/
aligner_sw.cpp
2634 lines (2634 loc) · 55.8 KB
/
aligner_sw.cpp
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extern "C"
{
#include "semiWFA/gap_affine/affine_wavefront_align.h"
extern mm_allocator_t *mm_allocator_new(const uint64_t segment_size);
extern affine_wavefronts_t *affine_wavefronts_new_complete(const int pattern_length, const int text_length, affine_penalties_t *const penalties, wavefronts_stats_t *const wavefronts_stats, mm_allocator_t *const mm_allocator);
extern void affine_wavefronts_align(affine_wavefronts_t *const affine_wavefronts, const char *const pattern, const int pattern_length, const char *const text, const int text_length);
extern int edit_cigar_score_gap_affine(edit_cigar_t *const edit_cigar, affine_penalties_t *const penalties);
extern void edit_cigar_print_pretty(FILE *const stream, const char *const pattern, const int pattern_length, const char *const text, const int text_length, edit_cigar_t *const edit_cigar, mm_allocator_t *const mm_allocator);
extern void affine_wavefronts_delete(affine_wavefronts_t *const affine_wavefronts);
extern void mm_allocator_delete(mm_allocator_t *const mm_allocator);
}
#ifndef myNDEBUG
#define jj printf
#else
#define jj
#endif
#include <limits>
#include "aligner_sw.h"
#include "aligner_result.h"
#include "search_globals.h"
#include "scoring.h"
#include "mask.h"
#include "embedding.h"
#include "aln_search.h"
static void parse(char seq[], char fwd[])
{
unsigned len = strlen(seq);
for (size_t i = 0; i < len; i++)
{
uint8_t c = *(code + seq[i]);
fwd[i] = c;
}
*(fwd + len) = '\0';
}
void SwAligner::initRead(
const BTDnaString &rdfw,
const BTDnaString &rdrc,
const BTString &qufw,
const BTString &qurc,
size_t rdi,
size_t rdf,
const Scoring &sc)
{
assert_gt(rdf, rdi);
int nceil = sc.nCeil.f<int>((double)rdfw.length());
rdfw_ = &rdfw;
rdrc_ = &rdrc;
qufw_ = &qufw;
qurc_ = &qurc;
rdi_ = rdi;
rdf_ = rdf;
sc_ = ≻
nceil_ = nceil;
readSse16_ = false;
initedRead_ = true;
#ifndef NO_SSE
sseU8fwBuilt_ = false;
sseU8rcBuilt_ = false;
sseI16fwBuilt_ = false;
sseI16rcBuilt_ = false;
#endif
if (dpLog_ != NULL)
{
if (!firstRead_)
{
(*dpLog_) << '\n';
}
(*dpLog_) << rdfw.toZBuf() << '\t' << qufw.toZBuf();
}
firstRead_ = false;
}
void SwAligner::initRef(
bool fw,
TRefId refidx,
const DPRect &rect,
char *rf,
size_t rfi,
size_t rff,
TRefOff reflen,
const Scoring &sc,
TAlScore minsc,
bool enable8,
size_t cminlen,
size_t cpow2,
bool doTri,
bool extend)
{
size_t readGaps = sc.maxReadGaps(minsc, rdfw_->length());
size_t refGaps = sc.maxRefGaps(minsc, rdfw_->length());
assert_geq(readGaps, 0);
assert_geq(refGaps, 0);
assert_gt(rff, rfi);
rdgap_ = readGaps;
rfgap_ = refGaps;
state_ = STATE_INITED;
fw_ = fw;
rd_ = fw ? rdfw_ : rdrc_;
qu_ = fw ? qufw_ : qurc_;
refidx_ = refidx;
rf_ = rf;
rfi_ = rfi;
rff_ = rff;
reflen_ = reflen;
rect_ = ▭
minsc_ = minsc;
cural_ = 0;
initedRef_ = true;
enable8_ = enable8;
extend_ = extend;
cperMinlen_ = cminlen;
cperPerPow2_ = cpow2;
cperEf_ = true;
cperTri_ = doTri;
bter_.initRef(
fw_ ? rdfw_->buf() : rdrc_->buf(),
fw_ ? qufw_->buf() : qurc_->buf(),
rd_->length(),
rf_ + rfi_,
rff_ - rfi_,
reflen,
refidx_,
rfi_,
fw_,
rect_,
&cper_,
*sc_,
nceil_);
if (dpLog_ != NULL)
{
(*dpLog_) << '\t';
(*dpLog_) << refidx_ << ',';
(*dpLog_) << reflen_ << ',';
(*dpLog_) << minsc_ << ',';
(*dpLog_) << (fw ? '+' : '-') << ',';
rect_->write(*dpLog_);
(*dpLog_) << ',';
for (TRefOff i = rfi_; i < rff_; i++)
{
(*dpLog_) << mask2dna[(int)rf[i]];
}
}
}
void SwAligner::initRef(
bool fw,
TRefId refidx,
const DPRect &rect,
const BitPairReference &refs,
TRefOff reflen,
const Scoring &sc,
TAlScore minsc,
bool enable8,
size_t cminlen,
size_t cpow2,
bool doTri,
bool extend,
size_t upto,
size_t &nsUpto)
{
TRefOff rfi = rect.refl;
TRefOff rff = rect.refr + 1;
assert_gt(rff, rfi);
rff++;
const size_t rflen = (size_t)(rff - rfi);
size_t leftNs =
(rfi >= 0 ? 0 : (size_t)std::abs(static_cast<long>(rfi)));
leftNs = min(leftNs, rflen);
size_t rightNs =
(rff <= (TRefOff)reflen ? 0 : (size_t)std::abs(static_cast<long>(rff - reflen)));
rightNs = min(rightNs, rflen);
assert_geq(rflen, leftNs + rightNs);
const size_t rflenInner = rflen - (leftNs + rightNs);
#ifndef NDEBUG
bool haveRfbuf2 = false;
EList<char> rfbuf2(rflen);
if ((rand() % 10) == 0)
{
TRefOff rfii = rfi;
for (size_t i = 0; i < rflen; i++)
{
if (rfii < 0 || (TRefOff)rfii >= reflen)
{
rfbuf2.push_back(4);
}
else
{
rfbuf2.push_back(refs.getBase(refidx, (size_t)rfii));
}
rfii++;
}
haveRfbuf2 = true;
}
#endif
rfwbuf_.resize((rflen + 16) / 4);
int offset = refs.getStretch(
rfwbuf_.ptr(),
refidx,
(rfi < 0) ? 0 : (size_t)rfi,
rflenInner
ASSERT_ONLY(, tmp_destU32_));
assert_leq(offset, 16);
rf_ = (char *)rfwbuf_.ptr() + offset;
if (leftNs > 0)
{
for (size_t i = rflenInner; i > 0; i--)
{
rf_[i + leftNs - 1] = rf_[i - 1];
}
for (size_t i = 0; i < leftNs; i++)
{
rf_[i] = 4;
}
}
if (rightNs > 0)
{
for (size_t i = 0; i < rightNs; i++)
{
rf_[i + leftNs + rflenInner] = 4;
}
}
#ifndef NDEBUG
for (size_t i = 0; i < rflen; i++)
{
assert(!haveRfbuf2 || rf_[i] == rfbuf2[i]);
assert_range(0, 4, (int)rf_[i]);
}
#endif
nsUpto = 0;
for (size_t i = 0; i < rflen; i++)
{
if (i < upto && rf_[i] > 3)
{
nsUpto++;
}
rf_[i] = (1 << rf_[i]);
}
rff--;
initRef(
fw,
refidx,
rect,
rf_,
0,
(size_t)(rff - rfi),
reflen,
sc,
minsc,
enable8,
cminlen,
cpow2,
doTri,
extend);
}
int SwAligner::ungappedAlign(
const BTDnaString &rd,
const BTString &qu,
const Coord &coord,
const BitPairReference &refs,
size_t reflen,
const Scoring &sc,
bool ohang,
TAlScore minsc,
SwResult &res)
{
const size_t len = rd.length();
int nceil = sc.nCeil.f<int>((double)len);
int ns = 0;
TRefOff rfi = coord.off();
TRefOff rff = rfi + (TRefOff)len;
TRefId refidx = coord.ref();
assert_gt(rff, rfi);
size_t leftNs = 0;
if (rfi < 0)
{
if (ohang)
{
leftNs = (size_t)(-rfi);
}
else
{
return 0;
}
}
size_t rightNs = 0;
if (rff > (TRefOff)reflen)
{
if (ohang)
{
rightNs = (size_t)(rff - (TRefOff)reflen);
}
else
{
return 0;
}
}
if ((leftNs + rightNs) > (size_t)nceil)
{
return 0;
}
assert_geq(len, leftNs + rightNs);
const size_t rflenInner = len - (leftNs + rightNs);
#ifndef NDEBUG
bool haveRfbuf2 = false;
EList<char> rfbuf2(len);
if ((rand() % 10) == 0)
{
TRefOff rfii = rfi;
for (size_t i = 0; i < len; i++)
{
if (rfii < 0 || (size_t)rfii >= reflen)
{
rfbuf2.push_back(4);
}
else
{
rfbuf2.push_back(refs.getBase(refidx, (size_t)rfii));
}
rfii++;
}
haveRfbuf2 = true;
}
#endif
rfwbuf_.resize((len + 16) / 4);
int offset = refs.getStretch(
rfwbuf_.ptr(),
refidx,
(rfi < 0) ? 0 : (size_t)rfi,
rflenInner
ASSERT_ONLY(, tmp_destU32_));
assert_leq(offset, 16);
rf_ = (char *)rfwbuf_.ptr() + offset;
if (leftNs > 0)
{
for (size_t i = rflenInner; i > 0; i--)
{
rf_[i + leftNs - 1] = rf_[i - 1];
}
for (size_t i = 0; i < leftNs; i++)
{
rf_[i] = 4;
}
}
if (rightNs > 0)
{
for (size_t i = 0; i < rightNs; i++)
{
rf_[i + leftNs + rflenInner] = 4;
}
}
#ifndef NDEBUG
for (size_t i = 0; i < len; i++)
{
assert(!haveRfbuf2 || rf_[i] == rfbuf2[i]);
assert_range(0, 4, (int)rf_[i]);
}
#endif
TAlScore score = 0;
res.alres.reset();
size_t rowi = 0;
size_t rowf = len - 1;
if (sc.monotone)
{
for (size_t i = 0; i < len; i++)
{
assert_geq(qu[i], 33);
score += sc.score(rd[i], (int)(1 << rf_[i]), qu[i] - 33, ns);
assert_leq(score, 0);
if (score < minsc || ns > nceil)
{
return 0;
}
}
}
else
{
TAlScore floorsc = 0;
TAlScore scoreMax = floorsc;
size_t lastfloor = 0;
rowi = MAX_SIZE_T;
size_t sols = 0;
for (size_t i = 0; i < len; i++)
{
score += sc.score(rd[i], (int)(1 << rf_[i]), qu[i] - 33, ns);
if (score >= minsc && score >= scoreMax)
{
scoreMax = score;
rowf = i;
if (rowi != lastfloor)
{
rowi = lastfloor;
sols++;
}
}
if (score <= floorsc)
{
score = floorsc;
lastfloor = i + 1;
}
}
if (ns > nceil || scoreMax < minsc)
{
return 0;
}
if (sols > 1)
{
return -1;
}
score = scoreMax;
}
assert_geq(rowf, rowi);
EList<Edit> &ned = res.alres.ned();
size_t refns = 0;
ASSERT_ONLY(BTDnaString refstr);
for (size_t i = rowi; i <= rowf; i++)
{
ASSERT_ONLY(refstr.append((int)rf_[i]));
if (rf_[i] > 3 || rd[i] != rf_[i])
{
Edit e((int)i,
mask2dna[1 << (int)rf_[i]],
"ACGTN"[(int)rd[i]],
EDIT_TYPE_MM);
ned.push_back(e);
if (rf_[i] > 3)
{
refns++;
}
}
}
res.alres.setScore(AlnScore(score,
(int)(rd.length() - ned.size()),
(int)ned.size(), ns, 0));
assert(Edit::repOk(ned, rd));
bool fw = coord.fw();
assert_leq(rowf, len - 1);
size_t trimEnd = (len - 1) - rowf;
res.alres.setShape(
coord.ref(),
coord.off() + rowi,
reflen,
fw,
len,
true,
0,
0,
true,
fw ? rowi : trimEnd,
fw ? trimEnd : rowi);
res.alres.setRefNs(refns);
assert(res.repOk());
#ifndef NDEBUG
BTDnaString editstr;
Edit::toRef(rd, ned, editstr, true, rowi, trimEnd);
if (refstr != editstr)
{
cerr << "Decoded nucleotides and edits don't match reference:" << endl;
cerr << " score: " << res.alres.score().score() << endl;
cerr << " edits: ";
Edit::print(cerr, ned);
cerr << endl;
cerr << " decoded nucs: " << rd << endl;
cerr << " edited nucs: " << editstr << endl;
cerr << " reference nucs: " << refstr << endl;
assert(0);
}
#endif
if (!fw)
{
res.alres.invertEdits();
}
return 1;
}
unsigned long long int countAlign_Static = 0;
unsigned long long int countGather_Static = 0;
unsigned long long int align_time = 0;
unsigned long long int gather_time = 0;
unsigned long long int time_multiseedSearchWorker = 0;
unsigned long long int time_effaln = 0;
unsigned long long int time_exact = 0;
unsigned long long int time_1mm = 0;
unsigned long long int time_seed = 0;
unsigned long long int time_extendSeeds = 0;
unsigned long long int time_seed_extendSeeds = 0;
unsigned long long int time_seed_searchAllSeeds = 0;
unsigned long long int time_seed_mmSeeds = 0;
unsigned long long int time_seed_instantiateSeeds = 0;
unsigned long long int time_extendSeeds_eeSaTups = 0;
unsigned long long int time_extendSeeds_prioritizeSATups = 0;
unsigned long long int time_extendSeeds_advanceElement = 0;
unsigned long long int time_extendSeeds_joinedToTextOff = 0;
unsigned long long int redundants_Nums = 0;
unsigned long long int time_extendSeeds_resEe = 0;
unsigned long long int time_extendSeeds_resUngap = 0;
unsigned long long int time_extendSeeds_init = 0;
unsigned long long int time_extendSeeds_align = 0;
unsigned long long int bestFilter_Nums = 0;
unsigned long long int time_wfa0 = 0;
unsigned long long int time_wfa1 = 0;
unsigned long long int seed_prune = 0;
bool SwAligner::align(
TAlScore &best,
SwResult &res,
const Coord &coord)
{
#ifdef TIME_STATS
countAlign_Static++;
#endif
#ifdef TIME_STATS
auto start = std::chrono::system_clock::now();
#endif
assert(initedRef() && initedRead());
assert_eq(STATE_INITED, state_);
state_ = STATE_ALIGNED;
btncand_.clear();
btncanddone_.clear();
btncanddoneSucc_ = btncanddoneFail_ = 0;
best = std::numeric_limits<TAlScore>::min();
sse8succ_ = sse16succ_ = false;
int flag = 0;
size_t rdlen = rdf_ - rdi_;
bool checkpointed = rdlen >= cperMinlen_;
bool gathered = false;
if (sc_->monotone)
{
if (enable8_ && !readSse16_)
{
if (checkpointed)
{
}
else
{
#ifdef TIME_STATS
auto start_wfa0 = std::chrono::system_clock::now();
#endif
char pattern[MAX_ELEN], pat[MAX_ELEN];
for (int i = rfi_; i < rff_; i++)
{
pattern[i] = mask2iupac[(int)rf_[i]];
}
int a = 0;
if ((rff_ - rfi_) > rdlen)
{
a = ((rff_ - rfi_) - rdlen) * 0.5;
}
strncpy(pat, pattern + a, rdlen);
parse(pat, bianma[2]);
int thred = rdlen * CGK_THRED;
int loop = CGK_LOOP;
if (!embed_rd)
{
char *text = const_cast<char *>(rdfw_->toZBuf());
parse(text, bianma[0]);
text = const_cast<char *>(rdrc_->toZBuf());
parse(text, bianma[1]);
for (int i = 0; i < loop; i++)
{
embedding->cgk_embed((const char **)bianma, rdlen, thred, 0, 0, embeddedQ[i][0], i);
embedding->cgk_embed((const char **)bianma, rdlen, thred, 1, 0, embeddedQ[i][1], i);
}
embed_rd = true;
}
int last_hm = 99999, tmp = 99999;
for (int i = 0; i < loop; i++)
{
tmp = embedding->cgk_embed((const char **)bianma, rdlen, thred, 2, 0, fw_ ? embeddedQ[i][0] : embeddedQ[i][1], i);
if (last_hm > tmp)
last_hm = tmp;
}
#ifdef TIME_STATS
auto end_wfa0 = std::chrono::system_clock::now();
auto elapsed_wfa0 = std::chrono::duration_cast<std::chrono::microseconds>(end_wfa0 - start_wfa0);
time_wfa0 += elapsed_wfa0.count();
#endif
if (last_hm > (rdlen * CGK_THRED))
{
return false;
}
#ifdef TIME_STATS
auto start_wfa1 = std::chrono::system_clock::now();
#endif
char *text = const_cast<char *>(rd_->toZBuf());
affine_wavefronts_t *affine_wavefronts = affine_wavefronts_new_complete(strlen(pattern), strlen(text), &affine_penalties, NULL, mm_allocator);
affine_wavefronts_align(affine_wavefronts, pattern, strlen(pattern), text, strlen(text));
best = edit_cigar_score_gap_affine(&affine_wavefronts->edit_cigar, &affine_penalties);
edit_cigar_t *const edit_cigar = &affine_wavefronts->edit_cigar;
char *const operations = edit_cigar->operations;
char cur;
int num = 0;
string sb;
for (int i = edit_cigar->begin_offset; i < edit_cigar->end_offset; ++i)
{
cur = operations[i];
sb.push_back(cur);
}
res.alres.mycigar = sb;
res.alres.setScore(AlnScore(best-1, rdlen, 0, 0, 0));
res.alres.setShape(refidx_, coord.off(), reflen_, fw_, rdf_ - rdi_, true, 0, 0, true, 0, 0);
res.alres.setRefNs(0);
affine_wavefronts_delete(affine_wavefronts);
#ifdef TIME_STATS
auto end_wfa1 = std::chrono::system_clock::now();
auto elapsed_wfa1 = std::chrono::duration_cast<std::chrono::microseconds>(end_wfa1 - start_wfa1);
time_wfa1 += elapsed_wfa1.count();
#endif
#ifndef NDEBUG
#endif
}
sse8succ_ = (flag == 0);
#ifndef NDEBUG
{
}
#endif
}
else
{
}
}
else
{
}
#ifndef NDEBUG
if (!checkpointed && (rand() & 15) == 0 && sse8succ_ && sse16succ_)
{
}
#endif
assert(repOk());
cural_ = 0;
if (best == MIN_I64 || best < minsc_)
{
if (dpLog_ != NULL)
{
(*dpLog_) << ",0,0";
}
#ifdef TIME_STATS
bestFilter_Nums++;
#endif
return false;
}
if (!gathered)
{
assert(sse8succ_ || sse16succ_);
if (sc_->monotone)
{
if (sse8succ_)
{
btncand_.clear();
btncand_.expand();
btncand_.back().init(33, 33, best);
}
}
else
{
}
}
if (dpLog_ != NULL)
{
(*dpLog_) << ",1," << best;
}
#ifdef TIME_STATS
auto end = std::chrono::system_clock::now();
auto elapsed = std::chrono::duration_cast<std::chrono::microseconds>(end - start);
align_time += elapsed.count();
#endif
return !btncand_.empty();
}
bool SwAligner::nextAlignment(
SwResult &res,
TAlScore minsc,
RandomSource &rnd)
{
return true;
}
#ifdef MAIN_ALIGNER_SW
#include <sstream>
#include <utility>
#include <getopt.h>
#include "scoring.h"
#include "aligner_seed_policy.h"
int gGapBarrier;
int gSnpPhred;
static int bonusMatchType;
static int bonusMatch;
static int penMmcType;
static int penMmc;
static int penNType;
static int penN;
static bool nPairCat;
static int penRdExConst;
static int penRfExConst;
static int penRdExLinear;
static int penRfExLinear;
static float costMinConst;
static float costMinLinear;
static float costFloorConst;
static float costFloorLinear;
static float nCeilConst;
static float nCeilLinear;
static bool nCatPair;
static int multiseedMms;
static int multiseedLen;
static int multiseedIvalType;
static float multiseedIvalA;
static float multiseedIvalB;
static float posmin;
static float posfrac;
static float rowmult;
enum
{
ARG_TESTS = 256
};
static const char *short_opts = "s:m:r:d:i:";
static struct option long_opts[] = {
{(char *)"snppen", required_argument, 0, 's'},
{(char *)"misspen", required_argument, 0, 'm'},
{(char *)"seed", required_argument, 0, 'r'},
{(char *)"align-policy", no_argument, 0, 'A'},
{(char *)"test", no_argument, 0, ARG_TESTS},
};
template <typename T>
T parse(const char *s)
{
T tmp;
stringstream ss(s);
ss >> tmp;
return tmp;
}
static EList<bool> stbuf, enbuf;
static BTDnaString btread;
static BTString btqual;
static BTString btref;
static BTString btref2;
static BTDnaString readrc;
static BTString qualrc;
static void doTestCase(
SwAligner &al,
const BTDnaString &read,
const BTString &qual,
const BTString &refin,
TRefOff off,
EList<bool> *en,
const Scoring &sc,
TAlScore minsc,
SwResult &res,
bool nsInclusive,
bool filterns,
uint32_t seed)
{
RandomSource rnd(seed);
btref2 = refin;
assert_eq(read.length(), qual.length());
size_t nrow = read.length();
TRefOff rfi, rff;
size_t maxgaps;
size_t padi, padf;
{
int readGaps = sc.maxReadGaps(minsc, read.length());
int refGaps = sc.maxRefGaps(minsc, read.length());
assert_geq(readGaps, 0);
assert_geq(refGaps, 0);
int maxGaps = max(readGaps, refGaps);
padi = 2 * maxGaps;
padf = maxGaps;
maxgaps = (size_t)maxGaps;
}
size_t nceil = (size_t)sc.nCeil.f((double)read.length());
size_t width = 1 + padi + padf;
rfi = off;
off = 0;
if (rfi < padi)
{
size_t beginpad = (size_t)(padi - rfi);
for (size_t i = 0; i < beginpad; i++)
{
btref2.insert('N', 0);
off--;
}
rfi = 0;
}
else
{
rfi -= padi;
}
assert_geq(rfi, 0);
while (rfi + nrow + padi + padf > btref2.length())
{
btref2.append('N');
}
rff = rfi + nrow + padi + padf;
for (size_t i = 0; i < btref2.length(); i++)
{
if (toupper(btref2[i]) == 'N' && !nsInclusive)
{
btref2.set(16, i);
}
else
{
int num = 0;
int alts[] = {4, 4, 4, 4};
decodeNuc(toupper(btref2[i]), num, alts);
assert_leq(num, 4);
assert_gt(num, 0);
btref2.set(0, i);
for (int j = 0; j < num; j++)
{
btref2.set(btref2[i] | (1 << alts[j]), i);
}
}
}
bool fw = true;
uint32_t refidx = 0;
size_t solwidth = width;
if (maxgaps >= solwidth)
{
solwidth = 0;
}
else
{
solwidth -= maxgaps;
}
if (en == NULL)
{
enbuf.resize(solwidth);
enbuf.fill(true);
en = &enbuf;
}
assert_geq(rfi, 0);
assert_gt(rff, rfi);
readrc = read;
qualrc = qual;
al.initRead(
read,
readrc,
qual,
qualrc,
0,
read.length(),
floorsc);
al.initRef(
fw,
refidx,
off,
btref2.wbuf(),
rfi,
rff,
width,
solwidth,
sc,
minsc,
maxgaps,
0,
en);
if (filterns)
{
al.filter((int)nceil);
}
al.align(rnd);
}
static void doTestCase2(
SwAligner &al,
const char *read,
const char *qual,
const char *refin,
TRefOff off,
const Scoring &sc,
float costMinConst,
float costMinLinear,
SwResult &res,
bool nsInclusive = false,
bool filterns = false,
uint32_t seed = 0)
{
btread.install(read, true);
TAlScore minsc = (TAlScore)(Scoring::linearFunc(
btread.length(),
costMinConst,
costMinLinear));
TAlScore floorsc = (TAlScore)(Scoring::linearFunc(
btread.length(),
costFloorConst,
costFloorLinear));
btqual.install(qual);
btref.install(refin);
doTestCase(
al,
btread,
btqual,
btref,
off,
NULL,
sc,
minsc,
floorsc,
res,
nsInclusive,
filterns,
seed);
}
static void doTestCase3(
SwAligner &al,
const char *read,
const char *qual,
const char *refin,
TRefOff off,
Scoring &sc,
float costMinConst,
float costMinLinear,
float nCeilConst,
float nCeilLinear,
SwResult &res,
bool nsInclusive = false,
bool filterns = false,
uint32_t seed = 0)
{
btread.install(read, true);
TAlScore minsc = (TAlScore)(Scoring::linearFunc(
btread.length(),
costMinConst,
costMinLinear));
TAlScore floorsc = (TAlScore)(Scoring::linearFunc(
btread.length(),
costFloorConst,
costFloorLinear));
btqual.install(qual);
btref.install(refin);
sc.nCeil.setType(SIMPLE_FUNC_LINEAR);
sc.nCeil.setConst(costMinConst);
sc.nCeil.setCoeff(costMinLinear);
doTestCase(
al,
btread,
btqual,
btref,
off,
NULL,
sc,
minsc,
floorsc,
res,
nsInclusive,
filterns,
seed);
}
static void doTestCase4(
SwAligner &al,
const char *read,
const char *qual,
const char *refin,
TRefOff off,
EList<bool> &en,
Scoring &sc,
float costMinConst,
float costMinLinear,
float nCeilConst,
float nCeilLinear,
SwResult &res,
bool nsInclusive = false,
bool filterns = false,
uint32_t seed = 0)
{
btread.install(read, true);
TAlScore minsc = (TAlScore)(Scoring::linearFunc(
btread.length(),
costMinConst,
costMinLinear));
TAlScore floorsc = (TAlScore)(Scoring::linearFunc(
btread.length(),
costFloorConst,
costFloorLinear));
btqual.install(qual);
btref.install(refin);
sc.nCeil.setType(SIMPLE_FUNC_LINEAR);
sc.nCeil.setConst(costMinConst);
sc.nCeil.setCoeff(costMinLinear);
doTestCase(
al,
btread,
btqual,
btref,
off,
&en,
sc,
minsc,
floorsc,
res,
nsInclusive,
filterns,
seed);
}
static void doTests()
{
bonusMatchType = DEFAULT_MATCH_BONUS_TYPE;
bonusMatch = DEFAULT_MATCH_BONUS;
penMmcType = DEFAULT_MM_PENALTY_TYPE;
penMmc = DEFAULT_MM_PENALTY;
penSnp = DEFAULT_SNP_PENALTY;
penNType = DEFAULT_N_PENALTY_TYPE;
penN = DEFAULT_N_PENALTY;
nPairCat = DEFAULT_N_CAT_PAIR;
penRdExConst = DEFAULT_READ_GAP_CONST;
penRfExConst = DEFAULT_REF_GAP_CONST;
penRdExLinear = DEFAULT_READ_GAP_LINEAR;