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NCBI C++ ToolKit: src/sra/readers/bam/bamread.cpp Source File

& message,

this->x_Init(

, message, prev_exc, severity);

& message,

this->x_Init(

, message, prev_exc, severity);

& message,

& param,

this->x_Init(

, message, prev_exc, severity);

m_Param(other.m_Param)

;

:

;

( acc.size() != 9 && acc.size() != 12 ) {

+acc);

prefix = acc.substr(0, 3);

( prefix !=

&& prefix !=

&& prefix !=

) {

+acc);

+acc);

level1 = num/1000;

snprintf(sub_dir,

(sub_dir),

,

prefix.c_str(), level1, prefix.c_str(), acc.c_str()+3);

sub_dir[

(sub_dir)-1] =

;

+acc);

( !

&&

.find(

) !=

) {

( !ids.empty() ) {

( external ||

.find(

) !=

) {

SraReleaseVersion release_version;

SraReleaseVersionGet(&release_version);

s << (release_version.version>>24) <<

<< ((release_version.version>>16)&0xff) <<

<< (release_version.version&0xffff);

( release_version.revision != 0 ||

release_version.type != SraReleaseVersion::eSraReleaseVersionTypeFinal ) {

*

=

;

( release_version.type ) {

SraReleaseVersion::eSraReleaseVersionTypeDev:

=

;

;

SraReleaseVersion::eSraReleaseVersionTypeAlpha:

=

;

;

SraReleaseVersion::eSraReleaseVersionTypeBeta:

=

;

;

SraReleaseVersion::eSraReleaseVersionTypeRC:

=

;

;

:

=

;

;

s <<

<<

<< release_version.revision;

{

,

},

{

,

},

( !token.

() && token[token.

()-1] ==

) {

( token ==

.tag ) {

thread::id s_DiagCheckThreadID;

s_DiagCheckThreadID = this_thread::get_id();

s_DiagCheckThreadID == this_thread::get_id();

(

token_pos = 0, token_end; token_pos <

.size(); token_pos = token_end + 1 ) {

token_end =

.find(

, token_pos);

( token_end ==

) {

token_end =

.size();

sev_manip =

->manip;

( sev_manip ==

) {

host = app->GetConfig().GetString(

,

,

);

port = app->GetConfig().GetInt(

,

, 0);

( !host.empty() && port != 0 ) {

, rc);

, path.c_str()) ) {

, rc);

,

) ) {

, rc);

req_ctx_version = req_ctx.

();

( &req_ctx == s_LastRequestContext && req_ctx_version == s_LastRequestContextVersion ) {

(

<<req_ctx_version);

s_LastRequestContext = &req_ctx;

s_LastRequestContextVersion = req_ctx_version;

, rc);

KNSManagerSetSessionID(kns_mgr, req_ctx.

().c_str());

KNSManagerSetClientIP(kns_mgr, req_ctx.

().c_str());

KNSManagerSetPageHitID(kns_mgr, req_ctx.

().c_str());

( app && app->

().

(

,

,

) ) {

(

rc = KNSManagerSetAllowAllCerts(kns_mgr,

) ) {

, rc);

<< NCBI_PRODUCTION_VER <<

;

KNSManagerSetUserAgent(kns_mgr,

,

initialized =

;

( !initialized ) {

ask_level = klogDebug;

ask_level = klogInfo;

KLogLevelSet(ask_level);

*

=

;

, rc);

, rc);

VFSManagerLogNamesServiceErrors(*

,

);

(

rc = VFSManagerGetKNSMgr(*

, kns_mgr.

()) ) {

, rc);

, rc);

s.length() >= 2 &&

(

(s[0])) && s[1] ==

;

( s.find_first_of(

) ==

) {

fixed_path = path;

replace(fixed_path.begin(), fixed_path.end(),

,

);

fixed_path[0] =

;

* c_path = fixed_path.c_str();

* c_path = path.c_str();

(

rc = VFSManagerMakePath(mgr, &kpath, c_path) ) {

, rc);

{ VPathRelease(kpath); }

& db_name)

kdb_name.

()) ) {

, rc, db_name);

& base_name,

dst.push_back(base_name.substr(0, base_name.size()-old_ext.

())+new_ext);

& db_name,

vector<string> index_name_candidates;

( idx_name.empty() || idx_name == db_name ) {

index_name_candidates.push_back(db_name+

);

index_name_candidates.push_back(idx_name);

(

= 0;

< index_name_candidates.size(); ++

) {

index_name_candidates[

]));

kidx_name.

()) ) {

(

< index_name_candidates.size()-1 &&

GetRCTarget(rc) == rcFile &&

GetRCState(rc) == rcNotFound ) {

*m_DB.x_InitPtr() = 0;

, rc, db_name);

idx_name = index_name_candidates[

];

& db_name,

& db_name,

& idx_name,

m_IndexName(idx_name)

= it.GetRefSeqId();

= it.GetLength();

(*lengths)[it.GetRefSeqId()] =

;

(

rc = AlignAccessDBExportBAMFile(

->m_DB,

.x_InitPtr()) ) {

, rc);

* header;

(

rc = BAMFileGetHeaderText(

, &header, &

) ) {

, rc);

EIntronMode intron_mode)

initialize(ref_range, intron_mode);

EIntronMode intron_mode)

m_RefToOpen = m_RefFrom = ref_range.

();

m_IntronMode = intron_mode;

(

& c : max_count ) c = 0;

cc_acgt.resize(

);

cc_match.resize(

);

cc_gap.resize(

);

( count_introns() ) {

cc_intron.resize(

);

(accumulate(&cc_gap[0], &cc_gap[m_RefToOpen-m_RefFrom+1], 0) == 0);

(accumulate(&cc_gap[

], &cc_gap[m_RefToOpen-m_RefFrom+1], 0) == 0);

(accumulate(&cc_intron[0], &cc_intron[m_RefToOpen-m_RefFrom+1], 0) == 0);

+= cc_intron[

];

cc_intron[

] =

;

(accumulate(&cc_intron[

], &cc_intron[m_RefToOpen-m_RefFrom+1], 0) == 0);

* src = read.

()+read_pos;

SPileupValues::SCountACGT* dst = cc_acgt.data()+pos;

SPileupValues::SCountACGT* dst_end = cc_acgt.data()+end;

TCount* dst_match = cc_match.data()+pos;

bits =

(1<<(

&0x1f), 1<<(

&0x1f), 1<<(

&0x1f), 1<<(

&0x1f));

( ; dst < dst_end; ++src, ++dst, ++dst_match ) {

= *src & 0x1f;

dst_match[0] +=

== (

& 0x1f);

add_bases_acgt(dst,

, bits,

);

add_bases_acgt(dst,

);

get_raw_base0(

)

get_raw_base1(

)

(

+ 0xf) & ~0xf;

* src = read.

()+read_pos/2;

SPileupValues::SCountACGT* dst = cc_acgt.data()+pos;

SPileupValues::SCountACGT* dst_end = cc_acgt.data()+end-1;

TCount* dst_match = cc_match.data()+pos;

= get_raw_base1(

);

dst_match[0] +=

== 0;

add_bases_acgt(dst,

, bits,

);

add_bases_acgt_raw(dst,

);

( ; dst < dst_end; ++src, dst += 2, dst_match += 2 ) {

b0 = get_raw_base0(

);

b1 = get_raw_base1(

);

dst_match[0] += b0 == 0;

dst_match[1] += b1 == 0;

add_bases_acgt(dst+0, b0, bits,

);

add_bases_acgt(dst+1, b1, bits,

);

add_bases_acgt_raw(dst+0, b0);

add_bases_acgt_raw(dst+1, b1);

( dst <= dst_end ) {

= get_raw_base0(

);

dst_match[0] +=

== 0;

add_bases_acgt(dst,

, bits,

);

add_bases_acgt_raw(dst,

);

( ref_pos > m_RefToOpen ) {

( ref_pos > m_RefToOpen+FLUSH_SIZE ) {

( m_RefToOpen != m_RefFrom ) {

advance_current_beg(m_RefToOpen, callback);

(m_RefToOpen == m_RefFrom);

add_zeros = ref_pos-m_RefToOpen;

flush_zeros = align_to_16_down(add_zeros);

(flush_zeros%16 == 0);

callback->AddZerosBy16(flush_zeros);

m_RefToOpen = m_RefFrom += flush_zeros;

( ref_pos > m_RefToOpen ) {

advance_current_end(ref_pos);

advance_current_end(ref_pos);

flush = ref_pos-m_RefFrom;

( ref_pos != m_RefStop ) {

flush = align_to_16_down(flush);

( count_introns() ) {

decode_intron(flush);

total = m_RefToOpen-m_RefFrom;

( flush >= 16 ) {

update_max_counts(flush);

callback->AddValuesBy16(flush, *

);

TCount gap_save = cc_gap[total];

cc_gap[

] = gap_save;

( count_introns() ) {

TCount intron_save = cc_intron[total];

cc_intron[

] = intron_save;

(accumulate(&cc_gap[0], &cc_gap[m_RefToOpen-m_RefFrom+1], 0) == 0);

accumulate(&cc_intron[0], &cc_intron[m_RefToOpen-m_RefFrom+1], 0) == 0);

(ref_pos == m_RefStop);

(ref_pos == m_RefToOpen);

update_max_counts(flush);

callback->AddValuesTail(flush, *

);

m_RefFrom = m_RefStop;

(ref_end > m_RefToOpen);

(ref_end <= m_RefStop);

cur_pos = m_RefToOpen-m_RefFrom;

new_pos = (

(m_RefStop + 15, ref_end + FLUSH_SIZE) - m_RefFrom) & ~15;

TCount gap_save = cc_gap[cur_pos];

cc_gap[cur_pos] = gap_save;

cc_gap[new_pos] = 0;

( count_introns() ) {

TCount intron_save = cc_intron[cur_pos];

cc_intron[cur_pos] = intron_save;

cc_intron[new_pos] = 0;

m_RefToOpen =

(m_RefStop, m_RefFrom + new_pos);

( m_RefToOpen < m_RefStop ) {

advance_current_end(m_RefStop);

(m_RefToOpen == m_RefStop);

decode_gap(m_RefStop - m_RefFrom);

(

flush = m_RefToOpen-m_RefFrom ) {

update_max_counts(flush);

callback->AddValuesTail(flush, *

);

update_max_counts(m_RefStop - m_RefFrom);

(m_RefFrom+length <= m_RefToOpen);

(length % 16 == 0 || m_RefToOpen == m_RefStop);

length = align_to_16_up(length);

( count_introns() ) {

max_count[kStat_Intron] = 0;

( m_SplitACGTLen <

) {

(

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

cc_split_acgt[k].clear();

cc_split_acgt[k].resize(len16);

cc_split_acgt[0].

(),

cc_split_acgt[1].

(),

cc_split_acgt[2].

(),

cc_split_acgt[3].

());

m_SplitACGTLen =

;

& ref_id,

ICollectPileupCallback* callback,

gap_to_intron_threshold)

values.initialize(graph_range, intron_mode);

( ; ait; ++ait ) {

( callback && !callback->AcceptAlign(ait) ) {

ref_pos = rit->GetRefSeqPos();

values.update_current_ref_start(ref_pos, callback);

read_len = rit->GetShortSequenceLength();

read_raw = rit->GetShortSequenceRaw();

( ref_pos >= graph_range.

() ) {

op = rit->GetCIGAROp(

);

seglen = op >> 4;

ref_end = ref_pos + seglen;

values.add_match_ref_range(ref_pos, ref_end);

( read_pos+ref_end > read_len+ref_pos ) {

values.add_match_ref_range(ref_pos, ref_end);

values.add_bases_ref_range_raw(ref_pos, ref_end, read_raw, read_pos);

values.add_intron_ref_range(ref_pos, ref_end);

( seglen > gap_to_intron_threshold ) {

values.add_intron_ref_range(ref_pos, ref_end);

values.add_gap_ref_range(ref_pos, ref_end);

( ; ait; ++ait ) {

( callback && !callback->AcceptAlign(ait) ) {

ref_pos = ait.GetRefSeqPos();

values.update_current_ref_start(ref_pos, callback);

((values.m_RefToOpen-values.m_RefFrom)%16 == 0 || values.m_RefToOpen == values.m_RefStop);

read_len = ait.GetShortSequenceLength();

read_pos = ait.GetCIGARPos();

* ptr = cigar.

();

* end = ptr + cigar.

();

( ptr != end ) {

( ref_pos >= graph_range.

() ) {

( ; ++ptr != end; ) {

( c >=

&& c <=

) {

seglen = seglen*10+(c-

);

( seglen == 0 ) {

(

<<

<<

<<cigar);

ref_end = ref_pos + seglen;

(

==

) {

values.add_match_ref_range(ref_pos, ref_end);

(

==

||

==

) {

( read_pos+ref_end > read_len+ref_pos ) {

values.add_match_ref_range(ref_pos, ref_end);

values.add_bases_ref_range(ref_pos, ref_end, read, read_pos);

(

==

) {

(

==

) {

(

==

) {

values.add_intron_ref_range(ref_pos, ref_end);

(

==

) {

( seglen > gap_to_intron_threshold ) {

values.add_intron_ref_range(ref_pos, ref_end);

values.add_gap_ref_range(ref_pos, ref_end);

(

!=

) {

(

<<

<<

<<cigar);

((values.m_RefToOpen-values.m_RefFrom)%16 == 0 || values.m_RefToOpen == values.m_RefStop);

( callback && graph_range.

() != values.m_RefFrom ) {

flush16 = align_to_16_down(flush);

flush_tail = flush - flush16;

values.advance_current_beg(values.m_RefFrom+flush16, callback);

values.advance_current_beg(values.m_RefFrom+flush_tail, callback);

values.finalize(callback);

(

.size() != 2 ) {

(

.size() != 2 ) {

AlignAccessRefSeqEnumerator* ptr = 0;

(

rc = AlignAccessDBEnumerateRefSequences(bam_db.

->m_DB, &ptr) ) {

( !(GetRCObject(rc) == rcRow &&

GetRCState(rc) == rcNotFound) ) {

->m_Iter.SetReferencedPointer(ptr);

(

!= &iter ) {

(

rc = AlignAccessRefSeqEnumeratorNext(

->m_Iter) ) {

( !(GetRCObject(rc) == rcRow &&

GetRCState(rc) == rcNotFound) ) {

, rc);

*

)

( GetRCState(rc) == rcInsufficient &&

>

.capacity() ) {

, rc,

);

*

, TGetString func)

(

.empty() ) {

AlignAccessRefSeqEnumeratorGetID);

(

rc = AlignAccessRefSeqEnumeratorGetLength(

->m_Iter, &length) ) {

, rc);

);

m_Iter(db, file_pos)

& ref_label,

m_Iter(db, ref_label, ref_pos, window,

& ref_label,

m_Iter(db, ref_label, ref_pos, window,

m_ShortSequence.clear();

AlignAccessAlignmentEnumerator* ptr)

m_ShortSeqId.clear();

m_ShortSeqAcc.clear();

m_ShortSequence.clear();

(

= 0;

< m_CIGAR.size(); ++

) {

( m_CIGAR[

] ==

) {

(

rc = AlignAccessAlignmentEnumeratorGetRefSeqPos(m_Iter, &pos) ) {

( GetRCObject(rc) == RCObject(rcData) &&

GetRCState(rc) == rcNotFound ) {

, rc);

m_BamFlagsAvailability(eBamFlags_NotTried)

( file_pos && *file_pos ) {

AlignAccessAlignmentEnumerator* ptr = 0;

(

rc = AlignAccessDBEnumerateAlignments(bam_db.

->m_DB, &ptr) ) {

( !AlignAccessAlignmentEnumeratorIsEOF(rc) ) {

& ref_id,

m_BamFlagsAvailability(eBamFlags_NotTried)

AlignAccessAlignmentEnumerator* ptr = 0;

(

rc = AlignAccessDBWindowedAlignments(bam_db.

->m_DB, &ptr,

ref_id.c_str(), ref_pos, window) ) {

AlignAccessAlignmentEnumeratorRelease(ptr);

( !AlignAccessAlignmentEnumeratorIsEOF(rc) ) {

(

->GetRefSeqPos() < ref_pos ) {

(

rc = AlignAccessAlignmentEnumeratorNext(ptr) ) {

( !AlignAccessAlignmentEnumeratorIsEOF(rc) ) {

& ref_id,

m_BamFlagsAvailability(eBamFlags_NotTried)

(

!= &iter ) {

(

rc = AlignAccessAlignmentEnumeratorNext(

->m_Iter) ) {

( !(GetRCObject(rc) == rcRow &&

GetRCState(rc) == rcNotFound) ) {

*

)

( GetRCState(rc) == rcInsufficient &&

>

.capacity() ) {

, rc,

);

*

, TGetString func)

(

.empty() ) {

*

, TGetString2 func)

(

.empty() ) {

->m_RawDB->GetData().GetHeader().GetRefName(

->m_Iter.GetRefSeqIndex());

AlignAccessAlignmentEnumeratorGetRefSeqID);

->m_Iter.GetRefSeqPos();

->m_Iter.GetNextRefSeqIndex();

next_ref_index =

->m_Iter.GetNextRefSeqIndex();

( next_ref_index == -1 ) {

->m_RawDB->GetData().GetHeader().GetRefName(next_ref_index);

->m_Iter.GetNextRefSeqPos();

->m_Iter.GetShortSeqId();

AlignAccessAlignmentEnumeratorGetShortSeqID);

->m_Iter.GetShortSeqAcc();

AlignAccessAlignmentEnumeratorGetShortSeqAccessionID);

(

->m_ShortSequence.empty() ) {

(

->m_ShortSequence.empty() ) {

AlignAccessAlignmentEnumeratorGetShortSequence);

->m_Iter.GetShortSequenceLength();

AlignAccessAlignmentEnumeratorGetCIGAR);

->m_Iter.HasAmbiguousMatch();

->m_Iter.GetCIGARPos();

->m_Iter.GetCIGAR(raw_cigar);

* ptr =

->m_CIGAR.data();

* end = ptr +

->m_CIGAR.size();

( ptr != end ) {

(

= 0; ++ptr != end; ) {

( c >=

&& c <=

) {

*

=

;

* ptr = strchr(

,

);

op = ptr? unsigned(ptr-

): 15u;

raw_cigar.push_back((

<<4)|(op));

->m_Iter.GetCIGARRefSize();

* ptr =

->m_CIGAR.data();

* end = ptr +

->m_CIGAR.size();

( ptr != end ) {

(

= 0; ++ptr != end; ) {

( c >=

&& c <=

) {

(

==

||

==

) {

(

==

||

==

) {

(

!=

) {

<<

<<

<<

->m_CIGAR);

->m_Iter.GetCIGARShortSize();

* ptr =

->m_CIGAR.data();

* end = ptr +

->m_CIGAR.size();

( ptr != end ) {

(

= 0; ++ptr != end; ) {

( c >=

&& c <=

) {

(

==

||

==

) {

(

==

||

==

) {

(

!=

) {

<<

<<

<<

->m_CIGAR);

->m_Iter.GetCIGARAlignment();

ref_size = 0, short_size = 0;

* ptr =

->m_CIGAR.data();

* end = ptr +

->m_CIGAR.size();

( ptr != end ) {

(

= 0; ++ptr != end; ) {

( c >=

&& c <=

) {

(

==

||

==

) {

(

==

||

==

) {

(

!=

) {

<<

<<

<<

->m_CIGAR);

ret.first.SetLength(ref_size);

ret.second.SetLength(short_size);

paired =

(), is_1st =

, is_2nd =

;

paired = (

& (BAMFlags_WasPaired |

BAMFlags_IsMappedAsPair)) != 0;

is_1st = (

& BAMFlags_IsFirst) != 0;

is_2nd = (

& BAMFlags_IsSecond) != 0;

( is_1st && !is_2nd ) {

( is_2nd && !is_1st ) {

detector->AddSpotId(

,

);

AlignmentStrandDirection dir;

( AlignAccessAlignmentEnumeratorGetStrandDirection(

->m_Iter, &dir) != 0 ) {

->m_Iter.IsSetStrand();

);

->m_Iter.GetMapQuality();

(

rc = AlignAccessAlignmentEnumeratorGetMapQuality(

->m_Iter, &q) ) {

, rc);

(

rc = AlignAccessAlignmentEnumeratorGetIsPaired(

->m_Iter, &

) ) {

, rc);

->m_Iter.IsFirstInPair();

(

rc=AlignAccessAlignmentEnumeratorGetIsFirstInPair(

->m_Iter, &

) ) {

, rc);

->m_Iter.IsSecondInPair();

(

rc=AlignAccessAlignmentEnumeratorGetIsSecondInPair(

->m_Iter, &

) ) {

, rc);

->m_Iter.IsSecondary();

(

& BAMFlags_IsNotPrimary) != 0;

, rc);

(

rc = BAMAlignmentGetRefSeqId(*

, &

) ) {

, rc);

->m_Iter.GetRefSeqIndex();

(

rc = BAMAlignmentGetFlags(*

, &

) ) {

, rc);

BAMAlignmentGetFlags(*

, &

) == 0;

->GetAuxIterator();

( length == 0 ) {

& iupac = inst.

().SetIupacna().Set();

iupac.assign(

.data(), length);

cache->

().SetStr(

);

obj.

().SetStr(

);

obj.

(

,

);

->m_Iter.GetSegments(starts, lens);

segcount =

(lens.size());

* ptr =

->m_CIGAR.data();

* end = ptr +

->m_CIGAR.size();

refstart = 0, seqstart = 0;

( ptr != end ) {

( seglen = 0; ++ptr != end; ) {

( c >=

&& c <=

) {

seglen = seglen*10+(c-

);

(

==

||

==

) {

(

==

||

==

) {

(

==

) {

( seglen == 0 ) {

<<

<<

starts.push_back(refstart);

starts.push_back(seqstart);

lens.push_back(seglen);

strands.reserve(2*segcount);

(

= 0;

< segcount; ++

) {

starts[

*2+1] = end - (pos +

);

add_aux = !tags.empty();

next_ref_index = -1;

( next_ref_id.

() ) {

( add_cigar || add_aux ) {

obj->

().push_back(field);

CBamDb::TTagList::const_iterator info_iter = find(tags.begin(), tags.end(), name);

( info_iter == tags.end() ) {

( aux_it->IsArray() ) {

( aux_it->IsFloat() ) {

(

= 0;

< aux_it->size(); ++

) {

.push_back(aux_it->GetFloat(

));

(

= 0;

< aux_it->size(); ++

) {

( aux_it->IsChar() ) {

field->

().SetStr(

(1, aux_it->GetChar()));

( aux_it->IsString() ) {

field->

().SetStr(aux_it->GetString());

( aux_it->IsFloat() ) {

field->

().SetReal(aux_it->GetFloat());

obj->

().push_back(field);

align->

().push_back(obj);

obj->

().push_back(field);

field->

().SetInt(next_ref_pos);

obj->

().push_back(field);

( ; mate_iter; ++mate_iter ) {

obj->

().push_back(field);

align->

().push_back(obj);

annot->

().SetAlign();

annot->

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

entry->

().push_back(annot);

annot->

().SetAlign().push_back(align);

void x_Assign(CObject_id &dst, const CObject_id &src)

static CRef< CSeq_id > sx_GetShortSeq_id(const string &str, IIdMapper *idmapper, bool external)

static bool s_OmitAmbiguousMatchCigar(void)

static const SVDBSeverityTag kSeverityTags[]

static bool s_ExplicitMateInfo(void)

static char s_VDBVersion[32]

static bool s_HasWindowsDriveLetter(const string &s)

static rc_t VDBLogWriter(void *, const char *buffer, size_t size, size_t *written)

static void s_InitLocalKNS(KNSManager *kns_mgr)

static CBamRef< KConfig > s_InitProxyConfig()

static void s_InitAllKNS(KNSManager *kns_mgr)

static int s_GetDiagHandler(void)

NCBI_PARAM_DEF(bool, BAM, CIGAR_IN_ALIGN_EXT, true)

static const SVDBSeverityTag * s_GetVDBSeverityTag(CTempString token)

DEFINE_STATIC_FAST_MUTEX(sx_SDKMutex)

static void s_InitVDBVersion()

SPECIALIZE_BAM_REF_TRAITS(KConfig,)

static const char kBamExt[]

static VPath * sx_GetVPath(const CBamVFSManager &mgr, const string &path)

static void s_InitStaticKNS(KNSManager *kns_mgr)

NCBI_PARAM_DECL(string, SRZ, REP_PATH)

static bool s_IsSysPath(const string &s)

static void s_InitDiagCheck()

static bool s_DiagIsSafe()

#define NCBI_THROW2_FMT(exception_class, err_code, message, extra)

static CObject_id & sx_GetObject_id(CTempString name, CRef< CObject_id > &cache)

static void s_AddReplacedExt(vector< string > &dst, const string &base_name, CTempString old_ext, CTempString new_ext)

static CRef< CUser_object > sx_GetSecondaryIndicator(CRef< CUser_object > &cache)

NCBI_PARAM_DEF_EX(string, SRZ, REP_PATH, NCBI_SRZ_REP_PATH, eParam_NoThread, SRZ_REP_PATH)

static void sx_MapId(CSeq_id &id, IIdMapper *idmapper)

static CRef< CSeq_id > sx_GetRefSeq_id(const string &str, IIdMapper *idmapper)

static const char kBaiExt[]

static void s_UpdateVDBRequestContext(void)

static bool s_GetCigarInAlignExt(void)

ostream & operator<<(ostream &out, const CBamRcFormatter &rc)

DEFINE_BAM_REF_TRAITS(VFSManager,)

static CRef< CAnnotdesc > sx_GetMatchAnnotIndicator(CRef< CAnnotdesc > &cache)

static DECLARE_TLS_VAR(const CRequestContext *, s_LastRequestContext)

#define NCBI_THROW3(exc_cls, err_code, msg, extra1, extra2)

ncbi::TMaskedQueryRegions mask

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

virtual ~ISpotIdDetector(void)

ISpotIdDetector * GetSpotIdDetector(void) const

friend class CBamFileAlign

CIRef< ISpotIdDetector > m_SpotIdDetector

CRef< CSeq_align > GetMatchAlign(void) const

Int4 GetRefSeqIndex(void) const

bool TryGetFlags(Uint2 &flags) const

CRef< CBioseq > GetShortBioseq(void) const

CTempString GetShortSequence(void) const

TSeqPos GetShortSequenceLength(void) const

bool x_HasAmbiguousMatch() const

TSeqPos GetCIGARShortSize(void) const

void SetRefSeq_id(CRef< CSeq_id > seq_id)

TSeqPos GetNextRefSeqPos() const

CRef< CSeq_id > GetShortSeq_id(void) const

TSeqPos GetRefSeqPos(void) const

AutoPtr< SCreateCache > m_CreateCache

bool x_CheckRC(CBamString &buf, rc_t rc, size_t size, const char *msg) const

CRef< CSeq_annot > x_GetSeq_annot(const string *annot_name) const

void SetShortSeq_id(CRef< CSeq_id > seq_id)

CTempString GetCIGAR(void) const

CRef< SRawImpl > m_RawImpl

Uint2 GetFlags(void) const

void x_GetStrand(void) const

CRef< CSeq_id > GetRefSeq_id(void) const

TSeqPos GetCIGARRefSize(void) const

Int4 GetNextRefSeqIndex() const

SCreateCache & x_GetCreateCache(void) const

bool IsSecondary(void) const

CTempString GetRefSeqId(void) const

bool IsSecondInPair(void) const

CBamRawAlignIterator * GetRawIndexIteratorPtr() const

CBamAuxIterator GetAuxIterator() const

CTempString GetShortSeqId(void) const

IIdMapper * GetIdMapper(void) const

Uint1 GetMapQuality(void) const

TSeqPos GetCIGARPos(void) const

bool IsSetStrand(void) const

EBamFlagsAvailability m_BamFlagsAvailability

void GetRawCIGAR(vector< Uint4 > &raw_cigar) const

CRef< CSeq_id > m_ShortSeq_id

bool UsesRawIndex() const

CRef< SAADBImpl > m_AADBImpl

void x_GetString(CBamString &buf, const char *msg, TGetString func) const

CBamAlignIterator & operator++(void)

CTempString GetNextRefSeqId(void) const

void x_CheckValid(void) const

void x_GetCIGAR(void) const

bool IsPaired(void) const

CBamAlignIterator & operator=(const CBamAlignIterator &iter)

CRef< CSeq_id > m_RefSeq_id

bool IsFirstInPair(void) const

ENa_strand GetStrand(void) const

CTempString GetShortSeqAcc(void) const

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

CRef< CSeq_entry > x_GetMatchEntry(const string *annot_name) const

virtual ~ICollectPileupCallback()

virtual bool AcceptAlign(const CBamAlignIterator &ait)

AutoPtr< TRefSeqLengths > m_RefSeqLengths

static int GetDebugLevel()

TSeqPos GetPageSize() const

string GetHeaderText(void) const

bool ExcludeAlignTag(CTempString tag)

CRef< CSeq_id > GetShortSeq_id(const string &str, bool external=false) 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)

CRef< CSeq_id > GetRefSeq_id(const string &label) const

TTagList m_IncludedAlignTags

vector< STagInfo > TTagList

unordered_map< string, CRef< CSeq_id > > TRefSeqIds

AutoPtr< TRefSeqIds > m_RefSeqIds

IIdMapper * GetIdMapper(void) const

TSeqPos GetRefSeqLength(const string &str) const

const TTagList & GetIncludedAlignTags() const

static bool UseRawIndex(EUseAPI use_api)

CRef< CObjectFor< CBamRawDb > > m_RawDB

unordered_map< string, TSeqPos > TRefSeqLengths

virtual const char * GetErrCodeString(void) const

Translate from the error code value to its string representation.

EErrCode

Error types that CBamXxx classes can generate.

@ eAddRefFailed

AddRef failed.

@ eInvalidArg

Invalid argument error.

@ eInitFailed

Initialization failed.

@ eInvalidBAIFormat

Invalid data in BAM index file.

@ eInvalidBAMFormat

Invalid data in BAM file.

@ eFileNotFound

File not found.

@ eBadCIGAR

Bad CIGAR string.

@ eNoData

Data not found.

@ eNullPtr

Null pointer error.

virtual const CException * x_Clone(void) const

Helper clone method.

int TErrCode

Translate from the error code value to its string representation.

virtual const char * GetType(void) const

CBamException(void)

Constructor.

virtual TErrCode GetErrCode(void) const

virtual void ReportExtra(ostream &out) const

Report "non-standard" attributes.

~CBamException(void) noexcept

static void ReportError(const char *msg, rc_t rc)

bool TryGetFlags(Uint2 &flags) const

Uint2 GetFlags(void) const

CBamFileAlign(const CBamAlignIterator &iter)

Int4 GetRefSeqIndex(void) const

const CBamRef< const AlignAccessMgr > & GetAlignAccessMgr() const

const CBamVFSManager & GetVFSManager() const

CBamRef< const AlignAccessMgr > m_AlignAccessMgr

void x_GetString(CBamString &buf, const char *msg, TGetString func) const

CRef< CObjectFor< CBamRawDb > > m_RawDB

CRef< CSeq_id > GetRefSeq_id(void) const

TSeqPos GetLength(void) const

CTempString GetRefSeqId(void) const

bool x_CheckRC(CBamString &buf, rc_t rc, size_t size, const char *msg) const

CRef< CSeq_id > m_CachedRefSeq_id

CBamRefSeqIterator & operator++(void)

void x_InvalidateBuffers(void)

void x_CheckValid(void) const

CBamRefSeqIterator & operator=(const CBamRefSeqIterator &iter)

CRef< SAADBImpl > m_AADBImpl

void x_AllocBuffers(void)

void SetReferencedPointer(TObject *ptr)

TObject ** x_InitPtr(void)

void reserve(size_t min_capacity)

AutoArray< char > m_Buffer

void x_reserve(size_t min_capacity)

Incapsulate compile time information such as __FILE__, __LINE__, NCBI_MODULE, current function.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

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

@ eBadFormat

Invalid SRZ accession format.

@ eNotFound

Accession not found.

virtual const char * GetErrCodeString(void) const override

Get error code interpreted as text.

vector< string > m_VolPath

static string GetDefaultRepPath(void)

void AddRepPath(const string &rep_path)

vector< string > m_RepPath

string FindAccPath(const string &acc, EMissing mising)

void AddVolPath(const string &vol_path)

static string GetDefaultVolPath(void)

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

CUser_object & AddField(const string &label, const string &value, EParseField parse=eParse_String)

add a data field to the user object that holds a given value

General IdMapper interface.

virtual void MapObject(CSerialObject &)=0

Map all embedded IDs in a given object at once.

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 void Find4MaxElements(const unsigned int *src, size_t count, unsigned int dest[4])

Find maximum values in 4 arrays, or dest Source buffer contains 4*count elements with the following l...

static void ClearBuffer(char *dest, size_t count)

Fill destination memory buffer with zeros.

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

Copy memory buffer when source and destination overlap.

static unsigned int FindMaxElement(const unsigned int *src, size_t count)

Find maximum value in an array.

static vector< string > arr

std::ofstream out("events_result.xml")

main entry point for tests

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

static const struct type types[]

static string GetAppName(EAppNameType name_type=eBaseName, int argc=0, const char *const *argv=NULL)

static CNcbiApplicationGuard InstanceGuard(void)

Singleton method.

const CNcbiRegistry & GetConfig(void) const

Get the application's cached configuration parameters (read-only).

unsigned int TSeqPos

Type for sequence locations and lengths.

CVersionInfo GetVersion(void) const

Get the program version information.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

element_type * get(void) const

Get pointer.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

void reset(element_type *p=0)

Reset will delete the old pointer, set content to the new value, and assume the ownership upon the ne...

const CNcbiDiag &(* FManip)(const CNcbiDiag &)

Diagnostic stream manipulator.

string GetSessionID(void) const

Session ID.

CAtomicCounter::TValue TVersion

bool IsSetSessionID(void) const

static CRequestContext & GetRequestContext(void)

Shortcut to CDiagContextThreadData::GetThreadData().GetRequestContext()

string GetClientIP(void) const

Client IP/hostname.

bool IsSetHitID(EHitIDSource src=eHitID_Any) const

Check if there's an explicit hit id or the default one.

bool IsSetClientIP(void) const

string GetHitID(void) const

Get explicit hit id or the default one (from HTTP_NCBI_PHID etc).

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

TVersion GetVersion(void) const

Return version increased on every context change (hit/subhit id, client ip, session id).

EDiagSev

Severity level for the posted diagnostics.

void Error(CExceptionArgs_Base &args)

TErrCode GetErrCode(void) const

Get error code.

#define NCBI_THROW(exception_class, err_code, message)

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

void Trace(CExceptionArgs_Base &args)

void Warning(CExceptionArgs_Base &args)

void Fatal(CExceptionArgs_Base &args)

#define NCBI_THROW2(exception_class, err_code, message, extra)

Throw exception with extra parameter.

EErrCode

Error types that an application can generate.

#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 * GetErrCodeString(void) const

Get error code interpreted as text.

void Info(CExceptionArgs_Base &args)

static string CreateAbsolutePath(const string &path, ERelativeToWhat rtw=eRelativeToCwd)

Get an absolute path from some, possibly relative, path.

static string MakePath(const string &dir=kEmptyStr, const string &base=kEmptyStr, const string &ext=kEmptyStr)

Assemble a path from basic components.

const string AsFastaString(void) const

static SIZE_TYPE ParseIDs(CBioseq::TId &ids, const CTempString &s, TParseFlags flags=fParse_Default)

Parse a string representing one or more Seq-ids, appending the results to IDS.

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

@ eContent

Untagged human-readable accession or the like.

T & GetData(void)

Get data as a reference.

void Reset(void)

Reset reference object.

TObjectType & GetNCObject(void) const

Get object.

#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

int32_t Int4

4-byte (32-bit) signed integer

unsigned char Uchar

Alias for unsigned char.

uint32_t Uint4

4-byte (32-bit) unsigned integer

uint16_t Uint2

2-byte (16-bit) unsigned integer

position_type GetLength(void) const

TThisType & SetFrom(position_type from)

position_type GetToOpen(void) const

virtual bool GetBool(const string &section, const string &name, bool default_value, TFlags flags=0, EErrAction err_action=eThrow) const

Get boolean value of specified parameter name.

#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.

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.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

const char * data(void) const

Return a pointer to the array represented.

bool empty(void) const

Return true if the represented string is empty (i.e., the length is zero)

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static unsigned int StringToUInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to unsigned int.

static string & ToUpper(string &str)

Convert string to upper case – string& version.

size_type size(void) const

Return the length of the represented array.

virtual string Print(void) const

Print version information.

static const char label[]

TFrom GetFrom(void) const

Get the From member data.

bool IsSetData(void) const

the object itself Check if a value has been assigned to Data data member.

TData & SetData(void)

Assign a value to Data data member.

void SetLabel(TLabel &value)

Assign a value to Label data member.

TStr & SetStr(void)

Select the variant.

void SetType(TType &value)

Assign a value to Type data member.

void SetData(TData &value)

Assign a value to Data data member.

TLens & SetLens(void)

Assign a value to Lens data member.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

vector< ENa_strand > TStrands

vector< TSignedSeqPos > TStarts

void SetType(TType value)

Assign a value to Type data member.

TExt & SetExt(void)

Assign a value to Ext data member.

TStarts & SetStarts(void)

Assign a value to Starts data member.

TStrands & SetStrands(void)

Assign a value to Strands data member.

void SetNumseg(TNumseg value)

Assign a value to Numseg data member.

TIds & SetIds(void)

Assign a value to Ids data member.

@ eType_diags

unbroken, but not ordered, diagonals

ENa_strand

strand of nucleic acid

TGi GetGi(void) const

Get the variant data.

bool IsGi(void) const

Check if variant Gi is selected.

TSet & SetSet(void)

Select the variant.

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

void SetData(TData &value)

Assign a value to Data data member.

TId & SetId(void)

Assign a value to Id data member.

void SetDesc(TDesc &value)

Assign a value to Desc data member.

TName & SetName(void)

Select the variant.

TUser & SetUser(void)

Select the variant.

list< CRef< CSeq_id > > TId

void SetInst(TInst &value)

Assign a value to Inst data member.

void SetRepr(TRepr value)

Assign a value to Repr data member.

void SetLength(TLength value)

Assign a value to Length data member.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

void SetMol(TMol value)

Assign a value to Mol data member.

@ eRepr_raw

continuous sequence

@ eMol_na

just a nucleic acid

unsigned int

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

#define NCBI_DEVELOPMENT_VER

static void hex(unsigned char c)

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

string s_Value(TValue value)

const GenericPointer< typename T::ValueType > T2 value

#define NCBI_PACKAGE_NAME

#define NCBI_PACKAGE_VERSION

#define NCBI_SRZ_VOL_PATH

#define NCBI_SRZ_REP_PATH

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

Defines CRequestContext class for NCBI C++ diagnostic API.

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

static __m128i _mm_cvtsi32_si128(int a)

static __m128i _mm_srl_epi32(__m128i a, __m128i count)

static void _mm_store_si128(__m128i *p, __m128i a)

static __m128i _mm_load_si128(const __m128i *p)

static __m128i _mm_add_epi32(__m128i a, __m128i b)

static __m128i _mm_set_epi32(int, int, int, int)

static __m128i _mm_set1_epi32(int)

static __m128i _mm_and_si128(__m128i, __m128i)

bool x_HasAmbiguousMatch() const

SAADBImpl(const CBamDb::SAADBImpl &db, AlignAccessAlignmentEnumerator *ptr)

CBamRef< AlignAccessAlignmentEnumerator > m_Iter

TSeqPos GetRefSeqPos() const

void x_InvalidateBuffers()

CBamString m_ShortSequence

TObjectIdCache m_ObjectIdLcl

TObjectIdCache m_ObjectIdCIGAR

TObjectIdCache m_ObjectIdRefId

TObjectIdCache m_ObjectIdMateRead

CRef< CUser_object > m_SecondaryIndicator

TObjectIdCache m_ObjectIdHP

CRef< CAnnotdesc > m_MatchAnnotIndicator

TObjectIdCache m_ObjectIdTracebacks

TObjectIdCache m_ObjectIdRefPos

SRawImpl(CObjectFor< CBamRawDb > &db, const CBGZFPos *file_pos=nullptr)

CBamString m_ShortSequence

void x_InvalidateBuffers()

SAADBImpl(const CBamMgr &mgr, const string &db_name)

CBamRef< const AlignAccessDB > m_DB

void advance_current_end(TSeqPos ref_end)

void decode_intron(TSeqPos len)

void add_bases_graph_range_raw(TSeqPos pos, TSeqPos end, CTempString read, TSeqPos read_pos)

void update_max_counts(TSeqPos len)

void add_bases_graph_range(TSeqPos pos, TSeqPos end, CTempString read, TSeqPos read_pos)

void finalize(ICollectPileupCallback *callback)

void initialize(CRange< TSeqPos > ref_range, EIntronMode intron_mode=eNoCountIntron)

void advance_current_beg(TSeqPos ref_pos, ICollectPileupCallback *callback)

void decode_gap(TSeqPos len)

void make_split_acgt(TSeqPos len)

static const TShift kBAI_min_shift

static void Delete(const VPath *kpath)

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

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