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hisat-3n/aligner_seed2.cpp

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2025-01-18 13:09:52 +00:00
/*
* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Bowtie 2 is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
*/
#include <limits>
#include <ctype.h>
#include "aligner_seed2.h"
#include "assert_helpers.h"
#include "gfm.h"
#ifdef ALIGNER_SEED2_MAIN
#include <string>
#include "sstring.h"
using namespace std;
/**
* A way of feeding simply tests to the seed alignment infrastructure.
*/
int main(int argc, char **argv) {
EList<string> strs;
// GCTATATAGCGCGCTCGCATCATTTTGTGT
strs.push_back(string("CATGTCAGCTATATAGCGCGCTCGCATCATTTTGTGTGTAAACCA"
"NNNNNNNNNN"
"CATGTCAGCTATATAGCGCGCTCGCATCATTTTGTGTGTAAACCA"));
// GCTATATAGCGCGCTTGCATCATTTTGTGT
// ^
bool packed = false;
int color = 0;
pair<GFM*, GFM*> gfms = GFM::fromStrings<SString<char> >(
strs,
packed,
REF_READ_REVERSE,
Ebwt::default_bigEndian,
Ebwt::default_lineRate,
Ebwt::default_offRate,
Ebwt::default_ftabChars,
".aligner_seed2.cpp.tmp",
Ebwt::default_useBlockwise,
Ebwt::default_bmax,
Ebwt::default_bmaxMultSqrt,
Ebwt::default_bmaxDivN,
Ebwt::default_dcv,
Ebwt::default_seed,
false, // verbose
false, // autoMem
false); // sanity
gfms.first->loadIntoMemory (-1, true, true, true, true, false);
gfms.second->loadIntoMemory(1, true, true, true, true, false);
int testnum = 0;
// Query is longer than ftab and matches exactly twice
for(int rc = 0; rc < 2; rc++) {
for(int i = 0; i < 2; i++) {
cerr << "Test " << (++testnum) << endl;
cerr << " Query with length greater than ftab" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
// Set up the read
BTDnaString seq ("GCTATATAGCGCGCTCGCATCATTTTGTGT", true);
BTString qual("ABCDEFGHIabcdefghiABCDEFGHIabc");
if(rc) {
seq.reverseComp();
qual.reverse();
}
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
conf.cons.init(GFM::default_ftabChars, 1.0);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
(i == 0) ? 0 : (seq.length() - 1), // 5' offset into read of root
(i == 0) ? true : false, // left-to-right?
rc == 0, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert_eq(2, dr.sink().nelt());
}
}
// Query has length euqal to ftab and matches exactly twice
for(int i = 0; i < 2; i++) {
cerr << "Test " << (++testnum) << endl;
cerr << " Query with length equal to ftab" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
// Set up the read
BTDnaString seq ("GCTATATAGC", true);
BTString qual("ABCDEFGHIa");
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
conf.cons.init(GFM::default_ftabChars, 1.0);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
(i == 0) ? 0 : (seq.length() - 1), // 5' offset into read of root
(i == 0) ? true : false, // left-to-right?
true, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert_eq(2, dr.sink().nelt());
}
// Query has length less than ftab length and matches exactly twice
for(int i = 0; i < 2; i++) {
cerr << "Test " << (++testnum) << endl;
cerr << " Query with length less than ftab" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
// Set up the read
BTDnaString seq ("GCTATATAG", true);
BTString qual("ABCDEFGHI");
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
conf.cons.init(GFM::default_ftabChars, 1.0);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
(i == 0) ? 0 : (seq.length() - 1), // 5' offset into read of root
(i == 0) ? true : false, // left-to-right?
true, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert_eq(2, dr.sink().nelt());
}
// Search root is in the middle of the read, requiring a bounce
for(int i = 0; i < 2; i++) {
cerr << "Test " << (++testnum) << endl;
cerr << " Search root in middle of read" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
// Set up the read
// 012345678901234567890123456789
BTDnaString seq ("GCTATATAGCGCGCTCGCATCATTTTGTGT", true);
BTString qual("ABCDEFGHIabcdefghiABCDEFGHIabc");
TIndexOffU top, bot;
top = bot = 0;
bool ret = gfms.first->contains("GCGCTCGCATCATTTTGTGT", &top, &bot);
cerr << ret << ", " << top << ", " << bot << endl;
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
conf.cons.init(GFM::default_ftabChars, 1.0);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
(i == 0) ? 10 : (seq.length() - 1 - 10), // 5' offset into read of root
(i == 0) ? true : false, // left-to-right?
true, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert_eq(2, dr.sink().nelt());
}
delete gfms.first;
delete gfms.second;
strs.clear();
strs.push_back(string("CATGTCAGCTATATAGCGCGCTCGCATCATTTTGTGTGTAAACCA"
"NNNNNNNNNN"
"CATGTCAGCTATATAGCG"));
gfms = GFM::fromStrings<SString<char> >(
strs,
packed,
REF_READ_REVERSE,
GFM::default_bigEndian,
GFM::default_lineRate,
GFM::default_offRate,
GFM::default_ftabChars,
".aligner_seed2.cpp.tmp",
GFM::default_useBlockwise,
GFM::default_bmax,
GfM::default_bmaxMultSqrt,
GFM::default_bmaxDivN,
GFM::default_dcv,
GFM::default_seed,
false, // verbose
false, // autoMem
false); // sanity
gfms.first->loadIntoMemory (-1, true, true, true, true, false);
gfms.second->loadIntoMemory(1, true, true, true, true, false);
// Query is longer than ftab and matches exactly once. One search root for
// forward read.
{
size_t last_topf = std::numeric_limits<size_t>::max();
size_t last_botf = std::numeric_limits<size_t>::max();
for(int i = 0; i < 2; i++) {
BTDnaString seq ("GCTATATAGCGCGCTCGCATCATTTTGTGT", true);
BTString qual("ABCDEFGHIabcdefghiABCDEFGHIabc");
for(size_t j = 0; j < seq.length(); j++) {
cerr << "Test " << (++testnum) << endl;
cerr << " Query with length greater than ftab and matches exactly once" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
// Set up the read
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
conf.cons.init(GFM::default_ftabChars, 1.0);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
i == 0, // left-to-right?
true, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert(last_topf == std::numeric_limits<size_t>::max() || last_topf == dr.sink()[0].topf);
assert(last_botf == std::numeric_limits<size_t>::max() || last_botf == dr.sink()[0].botf);
assert_eq(1, dr.sink().nelt());
}
}
}
// Query is longer than ftab and its reverse complement matches exactly
// once. Search roots on forward and reverse-comp reads.
{
size_t last_topf = std::numeric_limits<size_t>::max();
size_t last_botf = std::numeric_limits<size_t>::max();
for(int i = 0; i < 2; i++) {
BTDnaString seq ("GCTATATAGCGCGCTCGCATCATTTTGTGT", true);
BTString qual("ABCDEFGHIabcdefghiABCDEFGHIabc");
for(size_t j = 0; j < seq.length(); j++) {
cerr << "Test " << (++testnum) << endl;
cerr << " Query with length greater than ftab and reverse complement matches exactly once" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
// Set up the read
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
conf.cons.init(GFM::default_ftabChars, 1.0);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
i == 0, // left-to-right?
true, // forward?
0.0f); // root priority
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
i == 0, // left-to-right?
false, // forward?
1.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert(last_topf == std::numeric_limits<size_t>::max() || last_topf == dr.sink()[0].topf);
assert(last_botf == std::numeric_limits<size_t>::max() || last_botf == dr.sink()[0].botf);
assert_eq(1, dr.sink().nelt());
}
}
}
// Query is longer than ftab and matches exactly once with one mismatch
{
size_t last_topf = std::numeric_limits<size_t>::max();
size_t last_botf = std::numeric_limits<size_t>::max();
for(int i = 0; i < 2; i++) {
// Set up the read
// Ref: CATGTCAGCTATATAGCGCGCTCGCATCATTTTGTGTGTAAACCA
// ||||||||||||||||||||||||||||||
BTDnaString orig("GCTATATAGCGCGCTCGCATCATTTTGTGT", true);
// 012345678901234567890123456789
BTString qual("ABCDEFGHIabcdefghiABCDEFGHIabc");
for(size_t k = 0; k < orig.length(); k++) {
BTDnaString seq = orig;
seq.set(seq[k] ^ 3, k);
for(size_t j = 0; j < seq.length(); j++) {
// Assume left-to-right
size_t beg = j;
size_t end = j + GFM::default_ftabChars;
// Mismatch penalty is 3, so we have to skip starting
// points that are within 2 from the mismatch
if((i > 0 && j > 0) || j == seq.length()-1) {
// Right-to-left
if(beg < GFM::default_ftabChars) {
beg = 0;
} else {
beg -= GFM::default_ftabChars;
}
end -= GFM::default_ftabChars;
}
size_t kk = k;
//if(rc) {
// kk = seq.length() - k - 1;
//}
if(beg <= kk && end > kk) {
continue;
}
if((j > kk) ? (j - kk <= 2) : (kk - j <= 2)) {
continue;
}
cerr << "Test " << (++testnum) << endl;
cerr << " Query with length greater than ftab and matches exactly once with 1mm" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
// Changed
conf.cons.init(0, 1.0);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
i == 0, // left-to-right?
true, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert(last_topf == std::numeric_limits<size_t>::max() || last_topf == dr.sink()[0].topf);
assert(last_botf == std::numeric_limits<size_t>::max() || last_botf == dr.sink()[0].botf);
cerr << dr.sink()[0].topf << ", " << dr.sink()[0].botf << endl;
assert_eq(1, dr.sink().nelt());
last_topf = dr.sink()[0].topf;
last_botf = dr.sink()[0].botf;
}
}
}
}
// Query is longer than ftab and matches exactly once with one N mismatch
{
size_t last_topf = std::numeric_limits<size_t>::max();
size_t last_botf = std::numeric_limits<size_t>::max();
for(int i = 0; i < 2; i++) {
// Set up the read
// Ref: CATGTCAGCTATATAGCGCGCTCGCATCATTTTGTGTGTAAACCA
// ||||||||||||||||||||||||||||||
BTDnaString orig("GCTATATAGCGCGCTCGCATCATTTTGTGT", true);
// 012345678901234567890123456789
BTString qual("ABCDEFGHIabcdefghiABCDEFGHIabc");
for(size_t k = 0; k < orig.length(); k++) {
BTDnaString seq = orig;
seq.set(4, k);
for(size_t j = 0; j < seq.length(); j++) {
// Assume left-to-right
size_t beg = j;
size_t end = j + GFM::default_ftabChars;
// Mismatch penalty is 3, so we have to skip starting
// points that are within 2 from the mismatch
if((i > 0 && j > 0) || j == seq.length()-1) {
// Right-to-left
if(beg < GFM::default_ftabChars) {
beg = 0;
} else {
beg -= GFM::default_ftabChars;
}
end -= GFM::default_ftabChars;
}
if(beg <= k && end > k) {
continue;
}
if((j > k) ? (j - k <= 2) : (k - j <= 2)) {
continue;
}
cerr << "Test " << (++testnum) << endl;
cerr << " Query with length greater than ftab and matches exactly once with 1mm" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
// Changed
conf.cons.init(0, 1.0);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
i == 0, // left-to-right?
true, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert_eq(sc.n(40), dr.sink()[0].pen);
assert(last_topf == std::numeric_limits<size_t>::max() || last_topf == dr.sink()[0].topf);
assert(last_botf == std::numeric_limits<size_t>::max() || last_botf == dr.sink()[0].botf);
cerr << dr.sink()[0].topf << ", " << dr.sink()[0].botf << endl;
assert_eq(1, dr.sink().nelt());
last_topf = dr.sink()[0].topf;
last_botf = dr.sink()[0].botf;
}
}
}
}
// Throw a bunch of queries with a bunch of Ns in and try to force an assert
{
RandomSource rnd(79);
for(int i = 0; i < 2; i++) {
// Set up the read
// Ref: CATGTCAGCTATATAGCGCGCTCGCATCATTTTGTGTGTAAACCA
// ||||||||||||||||||||||||||||||
BTDnaString orig("GCTATATAGCGCGCTCGCATCATTTTGTGT", true);
// 012345678901234567890123456789
BTString qual("ABCDEFGHIabcdefghiABCDEFGHIabc");
if(i == 1) {
orig.reverseComp();
qual.reverse();
}
for(size_t trials = 0; trials < 100; trials++) {
BTDnaString seq = orig;
size_t ns = 10;
for(size_t k = 0; k < ns; k++) {
size_t pos = rnd.nextU32() % seq.length();
seq.set(4, pos);
}
cerr << "Test " << (++testnum) << endl;
cerr << " Query with a bunch of Ns" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
// Changed
conf.cons.init(GFM::default_ftabChars, 1.0);
conf.expol = DESC_EX_NONE;
// Set up the search roots
for(size_t k = 0; k < ns; k++) {
size_t j = rnd.nextU32() % seq.length();
bool ltr = (rnd.nextU2() == 0) ? true : false;
bool fw = (rnd.nextU2() == 0) ? true : false;
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
ltr, // left-to-right?
fw, // forward?
0.0f); // root priority
}
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
}
}
}
// Query is longer than ftab and matches exactly once with one mismatch
{
RandomSource rnd(77);
size_t last_topf = std::numeric_limits<size_t>::max();
size_t last_botf = std::numeric_limits<size_t>::max();
for(int i = 0; i < 2; i++) {
// Set up the read
// Ref: CATGTCAGCTATATAGCGCGCTCGCATCATTTTGTGTGTAAACCA
// ||||||||||||||||||||||||||||||
BTDnaString orig("GCTATATAGCGCGCTCGCATCATTTTGTGT", true);
// 012345678901234567890123456789
BTString qual("ABCDEFGHIabcdefghiABCDEFGHIabc");
// revcomp: ACACAAAATGATGCGAGCGCGCTATATAGC
// revqual: cbaIHGFEDCBAihgfedcbaIHGFEDCBA
bool fwi = (i == 0);
if(!fwi) {
orig.reverseComp();
}
for(size_t k = 0; k < orig.length(); k++) {
BTDnaString seq = orig;
seq.set(seq[k] ^ 3, k);
cerr << "Test " << (++testnum) << endl;
cerr << " Query with length greater than ftab and matches exactly once with 1mm. Many search roots." << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
// Changed
conf.cons.init(0, 1.0);
conf.expol = DESC_EX_NONE;
// Set up several random search roots
bool onegood = false;
for(size_t y = 0; y < 10; y++) {
size_t j = rnd.nextU32() % seq.length();
bool ltr = (rnd.nextU2() == 0) ? true : false;
bool fw = (rnd.nextU2() == 0) ? true : false;
dr.addRoot(
conf, // DescentConfig
(TReadOff)j, // 5' offset into read of root
ltr, // left-to-right?
fw, // forward?
(float)((float)y * 1.0f)); // root priority
// Assume left-to-right
size_t beg = j;
size_t end = j + GFM::default_ftabChars;
// Mismatch penalty is 3, so we have to skip starting
// points that are within 2 from the mismatch
if(!ltr) {
// Right-to-left
if(beg < GFM::default_ftabChars) {
beg = 0;
} else {
beg -= GFM::default_ftabChars;
}
end -= GFM::default_ftabChars;
}
bool good = true;
if(fw != fwi) {
good = false;
}
if(beg <= k && end > k) {
good = false;
}
if((j > k) ? (j - k <= 2) : (k - j <= 2)) {
good = false;
}
if(good) {
onegood = true;
}
}
if(!onegood) {
continue;
}
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert(last_topf == std::numeric_limits<size_t>::max() || last_topf == dr.sink()[0].topf);
assert(last_botf == std::numeric_limits<size_t>::max() || last_botf == dr.sink()[0].botf);
cerr << dr.sink()[0].topf << ", " << dr.sink()[0].botf << endl;
assert_eq(1, dr.sink().nelt());
last_topf = dr.sink()[0].topf;
last_botf = dr.sink()[0].botf;
}
}
}
// Query is longer than ftab and matches exactly once with one read gap
{
size_t last_topf = std::numeric_limits<size_t>::max();
size_t last_botf = std::numeric_limits<size_t>::max();
for(int i = 0; i < 2; i++) {
for(int k = 0; k < 2; k++) {
// Set up the read
// GCTATATAGCGCGCCTGCATCATTTTGTGT
// Ref: CATGTCAGCTATATAGCGCGCTCGCATCATTTTGTGTGTAAACCA
// |||||||||||||||///////////////
BTDnaString seq ("GCTATATAGCGCGCTGCATCATTTTGTGT", true);
// 01234567890123456789012345678
// 87654321098765432109876543210
BTString qual("ABCDEFGHIabcdefghiABCDEFGHIab");
if(k == 1) {
seq.reverseComp();
qual.reverse();
}
assert_eq(seq.length(), qual.length());
// js iterate over offsets from 5' end for the search root
for(size_t j = 0; j < seq.length(); j++) {
// Assume left-to-right
size_t beg = j;
if(k == 1) {
beg = seq.length() - beg - 1;
}
size_t end = beg + GFM::default_ftabChars;
// Mismatch penalty is 3, so we have to skip starting
// points that are within 2 from the mismatch
if((i > 0 && j > 0) || j == seq.length()-1) {
// Right-to-left
if(beg < GFM::default_ftabChars) {
beg = 0;
} else {
beg -= GFM::default_ftabChars;
}
end -= GFM::default_ftabChars;
}
assert_geq(end, beg);
if(beg <= 15 && end >= 15) {
continue;
}
cerr << "Test " << (++testnum) << endl;
cerr << " Query matches once with a read gap of length 1" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
Read q("test", seq.toZBuf(), qual.toZBuf());
assert(q.repOk());
dr.initRead(q, -30, 30);
// Set up the DescentConfig
DescentConfig conf;
// Changed
conf.cons.init(0, 0.5);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
i == 0, // left-to-right?
k == 0, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert_eq(sc.readGapOpen() + 0 * sc.readGapExtend(), dr.sink()[0].pen);
assert(last_topf == std::numeric_limits<size_t>::max() || last_topf == dr.sink()[0].topf);
assert(last_botf == std::numeric_limits<size_t>::max() || last_botf == dr.sink()[0].botf);
cerr << dr.sink()[0].topf << ", " << dr.sink()[0].botf << endl;
assert_eq(1, dr.sink().nelt());
last_topf = dr.sink()[0].topf;
last_botf = dr.sink()[0].botf;
}
}}
}
// Query is longer than ftab and matches exactly once with one read gap of
// length 3
{
size_t last_topf = std::numeric_limits<size_t>::max();
size_t last_botf = std::numeric_limits<size_t>::max();
for(int i = 0; i < 2; i++) {
for(int k = 0; k < 2; k++) {
// Set up the read
// GCTATATAGCGCGCGCTCATCATTTTGTGT
// Ref: CATGTCAGCTATATAGCGCGCTCGCATCATTTTGTGTGTAAACCA
// |||||||||||||| |||||||||||||
BTDnaString seq ("GCTATATAGCGCGC" "CATCATTTTGTGT", true);
// 01234567890123 4567890123456
// 65432109876543 2109876543210
BTString qual("ABCDEFGHIabcde" "fghiABCDEFGHI");
if(k == 1) {
seq.reverseComp();
qual.reverse();
}
for(size_t j = 0; j < seq.length(); j++) {
// Assume left-to-right
size_t beg = j;
if(k == 1) {
beg = seq.length() - beg - 1;
}
size_t end = beg + GFM::default_ftabChars;
// Mismatch penalty is 3, so we have to skip starting
// points that are within 2 from the mismatch
if((i > 0 && j > 0) || j == seq.length()-1) {
// Right-to-left
if(beg < GFM::default_ftabChars) {
beg = 0;
} else {
beg -= GFM::default_ftabChars;
}
end -= GFM::default_ftabChars;
}
if(beg <= 14 && end >= 14) {
continue;
}
cerr << "Test " << (++testnum) << endl;
cerr << " Query matches once with a read gap of length 3" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
// Changed
conf.cons.init(0, 0.2);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
i == 0, // left-to-right?
k == 0, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
// Need to adjust the mismatch penalty up to avoid alignments
// with lots of mismatches.
sc.setMmPen(COST_MODEL_CONSTANT, 6, 6);
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert_eq(sc.readGapOpen() + 2 * sc.readGapExtend(), dr.sink()[0].pen);
assert(last_topf == std::numeric_limits<size_t>::max() || last_topf == dr.sink()[0].topf);
assert(last_botf == std::numeric_limits<size_t>::max() || last_botf == dr.sink()[0].botf);
cerr << dr.sink()[0].topf << ", " << dr.sink()[0].botf << endl;
assert_eq(1, dr.sink().nelt());
last_topf = dr.sink()[0].topf;
last_botf = dr.sink()[0].botf;
}
}}
}
// Query is longer than ftab and matches exactly once with one reference gap
{
size_t last_topf = std::numeric_limits<size_t>::max();
size_t last_botf = std::numeric_limits<size_t>::max();
for(int i = 0; i < 2; i++) {
// Set up the read
// Ref: CATGTCAGCTATATAGCGCGC" "TCGCATCATTTTGTGTGTAAACCA
// |||||||||||||| ||||||||||||||||
BTDnaString seq ("GCTATATAGCGCGCA""TCGCATCATTTTGTGT", true);
// 012345678901234 5678901234567890
BTString qual("ABCDEFGHIabcdef""ghiABCDEFGHIabcd");
for(size_t j = 0; j < seq.length(); j++) {
// Assume left-to-right
size_t beg = j;
size_t end = j + GFM::default_ftabChars;
// Mismatch penalty is 3, so we have to skip starting
// points that are within 2 from the mismatch
if((i > 0 && j > 0) || j == seq.length()-1) {
// Right-to-left
if(beg < GFM::default_ftabChars) {
beg = 0;
} else {
beg -= GFM::default_ftabChars;
}
end -= GFM::default_ftabChars;
}
if(beg <= 14 && end >= 14) {
continue;
}
cerr << "Test " << (++testnum) << endl;
cerr << " Query matches once with a reference gap of length 1" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
// Changed
conf.cons.init(1, 0.5);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
i == 0, // left-to-right?
true, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
// Need to adjust the mismatch penalty up to avoid alignments
// with lots of mismatches.
sc.setMmPen(COST_MODEL_CONSTANT, 6, 6);
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert_eq(sc.refGapOpen() + 0 * sc.refGapExtend(), dr.sink()[0].pen);
assert(last_topf == std::numeric_limits<size_t>::max() || last_topf == dr.sink()[0].topf);
assert(last_botf == std::numeric_limits<size_t>::max() || last_botf == dr.sink()[0].botf);
cerr << dr.sink()[0].topf << ", " << dr.sink()[0].botf << endl;
assert_eq(1, dr.sink().nelt());
last_topf = dr.sink()[0].topf;
last_botf = dr.sink()[0].botf;
}
}
}
// Query is longer than ftab and matches exactly once with one reference gap
{
size_t last_topf = std::numeric_limits<size_t>::max();
size_t last_botf = std::numeric_limits<size_t>::max();
for(int i = 0; i < 2; i++) {
// Set up the read
// Ref: CATGTCAGCTATATAGCGCGC" "TCGCATCATTTTGTGTGTAAACCA
// |||||||||||||| ||||||||||||||||
BTDnaString seq ("GCTATATAGCGCGCATG""TCGCATCATTTTGTGT", true);
// 01234567890123456 7890123456789012
BTString qual("ABCDEFGHIabcdefgh""iABCDEFGHIabcdef");
for(size_t j = 0; j < seq.length(); j++) {
// Assume left-to-right
size_t beg = j;
size_t end = j + GFM::default_ftabChars;
// Mismatch penalty is 3, so we have to skip starting
// points that are within 2 from the mismatch
if((i > 0 && j > 0) || j == seq.length()-1) {
// Right-to-left
if(beg < GFM::default_ftabChars) {
beg = 0;
} else {
beg -= GFM::default_ftabChars;
}
end -= GFM::default_ftabChars;
}
if(beg <= 14 && end >= 14) {
continue;
}
if(beg <= 15 && end >= 15) {
continue;
}
if(beg <= 16 && end >= 16) {
continue;
}
cerr << "Test " << (++testnum) << endl;
cerr << " Query matches once with a reference gap of length 1" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
// Changed
conf.cons.init(1, 0.25);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
i == 0, // left-to-right?
true, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
// Need to adjust the mismatch penalty up to avoid alignments
// with lots of mismatches.
sc.setMmPen(COST_MODEL_CONSTANT, 6, 6);
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert_eq(sc.refGapOpen() + 2 * sc.refGapExtend(), dr.sink()[0].pen);
assert(last_topf == std::numeric_limits<size_t>::max() || last_topf == dr.sink()[0].topf);
assert(last_botf == std::numeric_limits<size_t>::max() || last_botf == dr.sink()[0].botf);
cerr << dr.sink()[0].topf << ", " << dr.sink()[0].botf << endl;
assert_eq(1, dr.sink().nelt());
last_topf = dr.sink()[0].topf;
last_botf = dr.sink()[0].botf;
}
}
}
// Query is longer than ftab and matches exactly once with one read gap,
// one ref gap, and one mismatch
{
size_t last_topf = std::numeric_limits<size_t>::max();
size_t last_botf = std::numeric_limits<size_t>::max();
for(int i = 0; i < 2; i++) {
// Set up the read
// Ref: CATGTCAGCT ATATAGCGCGCT CGCATCATTTTGTGTGTAAACCA
// |||||||||| |||||||||||| |||||| |||||||||||||
BTDnaString seq ("CATGTCAGCT""GATATAGCGCGCT" "GCATCAATTTGTGTGTAAAC", true);
// 0123456789 0123456789012 34567890123456789012
BTString qual("ABCDEFGHIa""bcdefghiACDEF" "GHIabcdefghijkABCDEF");
for(size_t j = 0; j < seq.length(); j++) {
// Assume left-to-right
size_t beg = j;
size_t end = j + GFM::default_ftabChars;
// Mismatch penalty is 3, so we have to skip starting
// points that are within 2 from the mismatch
if((i > 0 && j > 0) || j == seq.length()-1) {
// Right-to-left
if(beg < GFM::default_ftabChars) {
beg = 0;
} else {
beg -= GFM::default_ftabChars;
}
end -= GFM::default_ftabChars;
}
if(beg <= 10 && end >= 10) {
continue;
}
if(beg <= 22 && end >= 22) {
continue;
}
if(beg <= 30 && end >= 30) {
continue;
}
cerr << "Test " << (++testnum) << endl;
cerr << " Query matches once with a read gap of length 1" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -50, 50);
// Set up the DescentConfig
DescentConfig conf;
// Changed
conf.cons.init(1, 0.5);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
i == 0, // left-to-right?
true, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert_eq(sc.readGapOpen() + sc.refGapOpen() + sc.mm((int)'d' - 33), dr.sink()[0].pen);
assert(last_topf == std::numeric_limits<size_t>::max() || last_topf == dr.sink()[0].topf);
assert(last_botf == std::numeric_limits<size_t>::max() || last_botf == dr.sink()[0].botf);
cerr << dr.sink()[0].topf << ", " << dr.sink()[0].botf << endl;
assert_eq(1, dr.sink().nelt());
last_topf = dr.sink()[0].topf;
last_botf = dr.sink()[0].botf;
}
}
}
delete gfms.first;
delete gfms.second;
// Ref CATGTCAGCT-ATATAGCGCGCTCGCATCATTTTGTGTGTAAAC
// |||||||||| |||||||||||| |||||| |||||||||||||
// Rd CATGTCAGCTGATATAGCGCGCT-GCATCAATTTGTGTGTAAAC
strs.clear();
strs.push_back(string("CATGTCAGCTATATAGCGCGCTCGCATCATTTTGTGTGTAAAC"
"NNNNNNNNNN"
"CATGTCAGCTGATATAGCGCGCTCGCATCATTTTGTGTGTAAAC" // same but without first ref gap
"N"
"CATGTCAGCTATATAGCGCGCTGCATCATTTTGTGTGTAAAC" // same but without first read gap
"N"
"CATGTCAGCTATATAGCGCGCTCGCATCAATTTGTGTGTAAAC" // same but without first mismatch
"N"
"CATGTCAGCTGATATAGCGCGCTGCATCAATTTGTGTGTAAAC" // Exact match for read
));
gfms = GFM::fromStrings<SString<char> >(
strs,
packed,
REF_READ_REVERSE,
GFM::default_bigEndian,
GFM::default_lineRate,
GFM::default_offRate,
GFM::default_ftabChars,
".aligner_seed2.cpp.tmp",
GFM::default_useBlockwise,
GFM::default_bmax,
GFM::default_bmaxMultSqrt,
GFM::default_bmaxDivN,
GFM::default_dcv,
GFM::default_seed,
false, // verbose
false, // autoMem
false); // sanity
gfms.first->loadIntoMemory (color, -1, true, true, true, true, false);
gfms.second->loadIntoMemory(color, 1, true, true, true, true, false);
// Query is longer than ftab and matches exactly once with one read gap,
// one ref gap, and one mismatch
{
size_t last_topf = std::numeric_limits<size_t>::max();
size_t last_botf = std::numeric_limits<size_t>::max();
for(int i = 0; i < 2; i++) {
// Set up the read
// Ref: CATGTCAGCT ATATAGCGCGCT CGCATCATTTTGTGTGTAAACCA
// |||||||||| |||||||||||| |||||| |||||||||||||
BTDnaString seq ("CATGTCAGCT""GATATAGCGCGCT" "GCATCAATTTGTGTGTAAAC", true);
// 0123456789 0123456789012 34567890123456789012
BTString qual("ABCDEFGHIa""bcdefghiACDEF" "GHIabcdefghijkABCDEF");
for(size_t j = 0; j < seq.length(); j++) {
// Assume left-to-right
size_t beg = j;
size_t end = j + GFM::default_ftabChars;
// Mismatch penalty is 3, so we have to skip starting
// points that are within 2 from the mismatch
if((i > 0 && j > 0) || j == seq.length()-1) {
// Right-to-left
if(beg < GFM::default_ftabChars) {
beg = 0;
} else {
beg -= GFM::default_ftabChars;
}
end -= GFM::default_ftabChars;
}
if(beg <= 10 && end >= 10) {
continue;
}
if(beg <= 22 && end >= 22) {
continue;
}
if(beg <= 30 && end >= 30) {
continue;
}
cerr << "Test " << (++testnum) << endl;
cerr << " Query matches once with a read gap of length 1" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -50, 50);
// Set up the DescentConfig
DescentConfig conf;
// Changed
conf.cons.init(1, 0.5);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
i == 0, // left-to-right?
true, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(5, dr.sink().nrange());
assert_eq(0, dr.sink()[0].pen);
assert_eq(min(sc.readGapOpen(), sc.refGapOpen()) + sc.mm((int)'d' - 33), dr.sink()[1].pen);
assert_eq(max(sc.readGapOpen(), sc.refGapOpen()) + sc.mm((int)'d' - 33), dr.sink()[2].pen);
assert_eq(sc.readGapOpen() + sc.refGapOpen(), dr.sink()[3].pen);
assert_eq(sc.readGapOpen() + sc.refGapOpen() + sc.mm((int)'d' - 33), dr.sink()[4].pen);
assert(last_topf == std::numeric_limits<size_t>::max() || last_topf == dr.sink()[0].topf);
assert(last_botf == std::numeric_limits<size_t>::max() || last_botf == dr.sink()[0].botf);
cerr << dr.sink()[0].topf << ", " << dr.sink()[0].botf << endl;
assert_eq(5, dr.sink().nelt());
last_topf = dr.sink()[0].topf;
last_botf = dr.sink()[0].botf;
}
}
}
// Query is longer than ftab and matches exactly once with one read gap,
// one ref gap, one mismatch, and one N
{
size_t last_topf = std::numeric_limits<size_t>::max();
size_t last_botf = std::numeric_limits<size_t>::max();
for(int i = 0; i < 2; i++) {
// Set up the read
// Ref: CATGTCAGCT ATATAGCGCGCT CGCATCATTTTGTGTGTAAACCA
// |||||||||| |||||||||||| |||||| |||||| ||||||
BTDnaString seq ("CATGTCAGCT""GATATAGCGCGCT" "GCATCAATTTGTGNGTAAAC", true);
// 0123456789 0123456789012 34567890123456789012
BTString qual("ABCDEFGHIa""bcdefghiACDEF" "GHIabcdefghijkABCDEF");
for(size_t j = 0; j < seq.length(); j++) {
// Assume left-to-right
size_t beg = j;
size_t end = j + GFM::default_ftabChars;
// Mismatch penalty is 3, so we have to skip starting
// points that are within 2 from the mismatch
if((i > 0 && j > 0) || j == seq.length()-1) {
// Right-to-left
if(beg < GFM::default_ftabChars) {
beg = 0;
} else {
beg -= GFM::default_ftabChars;
}
end -= GFM::default_ftabChars;
}
if(beg <= 10 && end >= 10) {
continue;
}
if(beg <= 22 && end >= 22) {
continue;
}
if(beg <= 30 && end >= 30) {
continue;
}
if(beg <= 36 && end >= 36) {
continue;
}
cerr << "Test " << (++testnum) << endl;
cerr << " Query matches with various patterns of gaps, mismatches and Ns" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -50, 50);
// Set up the DescentConfig
DescentConfig conf;
// Changed
conf.cons.init(1, 0.5);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
i == 0, // left-to-right?
true, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
sc.setNPen(COST_MODEL_CONSTANT, 1);
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(5, dr.sink().nrange());
assert_eq(sc.n(40), dr.sink()[0].pen);
assert_eq(sc.n(40) + min(sc.readGapOpen(), sc.refGapOpen()) + sc.mm((int)'d' - 33), dr.sink()[1].pen);
assert_eq(sc.n(40) + max(sc.readGapOpen(), sc.refGapOpen()) + sc.mm((int)'d' - 33), dr.sink()[2].pen);
assert_eq(sc.n(40) + sc.readGapOpen() + sc.refGapOpen(), dr.sink()[3].pen);
assert_eq(sc.n(40) + sc.readGapOpen() + sc.refGapOpen() + sc.mm((int)'d' - 33), dr.sink()[4].pen);
assert(last_topf == std::numeric_limits<size_t>::max() || last_topf == dr.sink()[0].topf);
assert(last_botf == std::numeric_limits<size_t>::max() || last_botf == dr.sink()[0].botf);
cerr << dr.sink()[0].topf << ", " << dr.sink()[0].botf << endl;
assert_eq(5, dr.sink().nelt());
last_topf = dr.sink()[0].topf;
last_botf = dr.sink()[0].botf;
}
}
}
delete gfms.first;
delete gfms.second;
cerr << "DONE" << endl;
}
#endif
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