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

: m_MinMapQuality(-1),

m_GraphType(eGraphType_linear),

m_GraphValueType(eGraphValueType_byte),

m_GraphBinSize(kDefaultGraphBinSize),

m_OutlierDetails(

),

& bam_file,

& bam_index)

db(mgr, bam_file, bam_index);

align_cov = 0;

TCovLevelChangeMap cov_level_change_map;

kMapBinCountThreshold = 20;

kWarnLongAlignThreshold = 10000;

kWarnLongAlignCount = 10;

invalid_align_count = 0;

long_align_count = 0;

( min_qual > 0 && ait.GetMapQuality() < min_qual ) {

pos = ait.GetRefSeqPos();

( end > ref_length ) {

( ++invalid_align_count <= kWarnLongAlignCount ) {

<<

<<

<< ait.GetCIGAR());

( invalid_align_count == kWarnLongAlignCount+1 ) {

);

( pos < min_pos ) {

( end > max_pos ) {

(

> max_align_span ) {

max_align_span =

;

(

> kWarnLongAlignThreshold ) {

( ++long_align_count <= kWarnLongAlignCount ) {

<<

<<

<< ait.GetCIGAR());

( long_align_count == kWarnLongAlignCount+1 ) {

);

end_bin = (end - 1) / bin_size;

( end_bin >= bin_cnt ) {

bin_cnt = end_bin + 1;

cap = ret.capacity();

( bin_cnt > cap ) {

<<cap<<

<<align_cnt<<

);

begin_bin = pos / bin_size;

( begin_bin == end_bin ) {

ret[begin_bin] +=

;

begin_bin_coverage = (begin_bin + 1) * bin_size - pos;

ret[begin_bin] += begin_bin_coverage;

end_bin_coverage = end - end_bin * bin_size;

ret[end_bin] += end_bin_coverage;

( end_bin > begin_bin + kMapBinCountThreshold ) {

cov_level_change_map[begin_bin] += bin_size;

cov_level_change_map[end_bin] -= bin_size;

(

bin = begin_bin; bin < end_bin; ++bin ) {

ret[bin] += bin_size;

( !cov_level_change_map.empty() ) {

bin = cov_level_change_map.begin()->first;

( TCovLevelChangeMap, it, cov_level_change_map ) {

( ; bin < next_bin; ++bin ) {

<<align_cnt<<

<<align_cov<<

<<

<<max_align_span);

align_cov = 0;

TCovLevelChangeMap cov_level_change_map;

kMapBinCountThreshold = 20;

kWarnLongAlignThreshold = 10000;

kWarnLongAlignCount = 10;

invalid_align_count = 0;

long_align_count = 0;

( min_qual > 0 && ait.GetMapQuality() < min_qual ) {

pos = ait.GetRefSeqPos();

( end > ref_length ) {

( ++invalid_align_count <= kWarnLongAlignCount ) {

<<

<<

<< ait.GetCIGAR());

( invalid_align_count == kWarnLongAlignCount+1 ) {

);

( pos < min_pos ) {

( end > max_pos ) {

(

> max_align_span ) {

max_align_span =

;

(

> kWarnLongAlignThreshold ) {

( ++long_align_count <= kWarnLongAlignCount ) {

<<

<<

<< ait.GetCIGAR());

( long_align_count == kWarnLongAlignCount+1 ) {

);

end_bin = (end - 1) / bin_size;

( end_bin >= bin_cnt ) {

bin_cnt = end_bin + 1;

cap = ret.capacity();

( bin_cnt > cap ) {

<<cap<<

<<align_cnt<<

);

begin_bin = pos / bin_size;

( begin_bin == end_bin ) {

ret[begin_bin] +=

;

begin_bin_coverage = (begin_bin + 1) * bin_size - pos;

ret[begin_bin] += begin_bin_coverage;

end_bin_coverage = end - end_bin * bin_size;

ret[end_bin] += end_bin_coverage;

( end_bin > begin_bin + kMapBinCountThreshold ) {

cov_level_change_map[begin_bin] += bin_size;

cov_level_change_map[end_bin] -= bin_size;

(

bin = begin_bin; bin < end_bin; ++bin ) {

ret[bin] += bin_size;

( !cov_level_change_map.empty() ) {

bin = cov_level_change_map.begin()->first;

( TCovLevelChangeMap, it, cov_level_change_map ) {

( ; bin < next_bin; ++bin ) {

<<align_cnt<<

<<align_cov<<

<<

<<max_align_span);

length =

(ret.size())*bin_size;

& bam_ind)

bam_index(bam_ind.empty()? bam_file+

: bam_ind);

& bam_ind)

bam_raw_db(bam_file, bam_ind.empty()? bam_file+

: bam_ind);

title,

name)

( name.empty() ) {

name =

;

( title.empty() ) {

annot.

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

& bam_file)

annot->

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

user_desc.

().SetStr(

);

annot->

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

user_desc.

(

,

);

val_count = 0;

( vector<Uint8>, it, cov ) {

( val_count == 0 ) {

avg_cov = double(sum_cov)/val_count;

user_desc.

(

, bam_file);

user_desc.

(

, min_cov*cov_mul);

user_desc.

(

, max_cov*cov_mul);

user_desc.

(

, avg_cov*cov_mul);

user_desc.

(

, max_cov*cov_mul);

vvb->reserve(cov.size());

vvi->reserve(cov.size());

user_desc.

(

,

);

base =

(

(min_cov));

byte_mul = double(

-1)/(

(

(max_cov))-base);

graph->

(1./byte_mul);

( vector<Uint8>, it, cov ) {

( c > max_cov ) {

= 1 +

((

(

(c))-base)*byte_mul+.5);

byte_mul = double(

-1)/(max_cov-min_cov);

graph->

(cov_mul/byte_mul);

graph->

(cov_mul*(min_cov - 1./byte_mul));

( vector<Uint8>, it, cov ) {

( c > max_cov ) {

field->

().SetId(

(it-cov.begin()));

field->

().SetReal(

(c));

outliers->push_back(field);

= 1 +

((c-min_cov)*byte_mul+.5);

& bam_file,

& bam_index)

& bam_file)

& bam_file)

& bam_file)

seq.

().push_back(

);

seq.

().push_back(

);

& bam_file,

& bam_index)

& bam_file)

& bam_file)

& bam_file)

static void sx_SetTitle(CSeq_graph &graph, CSeq_annot &annot, string title, string name)

static const int kDefaultOutlierMax_Int

static const Uint8 kDefaultMinMapQuality

static const int kDefaultOutlierMax_Byte

NCBI_DEFINE_ERR_SUBCODE_X(6)

#define DEFAULT_BAI_SUFFIX

const string & GetRefLabel(void) const

Label of the reference sequence in the BAM file.

void SetGraphBinSize(TSeqPos bin_size)

void SetRawAccess(bool raw_access=true)

EGraphValueType m_GraphValueType

vector< Uint8 > CollectRawAccessCoverage(const CBamHeader &header, const CBamIndex &bam_index)

int GetMinMapQuality(void) const

Minimal map quality of alignments to include in graph.

void SetGraphTitle(const string &title)

bool GetEstimated(void) const

make estimated graph using BAM index only the bin size will be derived from index

bool GetOutlierDetails(void) const

void SetOutlierMax(double x)

void SetEstimated(bool estimated=true)

const string & GetAnnotName(void) const

Annot name of generated Seq-graph.

void SetGraphValueType(EGraphValueType type)

vector< Uint8 > CollectCoverage(CBamMgr &mgr, const string &bam_file, const string &bam_index)

Generate raw align coverage for BAM file using BAM file index.

bool GetRawAccess(void) const

try to use raw BAM file access for efficiency

double GetOutlierMax(void) const

Limit too big graph values by a multiple of their average.

void SetAnnotName(const string &name)

void SetOutlierDetails(bool details=true)

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.

vector< Uint8 > CollectEstimatedCoverage(const CBamHeader &header, const CBamIndex &bam_index)

CRef< CSeq_entry > MakeSeq_entry(CBamMgr &mgr, const string &bam_file, const string &bam_index)

Generate Seq-entry for BAM file.

CRef< CSeq_inst > m_Seq_inst

void SetRefLabel(const string &ref_label)

void SetGraphType(EGraphType type)

void SetRefId(const CSeq_id &ref_id)

const string & GetGraphTitle(void) const

Title of generated Seq-graph.

EGraphType

Type of graph coverage axis - linear or logarithmic.

const CSeq_id & GetRefId(void) const

Seq-id for the reference sequence in generated entry.

EGraphType GetGraphType(void) const

void SetSeq_inst(CRef< CSeq_inst > inst)

Use specified Seq-inst object for the virtual sequence.

EGraphValueType GetGraphValueType(void) const

EGraphValueType

Type of graph values - byte (0-255) or int.

void SetMinMapQuality(int qual)

CRange< TSeqPos > m_TotalRange

TSeqPos GetGraphBinSize(void) const

bool UsesRawIndex() const

const string & GetDbName(void) const

TSeqPos GetRefSeqLength(const string &str) const

const string & GetIndexName(void) const

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

size_t GetRefIndex(const string &ref_label) const

const CBamHeader & GetHeader() const

const CBamIndex & GetIndex() const

TSeqPos GetRefSeqLength(size_t ref_index) const

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

CRef< CUser_field > SetFieldRef(const string &str, const string &delim=".", const string &obj_subtype=kEmptyStr, NStr::ECase use_case=NStr::eCase)

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.

#define LOG_POST_X(err_subcode, message)

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

void Warning(CExceptionArgs_Base &args)

void Info(CExceptionArgs_Base &args)

C * SerialClone(const C &src)

Create on heap a clone of the source object.

uint64_t Uint8

8-byte (64-bit) unsigned integer

position_type GetToOpen(void) const

#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.

static const char label[]

void SetFrom(TFrom value)

Assign a value to From data member.

vector< CRef< CUser_field > > TFields

void SetLabel(TLabel &value)

Assign a value to Label data member.

void SetType(TType &value)

Assign a value to Type data member.

void SetData(TData &value)

Assign a value to Data data member.

void SetA(TA value)

Assign a value to A data member.

void SetMin(TMin value)

Assign a value to Min data member.

void SetTitle(const TTitle &value)

Assign a value to Title data member.

void SetAxis(TAxis value)

Assign a value to Axis data member.

void SetNumval(TNumval value)

Assign a value to Numval data member.

void SetComp(TComp value)

Assign a value to Comp data member.

TValues & SetValues(void)

Assign a value to Values data member.

void SetGraph(TGraph &value)

Assign a value to Graph data member.

void SetB(TB value)

Assign a value to B data member.

void SetMax(TMax value)

Assign a value to Max data member.

void SetMax(TMax value)

Assign a value to Max data member.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

void SetAxis(TAxis value)

Assign a value to Axis data member.

void SetMin(TMin value)

Assign a value to Min data member.

TValues & SetValues(void)

Assign a value to Values data member.

TSeq & SetSeq(void)

Select the variant.

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.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

TName & SetName(void)

Select the variant.

TUser & SetUser(void)

Select the variant.

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 SetMol(TMol value)

Assign a value to Mol data member.

@ eRepr_virtual

no seq data

@ eMol_na

just a nucleic acid

unsigned int

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

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

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

static bool Equals(const CVariation::TPlacements &p1, const CVariation::TPlacements &p2)

#define MAX(a, b)

returns larger of a and b.

constexpr TSeqPos GetMinBinSize() const

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