/usr/include/blasr/suffixarray/SuffixArray.hpp is in libblasr-dev 0~20151014+gitbe5d1bf-2.
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#define _BLASR_SUFFIX_ARRAY_HPP_
#include <string.h>
#include <assert.h>
#include <iostream>
#include <fstream>
#include <string>
#include <vector>
#include "LCPTable.hpp"
#include "defs.h"
#include "utils.hpp"
#include "tuples/DNATuple.hpp"
#include "tuples/CompressedDNATuple.hpp"
#include "qvs/QualityValue.hpp"
#include "DNASequence.hpp"
#include "NucConversion.hpp"
#include "algorithms/compare/CompareStrings.hpp"
#include "algorithms/sorting/qsufsort.hpp"
#include "algorithms/sorting/LightweightSuffixArray.hpp"
/*
* Suffix array implementation, with a Manber and Meyers sort, but
* that is typically not used.
*
*/
typedef enum E_SAType {manmy, slow, mcilroy, larsson, kark, mafe, welter} SAType;
template<typename T>
class CompareSuffixes {
public:
T t;
int refLength;
CompareSuffixes(T tref, int prefLength) {
t = tref;
refLength = prefLength;
}
int operator()(int a, int b) {
int aSufLen = refLength - a;
int bSufLen = refLength - b;
int abMinLength = MIN(aSufLen, bSufLen);
int cmpRes = memcmp(&(t[a]), &(t[b]), abMinLength);
if (cmpRes == 0) {
if (aSufLen < bSufLen) {
return 1;
}
else {
return 0;
}
}
else {
return cmpRes < 0;
}
}
};
typedef uint32_t SAIndex;
typedef uint32_t SAIndexLength;
template<typename T,
typename Sigma,
typename Compare = DefaultCompareStrings<T>,
typename Tuple = DNATuple >
class SuffixArray {
public:
SAIndex *index;
bool deleteStructures;
T* target;
SAIndex length;
SAIndex *startPosTable, *endPosTable;
SAIndexLength lookupTableLength;
SAIndex lookupPrefixLength;
TupleMetrics tm;
unsigned int magicNumber;
unsigned int ckMagicNumber;
typedef Compare CompareType;
enum Component { CompArray, CompLookupTable, CompLCPTable};
static const int ComponentListLength = 2;
static const int FullSearch = -1;
int componentList[ComponentListLength];
// vector<SAIndex> leftBound, rightBound;
inline int LengthLongestCommonPrefix(T *a, int alen, T *b, int blen) {
int i;
for (i = 0 ; i < alen and i < blen; i++ )
if (a[i] != b[i])
break;
return i;
}
SuffixArray() {
// Not necessarily using the lookup table.
// The magic number is linked with a version
magicNumber = 0xacac0001;
startPosTable = endPosTable = NULL;
lookupPrefixLength = 0;
lookupTableLength = 0;
deleteStructures = true;
ckMagicNumber = 0;
length = 0;
int i;
for (i = 0; i < ComponentListLength; i++) {
componentList[i] = false;
}
// Must create a suffix array, but for now make it null.
target = NULL;
index = NULL;
}
~SuffixArray() {
if (deleteStructures == false) {
//
// It is possible this class is referencing another structrue. In
// this case, do not try and delete in the destructor.
//
return;
}
if (startPosTable != NULL) {
delete[] startPosTable;
}
if (endPosTable != NULL) {
delete[] endPosTable;
}
if (index != NULL) {
delete[] index;
}
}
int StringLessThanEqual(T *a, int aLen, T *b, int bLen) {
return Compare::LessThanEqual(a, aLen, b, bLen);
}
int StringEquals(T *a, int aLen, T *b, int bLen) {
return Compare::Equal(a, aLen, b, bLen);
}
int StringLessThan(T *a, int aLen, T *b, int bLen) {
return Compare::LessThan(a, aLen, b, bLen);
}
void InitAsciiCharDNAAlphabet(std::vector<int> &dnaAlphabet) {
int i;
for (i = 0; i < 127; i++) {
dnaAlphabet.push_back(i);
}
}
void InitTwoBitDNAAlphabet(std::vector<int> &dnaAlphabet) {
dnaAlphabet.push_back(0);
dnaAlphabet.push_back(1);
dnaAlphabet.push_back(2);
dnaAlphabet.push_back(3);
}
void InitThreeBitDNAAlphabet(std::vector<int> &dnaAlphabet) {
//
// This is initialized to have ACTG-0123, N=4, and EOF=5
//
dnaAlphabet.push_back(0);
dnaAlphabet.push_back(1);
dnaAlphabet.push_back(2);
dnaAlphabet.push_back(3);
dnaAlphabet.push_back(4);
dnaAlphabet.push_back(5);
}
void PrintSuffices(T *target, int targetLength, int maxPrintLength) {
std::string seq;
seq.resize(maxPrintLength+1);
SAIndex i, s;
seq[maxPrintLength] = '\0';
for (i = 0; i < length; i++) {
DNALength suffixLength = maxPrintLength;
if (index[i] + maxPrintLength > length) {
suffixLength = length - index[i];
}
std::cout << index[i] << " " << suffixLength << " ";
seq.resize(suffixLength);
for (s = 0; s < suffixLength; s++ ){
seq[s] = TwoBitToAscii[target[index[i] + s]];
}
seq[suffixLength] = '\0';
std::cout << seq << std::endl;
}
}
void BuildLookupTable(T *target, SAIndexLength targetLength, int prefixLengthP) {
//
// pprefixLength is the length used to lookup the index boundaries
// given a string.
//
SAIndexLength i;
tm.tupleSize = lookupPrefixLength = prefixLengthP;
tm.InitializeMask();
lookupTableLength = 1 << (2*lookupPrefixLength);
if (startPosTable) {delete [] startPosTable;}
startPosTable = ProtectedNew<SAIndex>(lookupTableLength);
if (endPosTable) {delete [] endPosTable;}
endPosTable = ProtectedNew<SAIndex>(lookupTableLength);
deleteStructures = true;
Tuple curPrefix, nextPrefix;
SAIndex tablePrefixIndex = 0;
for (i = 0; i < lookupTableLength; i++) {
startPosTable[i] = endPosTable[i] = 0;
}
i = 0;
VectorIndex tablePos;
SAIndex indexPos;
indexPos = 0;
do {
// Advance to the first position that may be translated into a tuple.
if (targetLength < lookupPrefixLength)
break;
while(indexPos < targetLength - lookupPrefixLength + 1 and
index[indexPos] + lookupPrefixLength > targetLength) {
indexPos++;
}
if (indexPos >= targetLength - lookupPrefixLength + 1) {
break;
}
while (indexPos < targetLength - lookupPrefixLength + 1 and
curPrefix.FromStringLR((Nucleotide*) &target[index[indexPos]], tm) == 0) {
++indexPos;
}
startPosTable[curPrefix.tuple] = indexPos;
indexPos++;
while(indexPos < targetLength - lookupPrefixLength + 1 and
index[indexPos] + lookupPrefixLength < targetLength) {
nextPrefix.tuple = 0;
nextPrefix.FromStringLR((Nucleotide*) &target[index[indexPos]], tm);
if (nextPrefix.tuple != curPrefix.tuple) {
break;
}
else {
indexPos++;
}
}
endPosTable[curPrefix.tuple] = indexPos;
}
while ((indexPos < targetLength - lookupPrefixLength + 1) and
(uint32_t(curPrefix.tuple) < uint32_t(lookupTableLength - 1)));
}
void AllocateSuffixArray(SAIndexLength stringLength) {
assert(index == NULL or not deleteStructures);
index = ProtectedNew<SAIndex>(stringLength + 1);
deleteStructures = true;
length = stringLength;
}
void LarssonBuildSuffixArray(T* target, SAIndexLength targetLength, Sigma &alphabet) {
assert(index == NULL or not deleteStructures);
index = ProtectedNew<SAIndex>(targetLength+1);
deleteStructures = true;
SAIndex *p = ProtectedNew<SAIndex>(targetLength+1);
SAIndexLength i;
for (i = 0; i < targetLength; i++) { index[i] = target[i] + 1;}
SAIndexLength maxVal = 0;
for (i = 0; i < targetLength; i++) { maxVal = index[i] > maxVal ? index[i] : maxVal;}
index[targetLength] = 0;
LarssonSuffixSort<SAIndex, UINT_MAX> sorter;
sorter(index, p, ((SAIndex) targetLength), ((SAIndex) maxVal+1), (SAIndex) 1 );
for (i = 0; i < targetLength; i++ ){ index[i] = p[i+1];};
length = targetLength;
delete[] p;
}
void LightweightBuildSuffixArray(T*target, SAIndexLength targetLength, int diffCoverSize=2281) {
assert(index == NULL or not deleteStructures);
index = ProtectedNew<SAIndex>(targetLength+1);
deleteStructures = true;
length = targetLength;
DNALength pos;
for (pos = 0; pos < targetLength; pos++) {
target[pos]++;
}
LightweightSuffixSort(target, targetLength, index, diffCoverSize);
for (pos = 0; pos < targetLength; pos++) {
target[pos]--;
}
}
void MMBuildSuffixArray(T* target, SAIndexLength targetLength, Sigma &alphabet) {
/*
* Manber and Myers suffix array construction.
*/
length = targetLength;
VectorIndex a;
std::vector<int> prm;
std::vector<int> bucket;
std::vector<int> count;
// To be changed to bit vectors
std::vector<bool> bh, b2h;
bucket.resize(alphabet.size());
prm.resize(targetLength);
count.resize(targetLength);
bh.resize(targetLength+1);
b2h.resize(targetLength+1);
std::fill(bh.begin(), bh.end(), false);
std::fill(b2h.begin(), b2h.end(), false);
std::fill(count.begin(), count.end(), 0);
assert(index == NULL or not deleteStructures);
index = ProtectedNew<SAIndex>(targetLength);
deleteStructures = true;
for (a = 0; a < alphabet.size(); a++ ) {
bucket[a] = -1;
}
SAIndexLength i;
for (i = 0; i < targetLength; i++) {
index[i] = bucket[target[i]];
bucket[target[i]] = i;
}
int j;
SAIndex c;
std::fill(prm.begin(), prm.end(), -1);
//
// Prepare the buckets.
//
c = 0;
int b;
for (a = 0; a < alphabet.size(); a++) {
b = bucket[alphabet[a]]; // position of last suffix starting with 'a'
while (b != -1) {
j = index[b];
prm[b] = c;
if (b == bucket[a]) {
bh[c] = true;
}
else {
bh[c] = false;
}
c = c + 1;
b = j;
}
}
b2h[targetLength] = bh[targetLength] = true;
// fill the index with positions sorted by the first character.
for (i = 0; i < targetLength; i++) {
index[prm[i]] = i;
}
SAIndex h;
h = 1;
SAIndex l, r;
while (h < targetLength) {
// re-order the buckets;
l = 0;
int bstart;
while (l < targetLength) {
bstart = l;
r = l + 1;
count[l] = 0;
// bh[l] = 0;
while (bh[r] == false) {r++;} // find the begining of the next bucket.
while (l < r) {
assert(l < targetLength);
prm[index[l]] = bstart;
l++;
}
}
SAIndex d = targetLength - h;
SAIndex e = prm[d];
/*
* Phase 1: Set up the buckets in the index and bh list.
*/
//
// suffix d needs to be moved to the front of it's bucket.
// d should exist in the bucket starting at prm[d]
SAIndex i;
l = 0;
r = 1;
//
// Move each d that is h backwards up in it's 2h bucket.
//
d = targetLength - h;
e = prm[d];
bh[e] = true; // e is bstart, the beginning of the bucket.
prm[d] = e + count[e];
count[e] = count[e] + 1;
b2h[prm[d]] = true;
for (c = 0; c < targetLength; c++ ){
// d is T_i
d = index[c] - h;
if (index[c] >= h and d < targetLength) {
e = prm[d];
prm[d] = e + count[e];
count[e] = count[e] + 1;
b2h[prm[d]] = true;
}
}
//
// Fix the bucket boundaries.
//
l = 0;
while(l < targetLength) {
// First assign b2h to be 1 on the entire portion of the
// current bucket (from l ... bh[c]==true).
for (c = l; c == l or bh[c] == false; c++) {
d = index[c] - h;
if (d < targetLength) {
b2h[prm[d]] = true;
}
}
//
// Mark the start boundaries of the 2h bucket.
//
for (c = l; c == l or bh[c] == false; c++) {
d = index[c] - h;
if (d < targetLength) {
if (b2h[prm[d]] == true) {
j = prm[d] + 1;
// advance j to the next bucket.
while (!(bh[j] == true or b2h[j] == false)) {
j++;
}
e = j;
SAIndex f;
for (f = prm[d] + 1; f <= e - 1; f++) {
b2h[f] = false;
}
}
}
}
l = c;
}
for (i = 0; i < targetLength; i++) {
index[prm[i]] = i;
}
for (i = 0 ; i < targetLength; i++) {
if (b2h[i] == true and bh[i] == false) {
bh[i] = b2h[i];
}
}
h <<= 1;
}
}
void BuildSuffixArray(T* target, SAIndex targetLength, Sigma &alphabet) {
length = targetLength;
assert(index == NULL or not deleteStructures);
index = ProtectedNew<SAIndex>(length);
deleteStructures = true;
CompareSuffixes<T*> cmp(target, length);
SAIndex i;
for (i = 0; i < length; i++ ){
index[i] = i;
}
std::sort(index, index + length, cmp);
}
void WriteArray(std::ofstream &out) {
out.write((char*) &length, sizeof(int));
out.write((char*) index, sizeof(int) * (length));
}
void WriteLookupTable(std::ofstream &out) {
out.write((char*) &lookupTableLength, sizeof(SAIndex));
out.write((char*) &lookupPrefixLength, sizeof(SAIndex));
out.write((char*) startPosTable, sizeof(SAIndex) * (lookupTableLength));
out.write((char*) endPosTable, sizeof(SAIndex) * (lookupTableLength));
}
void WriteComponentList(std::ofstream &out) {
//
// First build the component list.
//
if (index != NULL)
componentList[CompArray] = 1;
else
componentList[CompArray] = 0;
if (startPosTable != NULL)
componentList[CompLookupTable] = 1;
else
componentList[CompLookupTable] = 0;
out.write((char*) componentList, sizeof(int) * ComponentListLength);
}
void WriteLCPTable(std::ofstream &out) {
std::cout << "NOT YET IMPLEMENTED." << std::endl;
exit(1);
}
void Write(std::string &outFileName) {
//
// The suffix array is written in 2 or more parts:
// 1 - a preamble listing the components of the
// array that are written
// 2 - The components.
//
//
std::ofstream suffixArrayOut;
suffixArrayOut.open(outFileName.c_str(), std::ios::binary);
if (!suffixArrayOut.good()) {
std::cout << "Could not open " << outFileName << std::endl;
exit(1);
}
WriteMagicNumber(suffixArrayOut);
// write the preamble
WriteComponentList(suffixArrayOut);
// write the components
if (componentList[CompArray]) {
WriteArray(suffixArrayOut);
}
if (componentList[CompLookupTable]) {
WriteLookupTable(suffixArrayOut);
}
suffixArrayOut.close();
}
void WriteMagicNumber(std::ofstream &out) {
out.write((char*) &magicNumber, sizeof(int));
}
int ReadMagicNumber(std::ifstream &in) {
in.read((char*) &ckMagicNumber, sizeof(int));
if (ckMagicNumber != magicNumber) {
return 0;
}
else {
return 1;
}
}
void ReadComponentList(std::ifstream &in) {
in.read((char*) componentList, sizeof(int) * ComponentListLength);
}
void ReadAllocatedArray(std::ifstream &in) {
in.read((char*) index, sizeof(int) * length);
}
void LightReadArray(std::ifstream &in) {
in.read((char*) &length, sizeof(int));
// skip the actual array
in.seekg(length*sizeof(int), std::ios_base::cur);
}
void ReadArray(std::ifstream &in) {
in.read((char*) &length, sizeof(int));
assert(index == NULL or not deleteStructures);
index = ProtectedNew<SAIndex>(length);
deleteStructures = true;
ReadAllocatedArray(in);
}
void ReadAllocatedLookupTable(std::ifstream &in) {
in.read((char*) startPosTable, sizeof(int) * (lookupTableLength));
in.read((char*) endPosTable, sizeof(int) * (lookupTableLength));
}
void ReadLookupTableLengths(std::ifstream &in) {
in.read((char*) &lookupTableLength, sizeof(int));
in.read((char*) &lookupPrefixLength, sizeof(int));
}
void ReadLookupTable(std::ifstream &in) {
ReadLookupTableLengths(in);
tm.Initialize(lookupPrefixLength);
assert(startPosTable == NULL or not deleteStructures);
assert(endPosTable == NULL or not deleteStructures);
startPosTable = ProtectedNew<SAIndex>(lookupTableLength);
endPosTable = ProtectedNew<SAIndex>(lookupTableLength);
deleteStructures = true;
ReadAllocatedLookupTable(in);
}
void ReadLCPTable(std::ifstream &in) {
std::cout <<" NOT YET IMPLEMENTED!!!" << std::endl;
exit(1);
}
bool LightRead(std::string &inFileName) {
std::ifstream saIn;
saIn.open(inFileName.c_str(), std::ios::binary);
int hasMagicNumber;
hasMagicNumber = ReadMagicNumber(saIn);
if (hasMagicNumber == 1) {
ReadComponentList(saIn);
LightReadArray(saIn);
ReadLookupTable(saIn);
saIn.close();
return true;
}
else {
saIn.close();
return false;
}
}
bool Read(std::string &inFileName) {
std::ifstream saIn;
saIn.open(inFileName.c_str(), std::ios::binary);
int hasMagicNumber;
hasMagicNumber = ReadMagicNumber(saIn);
if (hasMagicNumber == 1) {
ReadComponentList(saIn);
if (componentList[CompArray]) {
ReadArray(saIn);
}
if (componentList[CompLookupTable]) {
ReadLookupTable(saIn);
}
saIn.close();
return true;
}
else {
saIn.close();
return false;
}
}
int SearchLCP(T* target, T* query, DNALength queryLength, SAIndex &low, SAIndex &high, DNALength &lcpLength, DNALength maxlcp) {
// cout << "searching lcp with query of length: " << queryLength << endl;
lcpLength = 0;
if (startPosTable != NULL and
queryLength >= lookupPrefixLength) {
Tuple lookupTuple;
int left, right;
// just in case this was changed.
lookupTuple.FromStringLR(query, tm);
left = startPosTable[lookupTuple.tuple];
right = endPosTable[lookupTuple.tuple];
//
// When left == right, the k-mer in the read did not exist in the
// genome. Don't even try and map it in this case.
//
if (left == right) {
low = high = 0;
return 0;
}
//
// Otherwise, the sequence of length 'lookupPrefixLength' was found
// in the genome. The bounds of this prefix in the suffix array
// are stored in the lookup tables, so begin the binary search there.
//
lcpLength = lookupPrefixLength;
low = left, high = right;
}
else {
low = 0; high = length - 1;
lcpLength = 0;
}
int prevLow = low;
int prevHigh = high;
int prevLCPLength = lcpLength - 1;
// When the boundaries and the string share a prefix, it is not necessary
// to use this as a comparison in further lcp searches.
prevLCPLength = lcpLength;
Search(target, query, queryLength, low, high, low, high, 0);
DNALength lowLCP = lookupPrefixLength, highLCP = lookupPrefixLength;
while (lowLCP < queryLength and index[low]+lowLCP < length and
target[index[low] + lowLCP] == query[lowLCP]) lowLCP++;
while (highLCP < queryLength and index[high]+highLCP < length and
target[index[high] + highLCP] == query[highLCP]) highLCP++;
DNALength minLCP = highLCP;
if (lowLCP < highLCP ) {
minLCP = lowLCP;
}
while (minLCP >= (lookupPrefixLength -2 )and
low > 0 and high < (length - minLCP) and high - low < 10) {
while(low > 0 and StringEquals(&target[index[low]], minLCP, &target[index[high]], minLCP)) low--;
while(high > 0 and StringEquals(&target[index[low]], minLCP, &target[index[high]], minLCP)) high++;
--minLCP;
}
//
// The LCP is not an exact match to the end of the string.
//
prevLow = low;
prevHigh = high;
low = prevLow; high = prevHigh;
if (low < high and high - low < 100) {
return queryLength;
}
else {
high = low - 1;
lcpLength = 0;
}
return lcpLength;
}
int Search(T* target, T* query, DNALength queryLength, SAIndex left, SAIndex right, SAIndex &low, SAIndex &high, unsigned int offset=0) {
if (offset >= queryLength) {
return high - low;
}
SearchLow(target, query, queryLength, left, right, low, offset);
SearchHigh(target, query, queryLength, left, right, high, offset);
return high - low;
}
int Search(T* target, T* query, DNALength queryLength, SAIndex &low, SAIndex &high, int offset = 0) {
int left = 0;
int right = length - 1;
//
// Constrain the lookup if a lookup table exists.
//
if (startPosTable != NULL and
queryLength >= lookupPrefixLength) {
Tuple lookupTuple;
lookupTuple.FromStringLR(query, tm);
left = startPosTable[lookupTuple.tuple];
right = endPosTable[lookupTuple.tuple];
}
return Search(target, query, queryLength, left, right, low, high, offset);
}
long SearchLeftBound(T* target, long targetLength, DNALength targetOffset, T queryChar, long l, long r) {
long ll, lr;
ll = l;
lr = r;
long m;
long targetSufLen = 0;
while (ll < lr) {
m = (ll + lr) / 2;
targetSufLen = targetLength - index[m];
if (targetSufLen == targetOffset) {
ll =m + 1;
continue;
}
//
// The suffix at index[m] is shorter than the lengths of the
// two sequences being compared. With the Larsson
// implementation, that means that the target suffix is lex-less
// than the read.
int comp;
if (targetSufLen < targetOffset) {
comp = -1;
}
else {
//
// There is enough sequence to compare the target suffix with
// the query suffix.
//
assert(index[m]+targetOffset < targetLength);
/*
if (ThreeBit[target[index[m]+targetOffset]] >= 4 or
ThreeBit[queryChar] >= 4) {
lr = ll;
break;
}
*/
comp = Compare::Compare(target[index[m]+targetOffset], queryChar);
}
if (comp < 0) {
ll = m + 1;
}
else {
lr = m;
}
}
return ll;
}
long SearchRightBound(T* target, long targetLength, DNALength targetOffset,
T queryChar, long l, long r) {
long rl, rr;
rl = l;
rr = r;
long m;
long targetSufLen;
while (rl < rr) {
m = (rl + rr) / 2;
targetSufLen = targetLength - index[m];
if (targetSufLen == targetOffset) {
rr = m;
break;
}
if (targetSufLen < targetOffset) {
rr = m ;
}
else {
/*
* Do not try and map stretches of N. These do not add
* infomrative anchors.
*/
/*
if (ThreeBit[target[index[m]+targetOffset]] >= 4 or
ThreeBit[queryChar] >= 4) {
rl = rr;
break;
}
*/
int comp = Compare::Compare(target[index[m] + targetOffset], queryChar);
if (comp <= 0) {
rl = m + 1;
}
else {
rr = m ;
}
}
}
return rr;
}
/*
* Search the suffix array for the bounds l and r that specify the
* indices in the suffix array that have the longest common prefix
* between the read and the genome.
*/
int SearchLCPBounds(T*target, long targetLength, T*query, DNALength queryLength, SAIndex &l, SAIndex &r, DNALength &refOffset, DNALength &queryOffset) {
// l = 0; r = targetLength;
for (; refOffset < targetLength and queryOffset < queryLength and l < r; queryOffset++, refOffset++) {
std::cout << "bounds: " << l << ", " << r << std::endl;
//
// Band l by the character at query[offset]
//
l = SearchLeftBound(target, targetLength, refOffset, query[queryOffset], l, r);
//
// If the current search is past the end of the suffix array, it
// will be impossible to extend.
//
if (index[l] + refOffset >= targetLength or
Compare::Compare(target[index[l] + refOffset], query[queryOffset]) != 0) {
break;
}
r = SearchRightBound(target, targetLength, refOffset, query[queryOffset], l, r);
if (Compare::Compare(query[queryOffset], target[index[l]+refOffset]) != 0 or
Compare::Compare(query[queryOffset], target[index[r]+refOffset]) != 0) {
break;
}
}
return refOffset;
}
int StoreLCPBounds(T *target, long targetLength,
T *query, long queryLength,
SAIndex &low, SAIndex &high) {
DNALength targetOffset = 0;
DNALength queryOffset = 0;
DNALength lcpLength = 0;
low = 0; high = targetLength;
for (; index[low] + targetOffset < targetLength and
targetOffset < targetLength and
queryOffset < queryLength and
low < high ;
targetOffset++, queryOffset++, lcpLength++) {
//
// Band l by the character at query[offset]
//
low = SearchLeftBound(target, targetLength, targetOffset, query[queryOffset], low, high);
//
// If the current search is past the end of the suffix array, it
// will be impossible to extend.
//
if (index[low] + targetOffset > targetLength or
Compare::Compare(target[index[low] + targetOffset], query[queryOffset]) != 0 or
ThreeBit[query[queryOffset]] > 3) {
break;
}
high = SearchRightBound(target, targetLength, targetOffset, query[queryOffset], low, high);
}
return lcpLength;
}
int CountNumBranches(T* target, DNALength targetLength, DNALength targetOffset, SAIndex low, SAIndex high) {
//
// look to see how many different characters start suffices between
// low and high at targetOffset
//
// Check some easy boundary conditions.
//
// 1. No branches (indices do not define any subset of the suffix
// array).
if (high <= low) {
return 0;
}
// 2. One branch,
if (target[index[low] + targetOffset ] == target[index[high-1] + targetOffset]) {
return 1;
}
int numBranches = 1;
// More than one branch.
while ( low < high ) {
//
// Find the band where the suffices share the same chatacter
// 'targetOffset' bases into the suffix as the first suffix in
// the band given to this function.
//
SAIndex curCharHigh = high;
curCharHigh = SearchRightBound(target, targetLength, targetOffset, target[index[low]+targetOffset], low, high);
if (curCharHigh != high) {
++numBranches;
}
low = curCharHigh;
}
return numBranches;
}
int StoreLCPBounds(T *target, long targetLength, // The string which the suffix array is built on.
T *query, DNALength queryLength, // The query string. search starts at pos 0 in this string
bool useLookupTable, // Should the indices of the first k bases be determined by a lookup table?
int maxMatchLength, // Stop extending match at lcp length = maxMatchLength,
// Vectors containing lcpLeft and lcpRight from 0 ... lcpLength.
std::vector<SAIndex> &lcpLeftBounds, std::vector<SAIndex> &lcpRightBounds,
bool stopOnceUnique=false) {
//
// Precondition: target[l][0] >= query[offset]
//
long l, r;
l = 0; r = targetLength;
DNALength lcpLength = 0;
Tuple lookupTuple;
lookupTuple.tuple = -1;
/*
* Various parameters may make the search through the SA not use
* the full binary search. If priorLCP is > 0, the search for an
* LCP is limited to lcpLeftBounds[priorLCP] and lcpRightBounds[priorLCP].
* This is the case when continuing a search using branched
* re-uses previous lcp searches.
*/
if (useLookupTable and
startPosTable != NULL) {
// just in case this was changed.
if (lookupTuple.FromStringLR(query, tm)) {
l = startPosTable[lookupTuple.tuple];
r = endPosTable[lookupTuple.tuple];
lcpLength = lookupPrefixLength;
}
else {
//
// Not able to find a match for this sequence, so do not
// register a hit.
//
l = 0;
r = 0;
lcpLength = 0;
return 0;
}
//
// the values of startPosTable and endPosTable are the same when
// there are no matches. When they are not equal, a valid range
// has been found, so store this.
//
if (l < r) {
VectorIndex off_i;
VectorIndex boundLength = lcpLeftBounds.size();
lcpLeftBounds.push_back(l);
lcpRightBounds.push_back(r);
}
else {
//
// No exact match found in the lookup table, do not bother
// searching, and return 0 lcp length.
//
return 0;
}
}
//
// Search the suffix array for the longest common prefix between
// the read and the genome.
//
while( l < r and
lcpLength < queryLength // stop searching when the end of
// the query is reached.
) {
//
// If there is only one match in the suffix array, and and not
// extending matches as far as possible (stopping the search once
// they are unique), halt the search.
if (stopOnceUnique and l == r - 1) {
break;
}
//
// If there is a maximal match length and it is reached, stop
// searchign as well.
//
if (maxMatchLength and lcpLength >= maxMatchLength) {
break;
}
//
// If the match extends into one or more N's, stop. The reason
// for this is that sometimes people will set up genome databases
// by appending a stretch of N's between matches (although they
// should just use a multi-fasta file). Since the reads also
// have stretches of N's, this tends to slow the search down
// dramatically.
if (ThreeBit[target[index[l] + lcpLength]] >= 4) {
break;
}
//
// Find the bounds in the suffix array matching query[0... lcp]
// and target.
//
l = SearchLeftBound(target, targetLength, lcpLength, query[lcpLength], l, r);
r = SearchRightBound(target, targetLength, lcpLength, query[lcpLength], l, r);
//
// If the current search is past the end of the suffix array, it
// will be impossible to extend.
//
if (l == r or // if this point is reached, stop loop now since
// otherwise the lcp length will be incremented by
// 1, which will give one longer than the actual
// LCP length.
index[l] + lcpLength >= targetLength or // This shouldn't
// happen
// End on a mismatch.
ThreeBit[query[lcpLength]] >= 4 or
Compare::Compare(target[index[l] + lcpLength], query[lcpLength]) != 0
) {
break;
}
//
// Store the bounds for the current offset. These are used later
// to expand the search if necessary.
//
lcpLeftBounds.push_back(l);
lcpRightBounds.push_back(r);
lcpLength++;
}
return lcpLength;
}
int SearchLow(T *target, T *query, DNALength queryLength, SAIndex l, SAIndex r, SAIndex &low, unsigned int offset=0) {
long midPos;
int high;
int numSteps = 0;
//
// Boundary conditions, the string is either before (lexicographically) the text
// or after.
//
if (StringLessThanEqual(&query[offset],
queryLength-offset,
&target[index[l]+offset],
length - index[l]-offset)) {
low = l;
return low;
}
else if (StringLessThan(&target[index[r]+offset],
length - index[r] - offset ,
&query[offset],
queryLength - offset)) {
low = length;
return low;
}
//
// The string fits somewhere in the text.
//
low = l;
high = r;
long diff = ((long) high) - ((long) low);
while (diff > 1) {
++numSteps;
midPos = ((long) high) + ((long) low);
midPos = midPos / 2;
if (StringLessThanEqual(&query[offset], queryLength-offset, &target[index[midPos]+offset], length - index[midPos]-offset)) {
high = midPos;
}
else {
low = midPos;
}
diff = ((long) high) - ((long) low);
}
//
// The search is for the least position such that the query is greater than or equal to the text.
// High tracks the positions that may be equal to the query, and low is strictly less than the query.
// At the end of the search, high is either pointing to the query, or the first element where the query
// could be placed before high without changing the order of target.
//
low = high;
diff = ((long) high) - ((long) low);
return low;
// cout << "search low took: " << numSteps << endl;
}
int SearchHigh(T *target, T *query, DNALength queryLength, SAIndex l, SAIndex r, SAIndex &high, unsigned int offset=0) {
//
// Find the last position where the query is less than the target.
//
long midPos;
int low;
int numSteps = 0;
//
// Boundary conditions, the string is either before (lexicographically) the text
// or after.
//
if (StringLessThan(&target[index[r]+offset], length - index[r] - offset, &query[offset], queryLength-offset)) {
high = -1;
return high;
}
//
// The string fits somewhere in the text.
//
low = l;
high = r;
long diff = ((long) high) - ((long) low);
while (diff > 1) {
++numSteps;
midPos = ((long) high) + ((long) low);
midPos = midPos / 2;
if (StringLessThan(&query[offset], queryLength - offset, &target[index[midPos]+offset], length - index[midPos] - offset)) {
high = midPos;
}
else {
low = midPos;
}
diff = ((long) high) - ((long) low);
}
//
// The search is for the last position where the query is less than or equal to the text. High is
// strictly greater than or the query. Low is less than or equal to the query. At the end, low will be
// the last spot where query could be inserted after and not wreck the ordering of the array.
//
high = low;
// cout << "search high took: " << numSteps << " steps." << endl;
}
};
#endif // _BLASR_SUFFIX_ARRAY_HPP_
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