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NCBI C++ ToolKit: src/algo/sequence/adapter_search.cpp Source File

* alphabet =

;

(

= 0;

< mer_size;

++) {

s[mer_size - 1 -

] = alphabet[w & 3];

(words.size() == 0) {

iupac.resize(words.size() - 1);

* alphabet =

;

(

= 0;

< words.size() - 1;

++) {

iupac[

] = alphabet[words[

] >> (mer_size * 2 - 2)];

iupac +=

(words.back(), mer_size);

vector<Uint1> counts(64, 0);

counts[w2 & 0x3F] += 1;

(

= 0;

< 64;

++) {

c = counts[

];

(144 - sumsq)/132.0;

*

seq,

char2letter[] = {

0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,

0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,

0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,

0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,

0, 0, 0, 1, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0,

0, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,

0, 0, 0, 1, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0,

0, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,

0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,

0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,

0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,

0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,

0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,

0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,

0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,

0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0

c = char2letter[

(seq[

])];

(

= 1;

< words.size();

++) {

c = char2letter[

(seq[

+ k])];

words[

] = ((words[

- 1] &

) << 2) | c;

c = 3 - char2letter[

(seq[seq_size - 1 -

])];

(

= 1;

< words.size();

++) {

c = 3 - char2letter[

(seq[k -

])];

words[

] = ((words[

- 1] &

) << 2) | c;

::CPairedEndAdapterDetector

TWords::const_iterator begin,

TWords::const_iterator end)

words_size = end - begin;

=

(words_size, m_len);

(

= 0;

<

;

++) {

x_IncrCount(

, *(begin +

) >> 4);

(words_size > 0 && words_size < m_len) {

= min<size_t>(2, m_len - words_size);

w = *(begin + words_size);

(

= 0;

<

;

++) {

pos = words_size +

;

w2 = (w >> (2 -

*2)) & 0xFFFFF;

x_IncrCount(pos, w2);

::CPairedEndAdapterDetector

::x_NextWord(

pos,

prev_word)

best_count = 0;

word = ((prev_word << 2) & 0xFFFFF) |

;

(

> best_count) {

NAdapterSearch

::CPairedEndAdapterDetector

::InferConsensus(

& params)

secondbest_sup(0);

(

word = 0; word < NMERS10; word++) {

sup = m_counts[word];

secondbest_sup = top_sup;

words[0] = best_word;

<< s_AsIUPAC(best_word,10)

<<

(

= 1;

< words.size();

++) {

last_word = words[

- 1];

last_sup = x_GetCount(

- 1, last_word);

curr_word = x_NextWord(

- 1, last_word);

curr_sup = x_GetCount(

, curr_word);

words[

] = curr_word;

s_AsIUPAC(words, 10);

pair<size_t, size_t> NAdapterSearch

::CPairedEndAdapterDetector

::s_FindAdapterStartPos(

pair<size_t, size_t>(

find(fwd_read.begin(), fwd_read.end(), rev_read.back())

- fwd_read.begin() + MER_LENGTH,

find(rev_read.begin(), rev_read.end(), fwd_read.front())

::CPairedEndAdapterDetector

= spot_len / 2;

* fwd_read = spot;

* rev_read = spot+

;

pair<size_t, size_t> pos = s_FindAdapterStartPos(fwd_words, rev_words);

is_consistent = (pos.first + pos.second ==

);

adapter_len =

- pos.first;

(is_consistent && adapter_len >= MER_LENGTH) {

m_cons5.AddExemplar(fwd_words.begin() + pos.first, fwd_words.end());

s_Translate(rev_read + pos.first, adapter_len,

, words2);

m_cons3.AddExemplar(words2.begin(), words2.end());

top_count = m_counts[

];

words.push_back(

);

x_ExtendSeed(words, top_count,

);

reverse(words.begin(), words.end());

x_ExtendSeed(words, top_count,

);

c = seq[seq.size() - 1];

(seq.size() > 0 && seq[seq.size() - 1] == c) {

seq.resize(seq.size() - 1);

::CUnpairedAdapterDetector

::x_FindAdapterSeed()

pair<TCount, TWord>

;

priority_queue< TPair, vector<TPair>, greater<TPair> > TTopWords;

(

w = 0; w < m_counts.size(); w++) {

(top_words.size() > m_params.top_n) {

= top_words.size();

(; !top_words.empty(); top_words.pop()) {

sup = top_words.top().first;

word = top_words.top().second;

sumlogs +=

(sup + 1.0);

gmean =

== 0 ? 0 : exp(sumlogs /

) - 1;

<<

<<

(gmean));

m_params.HaveInitialSupport(sup, gmean) ? word : 0;

: (w >> 2) | (

<< 22);

(

> best_count) {

prev_word = words.back();

curr_word = x_GetAdjacent(prev_word, right);

prev_sup = m_counts[prev_word];

curr_sup = m_counts[curr_word];

(!m_params.HaveContinuedSupport(top_sup, prev_sup, curr_sup)

|| find(words.begin(), words.end(), curr_word) != words.end())

words.push_back(curr_word);

.second <

.second;

::CSimpleUngappedAligner

::GetSeqRange(

pos)

TRanges::const_iterator it = lower_bound(

m_subseq_ranges.begin(),

m_subseq_ranges.end(),

it == m_subseq_ranges.end() ?

(NULLPOS, NULLPOS) : *it;

::CSimpleUngappedAligner

(

.len > 0 &&

.len == 0) {

}

(

.len == 0 &&

.len > 0) {

ar = GetSeqRange((

.second -

.first) / 2);

= GetSeqRange((

.second -

.first) / 2);

a_un = (ar.second - ar.first) -

.len/2;

b_un = (

.second -

.first) -

.len/2;

<<

<< (

.second -

.first) / 2

<<

<< m_seq.substr(ar.first, ar.second - ar.first));

<<

<< (

.second -

.first) / 2

<<

<< m_seq.substr(

.first,

.second -

.first));

a_score =

.len -

(1.0 + a_un)*5;

b_score =

.len -

(1.0 + b_un)*5;

a_score < b_score ?

:

;

s_PermuteMismatches(word, approx_words);

& pos_ref = vec_index[w];

(pos_ref == pos || pos_ref == NULLPOS) {

(pos_ref != MULTIPOS) {

positions.resize(coordset.

());

TPositions::iterator dest = positions.begin();

pos = it->second;

(map_index.

(w) == map_index.

()) {

map_index[w].first = dest;

map_index[w].second = dest;

m_seq.assign(seq,

);

m_subseq_ranges.clear();

fill(m_vec_index.begin(), m_vec_index.end(), (

)NULLPOS);

* endend = seq+

;

(

*begin = seq, *end = find(begin, endend,

);

begin = end + 1, end = find(begin, endend,

))

(begin - seq, end - seq);

m_subseq_ranges.push_back(

);

(

= 0;

< words.size();

++) {

s_IndexWord(words[

], pos, m_vec_index, coordset);

s_CoordSetToMapIndex(coordset, m_map_index, m_positions);

TWords::iterator dest = words.begin();

(

i1 = 3; i1 < 9; i1++) {

(

c1 = 0; c1 < 4; c1++) {

w1 = s_Put(w, i1, c1);

(

i2 = i1+1; i2 < 9; i2++) {

(

c2 = 0; c2 < 4; c2++) {

*(dest++) = s_Put(w1, i2, c2);

(m1.

== NULLPOS) {

m.

= q_pos - s_pos;

m.

= q_pos + s_pos;

query_len,

direction,

match_score,

mismatch_score,

dropoff_score)

delta_pos = direction ? 1 : -1;

pair<TPos, TPos> TPoint;

TPoint p(seg.

+ (direction ? seg.

- 1 : 0),

seg.

+ (direction ? seg.

- 1 : 0));

score(0), max_score(0);

q_bounds(0, query_len);

p.first += delta_pos;

p.second += delta_pos;

(score + dropoff_score > max_score

&& p.first >= q_bounds.first

&& p.first < q_bounds.second

&& p.second >= s_bounds.first

&& p.second < s_bounds.second)

score += (q_seq[p.first] == m_seq[p.second]) ? match_score

<<

<< q_seq[p.first]

<<

<< m_seq[p.second]

<<

<< best_p.first);

(score > max_score) {

p.first += delta_pos;

p.second += delta_pos;

seg.

= best_p.first - seg.

+ 1;

seg2.

= best_p.first;

seg2.

= best_p.second;

(

= 0;

< words.size();

++) {

m_vec_index.begin() + w + 1);

(*

.first == NULLPOS) {

}

(*

.first == MULTIPOS) {

= m_map_index.find(w)->second;

(TPositions::const_iterator it =

.first; it !=

.second; ++it) {

new_match = x_CreateMatch(

, *it);

(!

(old_match, new_match)) {

best_match = x_GetBetterOf(best_match, old_match);

old_match = new_match;

(TMatches, it, matches) {

best_match = x_GetBetterOf(best_match, it->

);

LargeInt< 1 > revcomp(const LargeInt< 1 > &x, size_t sizeKmer)

CLocalRange< TOffset > TRange

define for the fundamental building block of sequence ranges

ncbi::TMaskedQueryRegions mask

static void s_CoordSetToMapIndex(const TCoordSet &coordset, TMapIndex &map_index, TPositions &positions)

static void s_PermuteMismatches(TWord w, TWords &words)

SMatch FindSingleBest(const char *query, size_t len) const

Return best ungapped alignment of at least MER_LENGTH.

pair< TPositions::const_iterator, TPositions::const_iterator > TPosRange

void Init(const char *seq, size_t len)

IUPAC sequence of target sequence(s) Multiple sequences may be concatenated and '-'-delimited e....

SMatch x_CreateMatch(TPos q_start, TPos s_start) const

Create a match in diag/antidiag coordspace for a matched word.

static bool s_Merge(SMatch &m, const SMatch &m2)

void x_Extend(SMatch &match, const char *query_seq, const size_t query_len, const bool direction, const int match_score=3, const int mismatch_score=-2, const int dropoff=5) const

Ungapped extension (match is in normal coordinates)

static void s_IndexWord(TWord w, TPos pos, TPositions &vec_index, TCoordSet &coordset)

pair< TPos, TPos > TRange

vector< TPos > TPositions

TWord x_GetAdjacent(TWord w, bool right) const

if right, return most frequent word whose 11-prefix = 11-suffix of w; otherwise, return most frequent...

virtual void AddExemplar(const char *seq, size_t len)

Add sequence of a spot from an SRA run (single or paired-end read)

virtual string InferAdapterSeq() const

returns IUPAC seq of the inferred adapter seq; empty if not found.

void x_ExtendSeed(TWords &words, size_t top_count, bool right) const

Extend the seed one way, as long as it satisfies extension thresholds.

static bool s_IsLowComplexity(TWord word)

With threshold of 0.9, 0.7% of all words are classified as such.

static double s_GetWordComplexity(TWord word)

Complexity is a value between 0 (for a homopolymer) and 1 (max complexity).

static const size_t MER_LENGTH

Will use 24-bit 12-mers as words.

static string s_AsIUPAC(TWord w, size_t mer_size=MER_LENGTH)

Convert word to IUPAC string [ACGT]{MER_LENGTH}.

static void s_Translate(const char *const iupac_na, size_t len, bool apply_revcomp, TWords &words)

Translate IUPAC sequence to a sequence of overlapping words (A,C,G,T,*) <-> (0,1,2,...

static bool s_IsHomopolymer(TWord w)

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

parent_type::value_type value_type

SStaticPair< const char *, const char * > TPair

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERR_POST(message)

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

#define LOG_POST(message)

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

void Info(CExceptionArgs_Base &args)

uint8_t Uint1

1-byte (8-bit) unsigned integer

int64_t Int8

8-byte (64-bit) signed integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

void s_Merge(SExpression &l, SExpression &r)

NCBI C++ auxiliary debug macros.

Miscellaneous common-use basic types and functionality.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

static SLJIT_INLINE sljit_ins br(sljit_gpr target)

Represents single ungapped alignment.

An adapter sequence is presumed to occur at least min_support times in the input, and is overrepresen...

bool HaveContinuedSupport(size_t top_sup, size_t prev_sup, size_t candidate_sup) const

bool HaveInitialSupport(size_t top_candidate_sup, size_t non_candidate_sup) const

bool operator()(const NAdapterSearch::CSimpleUngappedAligner::TRange &a, const NAdapterSearch::CSimpleUngappedAligner::TRange &b) const

static Uint4 letter(char c)

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