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NCBI C++ ToolKit: src/objtools/snputil/snp_bins.cpp Source File

;

;

}

(

>= 0){

(iter.

() != 1) {

pos_start, pos_end;

title, comment;

(

= pos_start;

< pos_end; ++

) {

(res->m_SigEntry.

()) {

res->m_SigEntry = BinEntry;

res->m_SigEntry = BinEntry;

res->m_EntryList.push_back(BinEntry);

snpid, ClinSigID;

trait, pmids, rgenes, mgenes;

title, comment, population;

dbgaptext, geneName;

(col_pos.

(annot,

, pos)) {

entry->

= col_snpid.

(annot,

, snpid) ? (

)snpid : 0;

entry->

= (col_val.

(annot,

, pvalue) || col_val_synonym.

(annot,

, pvalue)) ? pvalue : 0;

entry->

= col_trait.

(annot,

, trait) ? trait :

;

entry->

= col_pmids.

(annot,

, pmids) ? pmids :

;

entry->

= col_hgvs.

(annot,

, sHGVS) ? sHGVS :

;

entry->

= col_geneName.

(annot,

, geneName) ? geneName :

;

entry->

= col_geneId.

(annot,

, geneId) ? geneId : -1;

list<string> GeneSymIDPairsList;

(list<string>, iGeneSymIDPairsList, GeneSymIDPairsList) {

list<string> GeneSymIDPair;

[GeneSymIDPair.front()] = GeneSymIDPair.

() == 2 ? GeneSymIDPair.back() :

();

sRes += (sRes.empty() ?

:

) + iGeneMap->first +

+ iGeneMap->second;

pos_value_from,

pos_value_to,

& pos_index_begin,

& pos_index_end)

pos_index_begin = -1;

pos_index_end = rows-1;

col_sub_type.

(annot, 0, trackSubType);

lower_pos_index_bound = 0;

upper_pos_index_bound = rows-1;

pos_index_k = (lower_pos_index_bound + upper_pos_index_bound)/2;

col_pos_end.

(annot, pos_index_k, pos_value_k);

(pos_value_k < pos_value_from) {

pos_index_begin = pos_index_k;

lower_pos_index_bound = pos_index_k+1;

upper_pos_index_bound = pos_index_k-1;

}

(pos_value_k != pos_value_from && lower_pos_index_bound <= upper_pos_index_bound);

pos_index_begin = (pos_value_from == pos_value_k ? pos_index_k : pos_index_begin+1);

SlidingBegin(pos_index_begin-1);

(SlidingBegin >= 0) {

col_pos_end.

(annot, SlidingBegin, pos_value_k);

(pos_value_k < pos_value_from)

pos_index_begin = SlidingBegin;

lower_pos_index_bound=0;

upper_pos_index_bound=rows-1;

pos_index_k = (lower_pos_index_bound+upper_pos_index_bound)/2;

col_pos.

(annot, pos_index_k, pos_value_k);

(pos_value_k < pos_value_to) {

lower_pos_index_bound = pos_index_k+1;

pos_index_end = pos_index_k;

upper_pos_index_bound = pos_index_k-1;

}

(pos_value_k != pos_value_to && lower_pos_index_bound <= upper_pos_index_bound);

SlidingEnd(pos_index_end);

(SlidingEnd < rows) {

col_pos.

(annot, SlidingEnd, pos_value_k);

(pos_value_k > pos_value_to)

pos_index_end = SlidingEnd+1;

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Checksum and hash calculation classes.

bool TryGet(const CFeat_CI &feat_ci, Value &v) const

void x_Init(const string &sSrc)

string AsString() const

recreate the string that was used for creation

static int ChooseSignificant(const SBinEntry *entry1, const SBinEntry *entry2, TBinType type)

choose a more significant entry of the two offered

static void GetBinSelector(const string &sTrackAccession, bool isAdaptive, int depth, objects::SAnnotSelector &sel)

get a selector for a bin from a NA track accession

static bool GetBinHandle(objects::CScope &scope, const objects::SAnnotSelector &sel, const objects::CSeq_loc &loc, objects::CSeq_annot_Handle &annot)

get an annotation handle that is needed to load a singular bin on range

static CRef< SBin > GetBin(const objects::CSeq_annot_Handle &annot, TSeqRange range)

get a singular bin corresponding to a position range

static void ReadAnnotDesc(const objects::CSeq_annot_Handle &handle, string &title, string &comment)

get title and comment out of annot.desc

@ eCLIN

Clinical Variations.

@ eGAP

dbGaP analysis files

static bool isGeneMarker(const string &trackSubType)

determine whether a string in TrackSubType describes a Gene Marker ("102_1" or "102_3")

static void FindPosIndexRange(const objects::CSeq_annot_Handle &annot, int pos_value_from, int pos_value_to, int &pos_index_begin, int &pos_index_end)

Perform iterative binary search to find table indexes (rows) 'pos_index_begin' and 'pos_index_end' in...

static string SourceAsString(TSource Source)

get human-readable text for various source types

static CRef< SBinEntry > GetEntry(const objects::CSeq_annot_Handle &annot, int row)

get a bin entry corresponding to a row position in the table presumed contained within the handle

static unsigned char depth[2 *(256+1+29)+1]

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

size_t GetSeq_tableNumRows(void) const

const CSeq_annot::TDesc & Seq_annot_GetDesc(void) const

bool Seq_annot_CanGetDesc(void) const

SAnnotSelector & SetExactDepth(bool value=true)

SetExactDepth() specifies that annotations will be searched on the segment level specified by SetReso...

SAnnotSelector & SetResolveAll(void)

SetResolveAll() is equivalent to SetResolveMethod(eResolve_All).

SAnnotSelector & SetOverlapTotalRange(void)

Check overlapping only of total ranges.

size_t size(void) const

Get number of collected Seq-annots.

SAnnotSelector & SetAdaptiveDepth(bool value=true)

SetAdaptiveDepth() requests to restrict subsegment resolution depending on annotations found on lower...

SAnnotSelector & SetResolveDepth(int depth)

SetResolveDepth sets the limit of subsegment resolution in searching annotations.

SAnnotSelector & IncludeNamedAnnotAccession(const string &acc, int zoom_level=0)

SAnnotSelector & SetAnnotType(TAnnotType type)

Set annotation type (feat, align, graph)

SAnnotSelector & AddNamedAnnots(const CAnnotName &name)

Add named annot to set of annots names to look for.

void Reset(void)

Reset reference object.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const Tdata & Get(void) const

Get the member data.

bool IsComment(void) const

Check if variant Comment is selected.

const TTitle & GetTitle(void) const

Get the variant data.

const TComment & GetComment(void) const

Get the variant data.

bool IsTitle(void) const

Check if variant Title is selected.

list< CRef< CAnnotdesc > > Tdata

@ eClinical_significance_probable_pathogenic

@ eClinical_significance_pathogenic

unsigned int

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

const CharType(& source)[N]

#define row(bind, expected)

TSeqPos pos_end

gene end when trackSubType is (Gene association)

string geneStringId

when external Gene IDs are used, it can be a string

string geneName

gene name when trackSubType is (Gene association)

string dbgaptext

specially formatted, see document

string population

population description for GWAS/pha tracks

string genes_reported

specially formatted, see document

int ClinSigID

clinical significance ID,

string trackSubType

used to further differentiate some GWAS/pha tracks (see SV-2201)

string genes_mapped

specially formatted, see document

string pmids

comma-delimited list of PubMed IDs

TSeqPos pos

! arrange member names as in the dumped file

int geneId

gene ID when trackSubType is (Gene association)

static CS_CONTEXT * context

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