator::ISpotIdDetector > m_SpotIdDetector

bool x_LoadRangesCov(void)

void x_InitAlignIterator(CBamAlignIterator &ait, TSeqPos &max_end_pos, CTSE_Chunk_Info &chunk_info, int base_id)

Blob state exceptions, used by GenBank loader.

void AddSpotId(string &short_id, const CBamAlignIterator *iter)

map< string, SShortSeqInfo > m_ShortSeqs

IdMapper implementation using an external configuration file.

IdMapper base class implementation.

Data loader exceptions, used by GenBank loader.

static SIZE_TYPE ReverseComplement(const string &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst)

const TAnnot & GetAnnot(void) const

const value_type * data() const

string FindAccPathNoThrow(const string &acc)

pair< TBioseqId, TBioseq_setId > TPlace

void x_LoadAnnot(const TPlace &place, const CSeq_annot &annot)

void x_LoadBioseqs(const TPlace &place, const list< CRef< CBioseq > > &bioseqs)

void x_AddUsedMemory(size_t size)

void SetLoaded(CObject *obj=0)

void x_AddBioseqPlace(TBioseq_setId id)

TChunkId GetChunkId(void) const

void x_AddAnnotType(const CAnnotName &annot_name, const SAnnotTypeSelector &annot_type, const TLocationId &location_id)

void x_SetLoadBytes(Uint4 bytes)

const CTSE_Split_Info & GetSplitInfo(void) const

void x_AddBioseqId(const TBioseqId &id)

CTSE_Split_Info & GetSplitInfo(void)

void SetSeq_entry(CSeq_entry &entry, CTSE_SetObjectInfo *set_info=0)

void AddChunk(CTSE_Chunk_Info &chunk_info)

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

CConstRef< CUser_field > GetFieldRef(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

const CUser_field & GetField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Access a named field in this user object.

static void CopyBuffer(const int *src, size_t count, int *dest)

Copy memory buffer (only when source and destination do not overlap!).

static void ConvertBuffer(const char *src, size_t count, int *dest)

Convert memory buffer elements from one type to another.

static void AppendZeros(vector< V, A > &dest, size_t count)

Append count zeros to dest vector vector must have enough memory reserved.

static void SplitBufferInto4(const int *src, size_t count, int *dest0, int *dest1, int *dest2, int *dest3)

Split source memory buffer into 4 buffers Source buffer contains 4*count elements Each destination bu...

static V * AppendUninitialized(vector< V, A > &dest, size_t count)

Append count unitialized elements to dest vector return pointer to appended elements for proper initi...

static void AppendZerosAligned16(vector< V, A > &dest, size_t count)

Append count zeros to dest vector vector must have enough memory reserved dst.end() pointer and count...

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator end() const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

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

static const struct name_t names[]

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

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

void reset(element_type *p=0, EOwnership ownership=eTakeOwnership)

Reset will delete the old pointer (if owned), set content to the new value, and assume the ownership ...

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

SStrictId_Tax::TId TTaxId

Taxon id type.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

element_type * release(void)

Release will release ownership of pointer to caller.

@ eNoOwnership

No ownership is assumed.

#define LOG_POST_X(err_subcode, message)

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

void Warning(CExceptionArgs_Base &args)

#define NCBI_THROW_FMT(exception_class, err_code, message)

The same as NCBI_THROW but with message processed as output to ostream.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

void Info(CExceptionArgs_Base &args)

string GetBase(void) const

Get the base entry name without extension.

C * SerialClone(const C &src)

Create on heap a clone of the source object.

@ eSerial_AsnBinary

ASN.1 binary.

CConstRef< CSeq_id > GetSeqId(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

string AsString(void) const

string GetLabel(const CSeq_id &id)

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

TObjectType * GetNCPointer(void) const THROWS_NONE

Get pointer,.

#define NCBI_PARAM_TYPE(section, name)

Generate typename for a parameter from its {section, name} attributes.

@ eParam_NoThread

Do not use per-thread values.

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

uint64_t Uint8

8-byte (64-bit) unsigned integer

position_type GetLength(void) const

TThisType & SetToOpen(position_type toOpen)

position_type GetToOpen(void) const

static TThisType GetWhole(void)

#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::ifstream CNcbiIfstream

Portable alias for ifstream.

NCBI_NS_STD::string::size_type SIZE_TYPE

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

const char * data(void) const

Return a pointer to the array represented.

size_type size(void) const

Return the length of the represented array.

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

void Stop(void)

Suspend the timer.

void Start(void)

Start the timer.

@ eStart

Start timer immediately after creating.

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

bool IsId(void) const

Check if variant Id is selected.

const TData & GetData(void) const

Get the Data member data.

const TFields & GetFields(void) const

Get the variant data.

vector< CRef< CUser_field > > TFields

bool IsSetLabel(void) const

field label Check if a value has been assigned to Label data member.

TInt GetInt(void) const

Get the variant data.

TReal GetReal(void) const

Get the variant data.

const TLabel & GetLabel(void) const

Get the Label member data.

TId GetId(void) const

Get the variant data.

void SetTo(TTo value)

Assign a value to To data member.

void SetId(TId &value)

Assign a value to Id data member.

void SetFrom(TFrom value)

Assign a value to From data member.

void SetTitle(const TTitle &value)

Assign a value to Title data member.

const TInt & GetInt(void) const

Get the variant data.

void SetNumval(TNumval value)

Assign a value to Numval data member.

const TGraph & GetGraph(void) const

Get the Graph member data.

TB GetB(void) const

Get the B member data.

const TByte & GetByte(void) const

Get the variant data.

void SetGraph(TGraph &value)

Assign a value to Graph data member.

bool IsByte(void) const

Check if variant Byte is selected.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

TNumval GetNumval(void) const

Get the Numval member data.

TA GetA(void) const

Get the A member data.

TComp GetComp(void) const

Get the Comp member data.

const TSeq & GetSeq(void) const

Get the variant data.

TSet & SetSet(void)

Select the variant.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

void SetId(TId &value)

Assign a value to Id data member.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

void SetData(TData &value)

Assign a value to Data data member.

const Tdata & Get(void) const

Get the member data.

const TGraph & GetGraph(void) const

Get the variant data.

list< CRef< CSeq_graph > > TGraph

void SetDesc(TDesc &value)

Assign a value to Desc data member.

const TAnnot & GetAnnot(void) const

Get the Annot member data.

TName & SetName(void)

Select the variant.

list< CRef< CSeq_align > > TAlign

const TDesc & GetDesc(void) const

Get the Desc member data.

const TData & GetData(void) const

Get the Data member data.

list< CRef< CSeq_annot > > TAnnot

list< CRef< CAnnotdesc > > Tdata

unsigned int

A callback function used to compare two keys in a database.

Definition of all error codes used in SRA C++ support libraries.

constexpr auto sort(_Init &&init)

constexpr bool empty(list< Ts... >) noexcept

const struct ncbi::grid::netcache::search::fields::SIZE size

string s_Value(TValue value)

const GenericPointer< typename T::ValueType > T2 value

void SleepMilliSec(unsigned long ml_sec, EInterruptOnSignal onsignal=eRestartOnSignal)

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

Helper classes and templates to implement plugins.

const unsigned int kDefaultRetryCount

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

vector< SBamFileName > m_BamFiles

TCount get_max_count(int type) const

const TCount * get_intron_counts() const

CSimpleBufferT< TCount > cc_gap

CSimpleBufferT< TCount > cc_intron

CSimpleBufferT< TCount > cc_match

CSimpleBufferT< SCountACGT > cc_acgt

const TCount * get_acgt_counts() const

const TCount * get_split_acgt_counts(int k, TSeqPos len) const

const TCount * get_gap_counts() const

Better replacement of GetAccVer(), this method should be defined in data loaders, GetAccVer() is left...

Better replacement of GetGi(), this method should be defined in data loaders, GetGi() is left for com...

constexpr TSeqPos GetMinBinSize() const

vector< Uint8 > EstimateDataSizeByAlnStartPos(TSeqPos seqlen=kInvalidSeqPos) const

TSeqPos gap_to_intron_threshold

void add_match(TSeqPos pos)

TCount get_max_count(int type) const

void add_gap(TSignedSeqPos gap_pos, TSeqPos gap_len)

void x_finish_add(EStat stat)

void add_base_raw(TSeqPos pos, Uint1 b)

void x_add_gap_or_intron(TSignedSeqPos gap_pos, TSeqPos gap_len, EStat stat)

void add_base(TSeqPos pos, char b)

void get_maxs(TCount(&c_max)[kNumStat]) const

vector< TCount > cc[kNumStat]

void add_intron(TSignedSeqPos gap_pos, TSeqPos gap_len)

int g(Seg_Gsm *spe, Seq_Mtf *psm, Thd_Gsm *tdg)

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