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#include "TestGenome_Index_TableQ.h"
SimulateLongRead::SimulateLongRead(CGenomeInBits* pgenomeNTInBits, unsigned int startIndex)
{
unsigned int halfLength = this->uiReadLength / 2;
this->goodRead = pgenomeNTInBits->fragACGTKmerInBits(this->half1st, startIndex, halfLength);
this->goodRead = this->goodRead & (pgenomeNTInBits->fragACGTKmerInBits(half2nd, startIndex + halfLength, halfLength));
if (goodRead) {
bool bOddReadLength = (this->uiReadLength % 2 == 1);
decodeLongRead(this->half1st, this->half2nd, this->read, bOddReadLength);
}
}
SimulateLongRead::~SimulateLongRead(void)
{
}
void introduceMutation(char* kmer, int mutationPattern)
{
if (mutationPattern == 2 || mutationPattern == 3 || mutationPattern == 4) {
mutateRead(kmer, mutationPattern);
} else if (mutationPattern == (int)FULL_SENSITIVE_OPT_TO_ONE_BASE_ONE_COLOR_MIS) {
mutatePairsOfConsecutiveBases(kmer, 1);
mutateRead(kmer, 1);
} else if (mutationPattern == (int)FULL_SENSITIVE_OPT_TO_TWO_BASE_MIS ) {
mutatePairsOfConsecutiveBases(kmer, 2);
} else if (mutationPattern == (int)FULL_SENSITIVE_OPT_TO_ONE_BASE_TWO_COLOR_MIS) {
mutatePairsOfConsecutiveBases(kmer, 1);
mutateRead(kmer, 2);
}
}
/*
int getTestChrId(CGenome_Index_TableQ* table) {
}
const char* getTestChr(CGenome_Index_TableQ* table) {
}*/
/*
* Test function which mutates every sliding windows on the reference genome and check if the all hits are found
*/
bool testGenome_Index_TableQ(CGenome_Index_TableQ* table)
{
bool pass = true;
CAlignmentsQ alignmentsQ('B');
CchromosomeNTdata* testChr;
unsigned int testChrId;
if (table->pgenomeNT->iNo_of_chromosome > 1) {
testChrId = 1; // If there are more than one chromosome, test the second one.
testChr = table->pgenomeNT->paChromosomes[1];
} else {
testChrId = 0;
testChr = table->pgenomeNT->paChromosomes[0];
}
unsigned int testGenomeIdStart = table->pgenomeNT->chrIndex2genomelocusID(testChrId, 0);
unsigned int testGenomeIdEnd = table->pgenomeNT->chrIndex2genomelocusID(testChrId, 0)
+ testChr->iChromosome_size - table->uiRead_Length;
for (unsigned int i = testGenomeIdStart; i < testGenomeIdEnd; i++) {
CReadInBits slideWindows;
bool goodRead;
goodRead = table->pgenomeNTInBits->fragACGTKmerInBits(slideWindows, i, table->uiRead_Length);
if (table->bMapReadInColors) {
slideWindows = bases2Colors(slideWindows);
}
if (goodRead) {
char read[wordSize + 1];
char originalRead[wordSize + 1];
slideWindows.decode(read);
CReadInBits readInBits(read);
alignmentsQ.clearHits();
// (1) Test exact match
if (table->bMapReadInColors) {
table->queryReadColors(readInBits, alignmentsQ, true, true);
} else {
table->queryReadBases(readInBits, alignmentsQ, true, true);
}
if (alignmentsQ.MinDiff != 0) {
cout << "Miss exact match " << i << endl;
pass = false;
PRINT_MASKED_REPERAT_FLAG(table, i);
}
// (2) Test mutated reads
myStrCpy(originalRead, read, MAX_READ_LENGTH);
introduceMutation(read, table->chosenSeedId);
CReadInBits mReadInBits(read);
alignmentsQ.clearHits();
if (table->bMapReadInColors) {
table->queryReadColors(mReadInBits, alignmentsQ, true, true);
} else {
table->queryReadBases(mReadInBits, alignmentsQ, true, true);
}
if (alignmentsQ.MinDiff > table->uiSubDiffThreshold) {
cout << "Miss mutated read" << i << endl;
pass = false;
// PRINT_MASKED_REPERAT_FLAG(table, i);
} else if (alignmentsQ.MinDiff < table->uiSubDiffThreshold) {
// cout << "Found better alignment!" << endl;
}
// (3) Check reversed complement reads
if (table->bMapReadInColors) {
table->pgenomeNTInBits->fragACGTKmerInBits(slideWindows, i, table->uiRead_Length);
CReadInBits rcRead = reverseCompliment(table->uiRead_Length, slideWindows);
CReadInBits rcReadInColors = bases2Colors(rcRead);
rcReadInColors.decode(read);
myStrCpy(originalRead, read, MAX_READ_LENGTH);
introduceMutation(read, table->chosenSeedId);
CReadInBits rcMreadInBits(read);
alignmentsQ.clearHits();
table->queryReadColors(rcMreadInBits, alignmentsQ, true, false);
} else {
reverseComplementKmer(read);
CReadInBits rcMreadInBits(read);
alignmentsQ.MinDiff = table->uiRead_Length; // SET A LARGE NUMBER
table->queryReadBases(rcMreadInBits, alignmentsQ, true, false);
}
if (alignmentsQ.MinDiff > table->uiSubDiffThreshold) {
cout << "Miss reversed mutated read" << i << endl;
pass = false;
// PRINT_MASKED_REPERAT_FLAG(table, i);
} else if (alignmentsQ.MinDiff < table->uiSubDiffThreshold) {
// cout << "Found better alignment!" << endl;
}
}
}
return(pass);
}
bool testMappingLongRead(CGenome_Index_TableQ* table)
{
bool bOddReadLength = false; // Currently only test even long read
bool pass = true;
CAlignmentsQ alignmentsQ('B');
CchromosomeNTdata* testChr;
unsigned int testChrId;
if (table->pgenomeNT->iNo_of_chromosome > 1) {
testChrId = 1; // If there are more than one chromosome, test the second one.
testChr = table->pgenomeNT->paChromosomes[1];
} else {
testChrId = 0;
testChr = table->pgenomeNT->paChromosomes[0];
}
const unsigned halfLength = table->uiRead_Length;
unsigned int testGenomeIdStart = table->pgenomeNT->chrIndex2genomelocusID(testChrId, 0);
unsigned int testGenomeIdEnd = table->pgenomeNT->chrIndex2genomelocusID(testChrId, 0)
+ testChr->iChromosome_size - halfLength;
for (unsigned int i = testGenomeIdStart; i < testGenomeIdEnd; i++) {
CReadInBits half1st, half2nd;
bool goodRead;
goodRead = table->pgenomeNTInBits->fragACGTKmerInBits(half1st, i, halfLength);
goodRead = goodRead & (table->pgenomeNTInBits->fragACGTKmerInBits(half2nd, i + halfLength, halfLength));
if (goodRead) {
char read[MAX_LINE];
char originalRead[MAX_LINE];
decodeLongRead(half1st, half2nd, read, bOddReadLength);
alignmentsQ.clearHits();
// (1) Test exact match
table->queryLongReadBases(half1st, half2nd, bOddReadLength, alignmentsQ, 1, true, true);
if (alignmentsQ.MinDiff != 0) {
cout << "Miss exact match " << i << endl;
pass = false;
PRINT_MASKED_REPERAT_FLAG(table, i);
}
// (2) Test mutated reads
myStrCpy(originalRead, read, MAX_LINE);
introduceMutation(read, table->chosenSeedId * 2);
encodeLongRead(read, half1st, half2nd);
alignmentsQ.clearHits();
table->queryLongReadBases(half1st, half2nd, bOddReadLength, alignmentsQ, 1, true, true);
if (alignmentsQ.MinDiff > table->uiSubDiffThreshold) {
cout << "Miss mutated read" << i << endl;
pass = false;
// PRINT_MASKED_REPERAT_FLAG(table, i);
} else if (alignmentsQ.MinDiff < table->uiSubDiffThreshold) {
// cout << "Found better alignment!" << endl;
}
// (3) Check reversed complement reads
reverseComplementKmer(read);
CReadInBits rcR1, rcR2;
encodeLongRead(read, rcR1, rcR2);
alignmentsQ.MinDiff = table->uiRead_Length; // SET A LARGE NUMBER
table->queryLongReadBases(rcR1, rcR2, bOddReadLength, alignmentsQ, 1, true, false);
table->queryLongReadBases(rcR1, rcR2, bOddReadLength, alignmentsQ, 2, true, false);
if (alignmentsQ.MinDiff > table->uiSubDiffThreshold) {
cout << "Miss reversed mutated read" << i << endl;
pass = false;
// PRINT_MASKED_REPERAT_FLAG(table, i);
} else if (alignmentsQ.MinDiff < table->uiSubDiffThreshold) {
// cout << "Found better alignment!" << endl;
}
}
}
return(pass);
}
bool testMappingLongSOLiDRead(CGenome_Index_TableQ* table)
{
bool bOddReadLength = false;
bool pass = true;
CAlignmentsQ alignmentsQ('B');
CchromosomeNTdata* testChr;
unsigned int testChrId;
if (table->pgenomeNT->iNo_of_chromosome > 1) {
testChrId = 1; // If there are more than one chromosome, test the second one.
testChr = table->pgenomeNT->paChromosomes[1];
} else {
testChrId = 0;
testChr = table->pgenomeNT->paChromosomes[0];
}
const unsigned halfLength = table->uiRead_Length;
unsigned int testGenomeIdStart = table->pgenomeNT->chrIndex2genomelocusID(testChrId, 0);
unsigned int testGenomeIdEnd = table->pgenomeNT->chrIndex2genomelocusID(testChrId, 0)
+ testChr->iChromosome_size - halfLength;
for (unsigned int i = testGenomeIdStart; i < testGenomeIdEnd; i++) {
CReadInBits half1st, half2nd, half1stInColors, half2ndInColors;
bool goodRead;
goodRead = table->pgenomeNTInBits->fragACGTKmerInBits(half1st, i, halfLength);
goodRead = goodRead & (table->pgenomeNTInBits->fragACGTKmerInBits(half2nd, i + halfLength, halfLength));
if (goodRead) {
char read[MAX_LINE];
char originalRead[MAX_LINE];
decodeLongRead(half1st, half2nd, read, bOddReadLength);
// TODO: encode each half in colors signals
alignmentsQ.clearHits();
// (1) Test exact match
table->queryLongReadColors(half1stInColors, half2ndInColors, bOddReadLength, alignmentsQ, 1, true, true);
if (alignmentsQ.MinDiff != 0) {
cout << "Miss exact match " << i << endl;
pass = false;
PRINT_MASKED_REPERAT_FLAG(table, i);
}
// (2) Test mutated reads
myStrCpy(originalRead, read, MAX_LINE);
introduceMutation(read, table->chosenSeedId * 2);
encodeLongRead(read, half1st, half2nd);
// TODO: encode each half in colors signals
alignmentsQ.clearHits();
table->queryLongReadColors(half1stInColors, half2ndInColors, bOddReadLength, alignmentsQ, 1, true, true);
if (alignmentsQ.MinDiff > table->uiSubDiffThreshold) {
cout << "Miss mutated read" << i << endl;
pass = false;
// PRINT_MASKED_REPERAT_FLAG(table, i);
} else if (alignmentsQ.MinDiff < table->uiSubDiffThreshold) {
// cout << "Found better alignment!" << endl;
}
// (3) Check reversed complement reads
reverseComplementKmer(read);
CReadInBits rcR1, rcR2;
encodeLongRead(read, rcR1, rcR2);
// TODO: encode each half in colors signals
alignmentsQ.MinDiff = table->uiRead_Length; // SET A LARGE NUMBER
table->queryLongReadBases(rcR1, rcR2, bOddReadLength, alignmentsQ, 1, true, false);
table->queryLongReadBases(rcR1, rcR2, bOddReadLength, alignmentsQ, 2, true, false);
if (alignmentsQ.MinDiff > table->uiSubDiffThreshold) {
cout << "Miss reversed mutated read" << i << endl;
pass = false;
// PRINT_MASKED_REPERAT_FLAG(table, i);
} else if (alignmentsQ.MinDiff < table->uiSubDiffThreshold) {
// cout << "Found better alignment!" << endl;
}
}
}
return(pass);
}
bool testMappingLongPairedRead(CGenome_Index_TableQ* table)
{
bool bOddReadLength = false;
bool pass = true;
/*
CAlignmentsQ alignmentsQ('B');
CchromosomeNTdata* testChr;
unsigned int testChrId;
if (table->pgenomeNT->iNo_of_chromosome > 1) {
testChrId = 1; // If there are more than one chromosome, test the second one.
testChr = table->pgenomeNT->paChromosomes[1];
} else {
testChrId = 0;
testChr = table->pgenomeNT->paChromosomes[0];
}
int separation = 300;
const unsigned halfLength = table->uiRead_Length;
SimulateLongRead::uiReadLength = table->uiRead_Length * 2;
unsigned int testGenomeIdStart = table->pgenomeNT->chrIndex2genomelocusID(testChrId, 0);
unsigned int testGenomeIdEnd = table->pgenomeNT->chrIndex2genomelocusID(testChrId, 0)
+ testChr->iChromosome_size - halfLength = separation;
for (unsigned int i = testGenomeIdStart; i < testGenomeIdEnd; i++) {
CReadInBits half1st, half2nd, half1stInColors, half2ndInColors;
SimulateLongRead r1(table->pgenomeNTInBits, i);
SimulateLongRead r2(table->pgenomeNTInBits, i + separation);
if (r1.goodRead && r2.goodRead) {
char originalRead[MAX_LINE];
alignmentsQ.clearHits();
// (1) Test exact match
table->queryLongReadColors(r1.half1st, r1.half2nd, bOddReadLength, alignmentsQ, 1, true, true);
if (alignmentsQ.MinDiff != 0) {
cout << "Miss exact match " << i << endl;
pass = false;
PRINT_MASKED_REPERAT_FLAG(table, i);
}
// (2) Test mutated reads
myStrCpy(originalRead, r.read, MAX_LINE);
introduceMutation(read, table->chosenSeedId * 2);
encodeLongRead(read, half1st, half2nd);
// TODO: encode each half in colors signals
alignmentsQ.clearHits();
table->queryLongReadColors(half1stInColors, half2ndInColors, bOddReadLength, alignmentsQ, 1, true, true);
if (alignmentsQ.MinDiff > table->uiSubDiffThreshold) {
cout << "Miss mutated read" << i << endl;
pass = false;
// PRINT_MASKED_REPERAT_FLAG(table, i);
} else if (alignmentsQ.MinDiff < table->uiSubDiffThreshold) {
// cout << "Found better alignment!" << endl;
}
// (3) Check reversed complement reads
reverseComplementKmer(read);
CReadInBits rcR1, rcR2;
encodeLongRead(read, rcR1, rcR2);
// TODO: encode each half in colors signals
alignmentsQ.MinDiff = table->uiRead_Length; // SET A LARGE NUMBER
table->queryLongReadBases(rcR1, rcR2, bOddReadLength, alignmentsQ, 1, true, false);
table->queryLongReadBases(rcR1, rcR2, bOddReadLength, alignmentsQ, 2, true, false);
if (alignmentsQ.MinDiff > table->uiSubDiffThreshold) {
cout << "Miss reversed mutated read" << i << endl;
pass = false;
// PRINT_MASKED_REPERAT_FLAG(table, i);
} else if (alignmentsQ.MinDiff < table->uiSubDiffThreshold) {
// cout << "Found better alignment!" << endl;
}
}
}
*/
return(pass);
}
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