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NCBI C++ ToolKit: src/algo/blast/unit_tests/api/blastextend_unit_test.cpp Source File

;

m_ScoringOpts =

;

m_HitSavingOpts =

;

m_ipInitHitlist =

;

m_ipScoreParams =

;

m_ipHitParams =

;

m_ipExtParams =

;

m_ipWordParams =

;

(m_ipScoreParams);

(m_ipHitParams);

(m_ipExtParams);

num_hsps = 8;

q_offsets[num_hsps] =

{8799, 1358, 14042, 27664, 5143, 27737, 5231, 3212 };

s_offsets[num_hsps] =

{ 2728, 2736, 2784, 2784, 2792, 2856, 2888, 3640 };

q_starts[num_hsps] =

{ 8794, 1355, 14015, 27637, 5131, 27732, 5226, 3201 };

s_starts[num_hsps] =

{ 2723, 2733, 2757, 2757, 2780, 2851, 2883, 3629 };

lengths[num_hsps] = { 174, 18, 141, 92, 38, 37, 28, 20 };

scores[num_hsps] = { 146, 18, 93, 40, 34, 21, 24, 16 };

(index = 0; index < num_hsps; ++index) {

ungapped_data->

= q_starts[index];

ungapped_data->

= s_starts[index];

ungapped_data->

= lengths[index];

ungapped_data->

= scores[index];

s_offsets[index], ungapped_data);

num_hsps = 14;

q_offsets[num_hsps] =

{ 8799, 1358, 8831, 14042, 27664, 5143, 8863, 8903, 8927, 14114,

27737, 8943, 5231, 3212 };

s_offsets[num_hsps] =

{ 2728, 2736, 2760, 2784, 2784, 2792, 2792, 2832, 2856, 2856,

2856, 2872, 2888, 3640 };

(index = 0; index < num_hsps; ++index) {

s_offsets[index],

);

db_num_seq, &eff_len_params);

m_ipScoreBlk, m_iclsQueryInfo,

);

greedy,

chaining =

,

expect_value = 10)

BOOST_REQUIRE(status == 0);

(m_ipScoreBlk->

) {

BOOST_REQUIRE(status == 0);

program, m_ipScoreBlk,

m_iclsQueryBlk->

, m_iclsQueryInfo,

BOOST_REQUIRE(message ==

);

BOOST_REQUIRE(status == 0);

program, m_iclsQueryInfo,

);

BOOST_REQUIRE(status == 0);

fillEffectiveLengths(program, m_ScoringOpts,

m_ipScoreBlk, &m_ipScoreParams);

BOOST_REQUIRE(status == 0);

m_ExtnOpts, m_ipScoreBlk,

m_iclsQueryInfo, &m_ipExtParams);

BOOST_REQUIRE(status == 0);

m_ipScoreBlk, m_iclsQueryInfo, subject_length, 0, &m_ipHitParams);

BOOST_REQUIRE(status == 0);

m_iclsQueryInfo.

(),

BOOST_REQUIRE(status == 0);

subject_length, m_ipScoreBlk, &m_ipGapAlign);

BOOST_REQUIRE(status == 0);

num_hsps = 7;

query_starts[num_hsps] =

{ 8794, 13982, 12612, 5131, 5226, 1355, 3201 };

subject_starts[num_hsps] =

{ 2723, 2723, 2733, 2780, 2883, 2733, 3629 };

query_lengths[num_hsps] = { 174, 174, 182, 38, 28, 18, 20 };

subject_lengths[num_hsps] = { 174, 175, 183, 38, 28, 18, 20 };

pair<TSeqPos, TSeqPos> range(20000, 35000);

unique_ptr<SSeqLoc> qsl(

unique_ptr<SSeqLoc> ssl(

queries.push_back(*qsl);

subjects.push_back(*ssl);

(queries, m_iclsQueryInfo, &m_iclsQueryBlk,

, strand_opt, blast_msg);

BOOST_REQUIRE(m->empty());

subject_length;

vector<BLAST_SequenceBlk*> subject_blk_v;

&subject_blk_v, &subject_length);

m_iclsQueryBlk, m_iclsQueryInfo, subject_blk_v[0],

m_ipGapAlign, m_ipScoreParams, m_ipExtParams,

m_ipHitParams, m_ipWordParams, m_ipInitHitlist,

&hsp_list, gapped_stats,

);

BOOST_REQUIRE_EQUAL(num_hsps, hsp_list->

);

BOOST_REQUIRE_EQUAL(num_hsps, gapped_stats->

);

(gapped_stats);

(index = 0; index < num_hsps; ++index) {

query_starts[index]);

subject_starts[index]);

query_lengths[index]);

subject_lengths[index]);

num_hsps = 7;

query_starts[num_hsps] =

{ 8794, 13982, 12612, 5131, 5226, 1355, 3201 };

subject_starts[num_hsps] =

{ 2723, 2723, 2733, 2780, 2883, 2733, 3629 };

query_lengths[num_hsps] =

{ 174, 174, 182, 38, 28, 18, 20 };

subject_lengths[num_hsps] =

{ 174, 175, 183, 38, 28, 18, 20 };

pair<TSeqPos, TSeqPos> range(20000, 35000);

unique_ptr<SSeqLoc> qsl(

unique_ptr<SSeqLoc> ssl(

queries.push_back(*qsl);

subjects.push_back(*ssl);

(queries, m_iclsQueryInfo, &m_iclsQueryBlk,

, strand_opt, blast_msg);

BOOST_REQUIRE(m->empty());

subject_length;

vector<BLAST_SequenceBlk*> subject_blk_v;

&subject_blk_v, &subject_length);

setupGreedyHitList();

m_iclsQueryBlk, m_iclsQueryInfo, subject_blk_v[0],

m_ipGapAlign, m_ipScoreParams, m_ipExtParams,

m_ipHitParams, m_ipWordParams, m_ipInitHitlist,

&hsp_list, gapped_stats,

);

BOOST_REQUIRE_EQUAL(num_hsps, hsp_list->

);

BOOST_REQUIRE(hsp_list ==

);

setupGreedyHitList();

m_ipHitParams->options->min_hit_length = 100;

m_ipHitParams->options->percent_identity = 99;

m_iclsQueryBlk, m_iclsQueryInfo, subject_blk_v[0],

m_ipGapAlign, m_ipScoreParams, m_ipExtParams,

m_ipHitParams, m_ipWordParams, m_ipInitHitlist,

&hsp_list, gapped_stats,

);

BOOST_REQUIRE_EQUAL(num_hsps, hsp_list->

);

BOOST_REQUIRE_EQUAL(2*num_hsps, gapped_stats->

);

(gapped_stats);

(index = 0; index < num_hsps; ++index) {

query_starts[index]);

subject_starts[index]);

query_lengths[index]);

subject_lengths[index]);

query_start = 2612;

query_end = 2754;

subject_start = 291;

subject_end = 438;

q_offset = 2754;

s_offset = 438;

ungapped.

= 42;

unique_ptr<SSeqLoc> qsl(

pair<TSeqPos, TSeqPos> range(1896999, 1897550);

unique_ptr<SSeqLoc> ssl(

queries.push_back(*qsl);

subjects.push_back(*ssl);

(queries, m_iclsQueryInfo, &m_iclsQueryBlk,

, strand_opt, blast_msg);

BOOST_REQUIRE(m->empty());

subject_length;

vector<BLAST_SequenceBlk*> subject_blk_v;

&subject_blk_v, &subject_length);

m_ipScoreParams->reward = 1;

m_ipScoreParams->penalty = -2;

m_ipScoreParams->gap_open = 0;

m_ipScoreParams->gap_extend = 0;

m_ipExtParams->gap_x_dropoff = 16;

m_ipExtParams->gap_x_dropoff_final = 54;

subject_length, m_ipScoreBlk, &m_ipGapAlign);

m_iclsQueryBlk, m_iclsQueryInfo, subject_blk_v[0],

m_ipGapAlign, m_ipScoreParams, m_ipExtParams,

m_ipHitParams, m_ipWordParams, m_ipInitHitlist,

&hsp_list, gapped_stats,

);

m_ipInitHitlist->init_hsp_array[0].ungapped_data =

;

BOOST_REQUIRE_EQUAL(1, hsp_list->

);

(gapped_stats);

BOOST_REQUIRE(m_ipGapAlign->greedy_query_seed_start >= query_start);

BOOST_REQUIRE(m_ipGapAlign->greedy_query_seed_start <= query_end);

BOOST_REQUIRE(m_ipGapAlign->greedy_subject_seed_start >= subject_start);

BOOST_REQUIRE(m_ipGapAlign->greedy_subject_seed_start <= subject_end);

qid(

);

unique_ptr<SSeqLoc> qsl(

unique_ptr<SSeqLoc> ssl(

queries.push_back(*qsl);

subjects.push_back(*ssl);

(queries, m_iclsQueryInfo, &m_iclsQueryBlk,

, strand_opt, blast_msg);

BOOST_REQUIRE(m->empty());

subject_length;

vector<BLAST_SequenceBlk*> subject_blk_v;

&subject_blk_v, &subject_length);

,

, 0.00001);

m_ipExtParams->options->chaining =

;

num_init_hsps = 1;

q_starts[num_init_hsps] = { 164 };

s_starts[num_init_hsps] = { 242 };

lengths[num_init_hsps] = { 9 };

scores[num_init_hsps] = { 42 };

(index = 0; index < num_init_hsps; ++index) {

ungapped_data->

= q_starts[index];

ungapped_data->

= s_starts[index];

ungapped_data->

= lengths[index];

ungapped_data->

= scores[index];

s_starts[index], ungapped_data);

m_iclsQueryBlk, m_iclsQueryInfo, subject_blk_v[0],

m_ipGapAlign, m_ipScoreParams, m_ipExtParams,

m_ipHitParams, m_ipWordParams, m_ipInitHitlist,

&hsp_list, gapped_stats,

);

BOOST_REQUIRE_EQUAL(hsp_list->

, 0);

BOOST_REQUIRE_EQUAL(gapped_stats->

, 0);

(gapped_stats);

kSize = 100;

kDefaultSize = 1000000;

BOOST_REQUIRE(retval);

kDefaultSize = 1000000;

BOOST_REQUIRE(retval);

kSize = 5000000;

BOOST_REQUIRE(retval);

null_output =

;

BOOST_REQUIRE_EQUAL(

, null_output);

null_output =

;

BOOST_REQUIRE_EQUAL(

, null_output);

Declares the CBl2Seq (BLAST 2 Sequences) class.

#define sfree(x)

Safe free a pointer: belongs to a higher level header.

Declarations of static arrays used to define some NCBI encodings to be used in a toolkit independent ...

BlastInitHitList * BLAST_InitHitListNew(void)

Allocate memory for the BlastInitHitList structure.

Boolean BLAST_SaveInitialHit(BlastInitHitList *init_hitlist, Int4 q_off, Int4 s_off, BlastUngappedData *ungapped_data)

Save the initial hit data into the initial hit list structure.

void Blast_InitHitListSortByScore(BlastInitHitList *init_hitlist)

Sort array of initial HSPs by score.

Blast_ExtendWord * BlastExtendWordFree(Blast_ExtendWord *ewp)

Deallocate memory for the word extension structure.

BlastInitHitList * BLAST_InitHitListFree(BlastInitHitList *init_hitlist)

Free memory for the BlastInitList structure.

Structures and functions prototypes used for BLAST gapped extension.

Int2 BLAST_GetGappedScore(EBlastProgramType program_number, BLAST_SequenceBlk *query, BlastQueryInfo *query_info, BLAST_SequenceBlk *subject, BlastGapAlignStruct *gap_align, const BlastScoringParameters *score_params, const BlastExtensionParameters *ext_params, const BlastHitSavingParameters *hit_params, const BlastInitialWordParameters *word_params, BlastInitHitList *init_hitlist, BlastHSPList **hsp_list_ptr, BlastGappedStats *gapped_stats, Boolean *fence_hit)

Performs gapped extension for all non-Mega BLAST programs, given that ungapped extension has been don...

Int2 BLAST_GapAlignStructNew(const BlastScoringParameters *score_params, const BlastExtensionParameters *ext_params, Uint4 max_subject_length, BlastScoreBlk *sbp, BlastGapAlignStruct **gap_align_ptr)

Initializes the BlastGapAlignStruct structure.

BlastGapAlignStruct * BLAST_GapAlignStructFree(BlastGapAlignStruct *gap_align)

Deallocates memory in the BlastGapAlignStruct structure.

BlastHSPList * Blast_HSPListNew(Int4 hsp_max)

Creates HSP list structure with a default size HSP array.

BlastHSPList * Blast_HSPListFree(BlastHSPList *hsp_list)

Deallocate memory for an HSP list structure as well as all it's components.

Blast_Message * Blast_MessageFree(Blast_Message *blast_msg)

Deallocates message memory.

Declares the CBlastNucleotideOptionsHandle class.

Definitions which are dependant on the NCBI C++ Object Manager.

BlastHitSavingOptions * BlastHitSavingOptionsFree(BlastHitSavingOptions *options)

Deallocate memory for BlastHitSavingOptions.

@ eGreedyScoreOnly

Greedy extension (megaBlast)

Int2 BlastEffectiveLengthsOptionsNew(BlastEffectiveLengthsOptions **options)

Allocate memory for BlastEffectiveLengthsOptions* and fill with default values.

BlastInitialWordOptions * BlastInitialWordOptionsFree(BlastInitialWordOptions *options)

Deallocate memory for BlastInitialWordOptions.

Int2 BlastScoringOptionsNew(EBlastProgramType program, BlastScoringOptions **options)

Allocate memory for BlastScoringOptions and fill with default values.

BlastEffectiveLengthsOptions * BlastEffectiveLengthsOptionsFree(BlastEffectiveLengthsOptions *options)

Deallocate memory for BlastEffectiveLengthsOptions*.

BlastExtensionOptions * BlastExtensionOptionsFree(BlastExtensionOptions *options)

Deallocate memory for BlastExtensionOptions.

Int2 BlastHitSavingOptionsNew(EBlastProgramType program, BlastHitSavingOptions **options, Boolean gapped_calculation)

Allocate memory for BlastHitSavingOptions.

Int2 BlastInitialWordOptionsNew(EBlastProgramType program, BlastInitialWordOptions **options)

Allocate memory for BlastInitialWordOptions and fill with default values.

BlastScoringOptions * BlastScoringOptionsFree(BlastScoringOptions *options)

Deallocate memory for BlastScoringOptions.

Int2 BlastExtensionOptionsNew(EBlastProgramType program, BlastExtensionOptions **options, Boolean gapped)

Allocate memory for BlastExtensionOptions and fill with default values.

BlastHitSavingParameters * BlastHitSavingParametersFree(BlastHitSavingParameters *parameters)

Deallocate memory for BlastHitSavingOptions*.

BlastEffectiveLengthsParameters * BlastEffectiveLengthsParametersFree(BlastEffectiveLengthsParameters *parameters)

Deallocate memory for BlastEffectiveLengthsParameters*.

Int2 BlastExtensionParametersNew(EBlastProgramType blast_program, const BlastExtensionOptions *options, BlastScoreBlk *sbp, BlastQueryInfo *query_info, BlastExtensionParameters **parameters)

Calculate the raw values for the X-dropoff parameters.

BlastInitialWordParameters * BlastInitialWordParametersFree(BlastInitialWordParameters *parameters)

Deallocate memory for BlastInitialWordParameters.

Int2 BlastScoringParametersNew(const BlastScoringOptions *options, BlastScoreBlk *sbp, BlastScoringParameters **parameters)

Calculate scaled cutoff scores and gap penalties.

Int2 BlastInitialWordParametersNew(EBlastProgramType program_number, const BlastInitialWordOptions *word_options, const BlastHitSavingParameters *hit_params, const LookupTableWrap *lookup_wrap, const BlastScoreBlk *sbp, BlastQueryInfo *query_info, Uint4 subject_length, BlastInitialWordParameters **parameters)

Allocate memory for BlastInitialWordParameters and set x_dropoff.

Int2 BlastHitSavingParametersNew(EBlastProgramType program_number, const BlastHitSavingOptions *options, const BlastScoreBlk *sbp, const BlastQueryInfo *query_info, Int4 avg_subject_length, Int4 compositionBasedStats, BlastHitSavingParameters **parameters)

Allocate memory and initialize the BlastHitSavingParameters structure.

Int2 BlastEffectiveLengthsParametersNew(const BlastEffectiveLengthsOptions *options, Int8 db_length, Int4 num_seqs, BlastEffectiveLengthsParameters **parameters)

Allocate memory for BlastEffectiveLengthsParameters.

Boolean Blast_QueryIsProtein(EBlastProgramType p)

Returns true if the query is protein.

EBlastProgramType

Defines the engine's notion of the different applications of the BLAST algorithm.

Utilities initialize/setup BLAST.

Int2 Blast_ScoreBlkKbpGappedCalc(BlastScoreBlk *sbp, const BlastScoringOptions *scoring_options, EBlastProgramType program, const BlastQueryInfo *query_info, Blast_Message **error_return)

Blast_ScoreBlkKbpGappedCalc, fills the ScoreBlkPtr for a gapped search.

Int2 Blast_ScoreBlkMatrixInit(EBlastProgramType program_number, const BlastScoringOptions *scoring_options, BlastScoreBlk *sbp, GET_MATRIX_PATH get_path)

Initializes the substitution matrix in the BlastScoreBlk according to the scoring options specified.

Int2 BLAST_CalcEffLengths(EBlastProgramType program_number, const BlastScoringOptions *scoring_options, const BlastEffectiveLengthsParameters *eff_len_params, const BlastScoreBlk *sbp, BlastQueryInfo *query_info, Blast_Message **blast_message)

Function to calculate effective query length and db length as well as effective search space.

BlastScoreBlk * BlastScoreBlkFree(BlastScoreBlk *sbp)

Deallocates BlastScoreBlk as well as all associated structures.

Int2 Blast_ScoreBlkKbpUngappedCalc(EBlastProgramType program, BlastScoreBlk *sbp, Uint1 *query, const BlastQueryInfo *query_info, Blast_Message **blast_message)

Calculate and fill the ungapped Karlin-Altschul parameters in the BlastScoreBlk structure (fields kbp...

BlastScoreBlk * BlastScoreBlkNew(Uint1 alphabet, Int4 number_of_contexts)

Allocates and initializes BlastScoreBlk.

BLAST_SequenceBlk * BlastSequenceBlkFree(BLAST_SequenceBlk *seq_blk)

Deallocate memory for a sequence block.

BOOST_AUTO_TEST_CASE(testGapAlignment)

int x_score_compare_hsps(const void *v1, const void *v2)

BOOST_AUTO_TEST_SUITE_END() static int s_GetSegmentFlags(const CBioseq &bioseq)

Wrapper class for BLAST_SequenceBlk .

Handle to the nucleotide-nucleotide options to the BLAST algorithm.

Encapsulates ALL the BLAST algorithm's options.

Wrapper class for BlastQueryInfo .

static CTestObjMgr & Instance()

typedef for the messages for an entire BLAST search, which could be comprised of multiple query seque...

static SQLCHAR output[256]

void MBSpaceFree(SMBSpace *sp)

Free the space structure.

SMBSpace * MBSpaceNew(int num_space_arrays)

Allocate a space structure for greedy alignment At least num_space_arrays will be allocated,...

BlastQueryInfo * Get() const

void SetupSubjects(TSeqLocVector &subjects, EBlastProgramType program, vector< BLAST_SequenceBlk * > *seqblk_vec, unsigned int *max_subjlen)

Sets up internal subject data structure for the BLAST search.

void SetupQueries(TSeqLocVector &queries, BlastQueryInfo *qinfo, BLAST_SequenceBlk **seqblk, EBlastProgramType prog, objects::ENa_strand strand_opt, TSearchMessages &messages)

Populates BLAST_SequenceBlk with sequence data for use in CORE BLAST.

objects::ENa_strand GetStrandOption() const

#define BLASTNA_SEQ_CODE

Identifies the blastna alphabet, for use in blast only.

#define BLASTAA_SEQ_CODE

== Seq_code_ncbistdaa

EBlastProgramType GetProgramType() const

Returns the CORE BLAST notion of program type.

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

char * BlastFindMatrixPath(const char *matrix_name, Boolean is_prot)

Returns the path to a specified matrix.

void SetupQueryInfo(TSeqLocVector &queries, EBlastProgramType prog, objects::ENa_strand strand_opt, BlastQueryInfo **qinfo)

Allocates the query information structure and fills the context offsets, in case of multiple queries,...

static CBlastOptionsHandle * CreateTask(string task, EAPILocality locality=CBlastOptions::eLocal)

Creates an options handle object configured with default options for the requested task,...

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int16_t Int2

2-byte (16-bit) signed integer

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

int64_t Int8

8-byte (64-bit) signed integer

ENa_strand

strand of nucleic acid

@ eNa_strand_both

in forward orientation

Magic spell ;-) needed for some weird compilers... very empiric.

Defines: CTimeFormat - storage class for time format.

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

Uint1 * sequence

Sequence used for search (could be translation).

Options for setting up effective lengths and search spaces.

Parameters for setting up effective lengths and search spaces.

Options used for gapped extension These include: a.

Boolean chaining

Use chaining for fast approximate gapped extension.

EBlastPrelimGapExt ePrelimGapExt

type of preliminary gapped extension (normally) for calculating score.

Computed values used as parameters for gapped alignments.

Structure supporting the gapped alignment.

Structure containing hit counts from the gapped stage of a BLAST search.

Int4 extensions

Total number of gapped extensions performed.

The structure to hold all HSPs for a given sequence after the gapped alignment.

Int4 hspcnt

Number of HSPs saved.

BlastHSP ** hsp_array

Array of pointers to individual HSPs.

Structure holding all information about an HSP.

BlastSeg query

Query sequence info.

BlastSeg subject

Subject sequence info.

Int4 score

This HSP's raw score.

Options used when evaluating and saving hits These include: a.

double expect_value

The expect value cut-off threshold for an HSP, or a combined hit if sum statistics is used.

Parameter block that contains a pointer to BlastHitSavingOptions and the values derived from it.

Structure to hold all initial HSPs for a given subject sequence.

Options needed for initial word finding and processing.

Parameter block that contains a pointer to BlastInitialWordOptions and the values derived from it.

Structure used for scoring calculations.

Blast_KarlinBlk ** kbp

Karlin-Altschul parameters.

Blast_KarlinBlk ** kbp_gap

K-A parameters for gapped alignments.

Blast_KarlinBlk ** kbp_gap_std

K-A parameters for std (not position-based) alignments.

Blast_KarlinBlk ** kbp_std

K-A parameters for ungapped alignments.

Blast_GumbelBlk * gbp

Gumbel parameters for FSC.

Scoring options block Used to produce the BlastScoreBlk structure This structure may be needed for lo...

Boolean gapped_calculation

gap-free search if FALSE

Scoring parameters block Contains scoring-related information that is actually used for the blast sea...

Int4 offset

Start of hsp.

Structure to hold ungapped alignment information.

Int4 score

Score of the ungapped alignment.

Int4 length

Length of the ungapped alignment.

Int4 q_start

Start of the ungapped alignment in query.

Int4 s_start

Start of the ungapped alignment in subject.

Structure for keeping initial word extension information.

Structure to hold the a message from the core of the BLAST engine.

void setupStructures(EBlastProgramType program, Uint4 subject_length, bool greedy, bool chaining=false, double expect_value=10)

BlastHitSavingParameters * m_ipHitParams

BlastHitSavingOptions * m_HitSavingOpts

CBLAST_SequenceBlk m_iclsQueryBlk

~CBlastExtendTestFixture()

CBlastExtendTestFixture()

BlastInitialWordParameters * m_ipWordParams

BlastInitialWordOptions * m_WordOpts

BlastGapAlignStruct * m_ipGapAlign

BlastScoringOptions * m_ScoringOpts

BlastScoreBlk * m_ipScoreBlk

BlastExtensionParameters * m_ipExtParams

CBlastQueryInfo m_iclsQueryInfo

BlastInitHitList * m_ipInitHitlist

BlastScoringParameters * m_ipScoreParams

void fillEffectiveLengths(EBlastProgramType program_type, const BlastScoringOptions *score_options, Int8 db_length, Int4 db_num_seq)

BlastExtensionOptions * m_ExtnOpts

void setupGreedyHitList()

Space structure for greedy alignment algorithm.

Int4 space_allocated

number of structures allocated

Utility stuff for more convenient using of Boost.Test library.

voidp calloc(uInt items, uInt size)

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