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e-mem.cpp
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e-mem.cpp
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/* ================================================================= *
* e-mem.cpp : Main program *
* *
* E-MEM: An efficient (MUMmer-like) tool to retrieve Maximum Exact *
* Matches using hashing based algorithm *
* *
* Copyright (c) 2014, Nilesh Khiste *
* All rights reserved *
* *
* This program 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. *
* *
* This program 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 this program. *
* *
* This file is subject to the terms and conditions defined in the *
* file 'LICENSE', which is part of this source code package. *
* ================================================================= */
#include <iostream>
#include <sstream>
#include <fstream>
#include <cstdint>
#include <cstdlib>
#include <cmath>
#include <iomanip>
#include <unordered_map>
#include <map>
#include <vector>
#include <iterator>
#include <omp.h>
#include <boost/algorithm/string.hpp>
#include <boost/tokenizer.hpp>
#include <sys/stat.h>
#include "e-mem.h"
#include "file.h"
using namespace std;
using namespace boost;
/*
* Function builds a kmer hash for a reference sequence.
* Input: empty refHash
* Output: populated refHash
*/
void buildRefHash(Knode* &refHash, uint64_t totalBits, seqFileReadInfo &RefFile)
{
uint64_t j=0;
uint64_t currKmerPos=0, currKmer=0;
int32_t offset=0;
int nextKmerPosition = commonData::minMemLen - commonData::kmerSize + 2;
vector<mapObject>::iterator it;
it = upper_bound(RefFile.blockOfNs.begin(), RefFile.blockOfNs.end(), currKmerPos, mapObject());
while (currKmerPos<=totalBits)
{
if (currKmerPos + commonData::kmerSize - 2 > totalBits)
break;
if(RefFile.checkKmerForNs(currKmerPos, it)){
currKmerPos+=nextKmerPosition; // Move L-K+2 bits = 50-28+1=23 char = 46 bits
continue;
}
offset = currKmerPos%DATATYPE_WIDTH;
j=currKmerPos/DATATYPE_WIDTH; // next loc in binReads
currKmer = RefFile.binReads[j];
currKmer <<= offset;
if (offset > DATATYPE_WIDTH-commonData::kmerSize) // Kmer split in two integers
currKmer |= ((RefFile.binReads[j+1] & global_mask_left[(commonData::kmerSize-(DATATYPE_WIDTH-offset))/2 -1])>>(DATATYPE_WIDTH-offset));
else
currKmer &= global_mask_left[commonData::kmerSize/2 - 1];
/* Add kmer to the hash table */
refHash->addKmerNode(currKmer, currKmerPos);
currKmerPos+=nextKmerPosition; // Move L-K+2 bits = 50-28+1=23 char = 46 bits
}
}
/*
* Function extends the kmer match in left/right direction for
* possible MEMs.
* Input: currRPos : current position of matching reference Kmer
* Input: currRPos : current position of matching query Kmer
* Input: totalRBits : total number of bits in reference
* Input: totalQBits : total number of bits in query
* Input: name : reference sequence string for output
*
*/
void helperReportMem(uint64_t &currRPos, uint64_t &currQPos, uint64_t totalRBits, uint64_t totalQBits, seqFileReadInfo &RefFile, seqFileReadInfo &QueryFile, tmpFilesInfo &arrayTmpFile, mapObject &RefNpos, mapObject &QueryNpos, uint32_t &revComplement)
{
/*
* lRef and lQue are local variables for left extension of
* reference and query sequence respectively. rRef and rQue
* are their right counterparts.
*/
uint64_t lRef=currRPos, lQue=currQPos; // Keeping lRef on currRPos-this makes offset computation simpler
uint64_t offsetR=0,offsetQ=0;
uint64_t rRef=currRPos+commonData::kmerSize, rQue=currQPos+commonData::kmerSize; // one character ahead of current match
uint64_t currR=0, currQ=0;
int i=0,j=0,mismatch=0;
uint64_t matchSize=0;
if (!(((QueryNpos.left==0x1)?true:QueryNpos.left<=lQue) && rQue<=QueryNpos.right))
QueryFile.getKmerLeftnRightBoundForNs(lQue, QueryNpos);
if (!(((RefNpos.left==0x1)?true:RefNpos.left<=lRef) && rRef<=RefNpos.right))
RefFile.getKmerLeftnRightBoundForNs(lRef, RefNpos);
if (RefNpos.right-((RefNpos.left==0x1)?0:RefNpos.left)+2 < static_cast<uint64_t>(commonData::minMemLen))
return;
if (QueryNpos.right-((QueryNpos.left==0x1)?0:QueryNpos.left)+2 < static_cast<uint64_t>(commonData::minMemLen))
return;
//match towards left
while (lRef && lQue && ((QueryNpos.left==0x1)?true:QueryNpos.left<=lQue) && ((RefNpos.left==0x1)?true:RefNpos.left<=lRef))
{
if (!mismatch)
{
offsetR=(lRef)%DATATYPE_WIDTH;
i=(lRef)/DATATYPE_WIDTH;
offsetQ=(lQue)%DATATYPE_WIDTH;
j=(lQue)/DATATYPE_WIDTH;
if (offsetR > offsetQ)
matchSize = offsetQ;
else
matchSize = offsetR;
if (!matchSize)
matchSize=2;
if ((QueryNpos.left!=0x1) && (matchSize > lQue-QueryNpos.left))
matchSize = lQue-QueryNpos.left;
if ((RefNpos.left!=0x1) && (matchSize > lRef-RefNpos.left))
matchSize = lRef-RefNpos.left;
if (!matchSize)
break;
/*
* There will never be case with offset=0 and i=0 because
* i=0 happens only when lRef=0 and in that case we do not
* enter this loop.
*/
currR = RefFile.binReads[offsetR?i:i-1];
if (offsetR)
currR >>= DATATYPE_WIDTH-offsetR;
currQ = QueryFile.binReads[offsetQ?j:j-1];
if (offsetQ)
currQ >>= DATATYPE_WIDTH-offsetQ;
}
if((currR & global_mask_right[matchSize/2 - 1]) != (currQ & global_mask_right[matchSize/2 - 1])) {
if (matchSize==2)
break;
mismatch=1;
matchSize/=2;
if (matchSize%2)
matchSize+=1;
}else {
lRef-=matchSize;
lQue-=matchSize;
if (mismatch) {
if (matchSize==2)
break;
currR >>= matchSize;
currQ >>= matchSize;
}
}
}
if (totalRBits-lRef+2 < static_cast<uint64_t>(commonData::minMemLen))
return;
if (totalQBits-lQue+2 < static_cast<uint64_t>(commonData::minMemLen))
return;
//match towards right
mismatch=0;
while ((rRef <= totalRBits) && (rQue <= totalQBits) && (rRef <= RefNpos.right) && (rQue <= QueryNpos.right))
{
if (!mismatch)
{
offsetR=rRef%DATATYPE_WIDTH;
i=rRef/DATATYPE_WIDTH;
offsetQ=rQue%DATATYPE_WIDTH;
j=rQue/DATATYPE_WIDTH;
if (offsetR > offsetQ)
matchSize = DATATYPE_WIDTH-offsetR;
else
matchSize = DATATYPE_WIDTH-offsetQ;
if (rRef+matchSize > totalRBits)
matchSize = totalRBits-rRef;
if (rQue+matchSize > totalQBits)
matchSize = totalQBits-rQue;
if (rQue+matchSize > QueryNpos.right)
matchSize = QueryNpos.right-rQue;
if (rRef+matchSize > RefNpos.right)
matchSize = RefNpos.right-rRef;
if(!matchSize)
matchSize=2;
currR = RefFile.binReads[i];
currR <<= offsetR;
currQ = QueryFile.binReads[j];
currQ <<= offsetQ;
}
if((currR & global_mask_left[matchSize/2 - 1]) != (currQ & global_mask_left[matchSize/2 - 1])) {
if (matchSize==2){
rRef-=2;
rQue-=2;
break;
}
/* if current rRef/rQue plus matchSize smaller than minMEMLength, then simply return.
* Note that one less character is compared due to a mismatch
*/
if (rRef+matchSize-lRef < static_cast<uint64_t>(commonData::minMemLen))
{
return;
}
mismatch=1;
matchSize/=2;
if (matchSize%2)
matchSize+=1;
}else {
if (mismatch) {
if (matchSize==2)
break;
}
if ((rRef == totalRBits) || (rQue == totalQBits))
break;
currR <<= matchSize;
currQ <<= matchSize;
rRef+=matchSize;
rQue+=matchSize;
}
}
/* Adjust rRef and rQue locations */
if (rRef > RefNpos.right){
rQue-=(rRef-RefNpos.right);
rRef=RefNpos.right;
}
if (rQue > QueryNpos.right){
rRef-=(rQue-QueryNpos.right);
rQue=QueryNpos.right;
}
if (rRef > totalRBits){
rQue-=(rRef-totalRBits);
rRef=totalRBits;
}
if (rQue > totalQBits){
rRef-=(rQue-totalQBits);
rQue=totalQBits;
}
arrayTmpFile.writeMemInTmpFiles(lRef, rRef, lQue, rQue, QueryFile, RefFile, revComplement);
}
void reportMEM(Knode * &refHash, uint64_t totalBases, uint64_t totalQBases, seqFileReadInfo &RefFile, seqFileReadInfo &QueryFile, tmpFilesInfo &arrayTmpFile, uint32_t &revComplement)
{
uint64_t totalQBits = CHARS2BITS(totalQBases);
uint32_t copyBits=0;
#pragma omp parallel num_threads(commonData::numThreads)
{
uint64_t currKmer=0, j=0;
int32_t offset=0;
uint32_t first=1;
int kmerWithNs=0;
mapObject QueryNpos, RefNpos;
vector<mapObject>::iterator it;
it = upper_bound(QueryFile.blockOfNs.begin(), QueryFile.blockOfNs.end(), 0, mapObject());
#pragma omp single
{
/*
* Number of copy bits during query kmer processing depends on kmer size.
*/
if (DATATYPE_WIDTH-commonData::kmerSize > 32 )
copyBits=32; //16 characters
else if (DATATYPE_WIDTH-commonData::kmerSize > 16)
copyBits=16; //8 characters
else
copyBits=8; //4 characters
/* If copyBits more than 8, the for loop parallelisation will give
* incorrect results - miss some Mems
*/
if(commonData::numThreads > 1)
copyBits=8; //4 characters
}
#pragma omp for
for (uint64_t currKmerPos=0; currKmerPos<=totalQBits; currKmerPos+=2)
{
if ((currKmerPos + commonData::kmerSize - 2) > totalQBits)
continue;
if(QueryFile.checkKmerForNs(currKmerPos, it)){
kmerWithNs=1;
}
j=currKmerPos/DATATYPE_WIDTH;// current location in binReads
offset = currKmerPos%DATATYPE_WIDTH;
if(first || !offset){
currKmer = QueryFile.binReads[j];
currKmer <<= offset;
if(offset > DATATYPE_WIDTH-commonData::kmerSize)
currKmer |= ((QueryFile.binReads[j+1] & global_mask_left[offset/2-1])>>(DATATYPE_WIDTH-offset));
first=0;
}else
currKmer <<= 2;
if(offset && !(offset % copyBits))
currKmer |= ((QueryFile.binReads[j+1] & global_mask_left[offset/2-1])>>(DATATYPE_WIDTH-offset));
if (kmerWithNs){
/* Do not process this Kmer, Ns in it */
kmerWithNs=0;
continue;
}
/* Find the K-mer in the refHash */
uint64_t *dataPtr=NULL;
if (refHash->findKmer(currKmer & global_mask_left[commonData::kmerSize/2 - 1], dataPtr))
{
// We have a match
for (uint64_t n=1; n<=dataPtr[0]; n++) {
helperReportMem(dataPtr[n], currKmerPos, CHARS2BITS(totalBases), CHARS2BITS(totalQBases), RefFile, QueryFile, arrayTmpFile, RefNpos, QueryNpos, revComplement);
}
}
}
}
}
void processQuery(Knode * &refHash, seqFileReadInfo &RefFile, seqFileReadInfo &QueryFile, tmpFilesInfo &arrayTmpFile, uint32_t &revComplement)
{
QueryFile.clearFileFlag();
QueryFile.resetCurrPos();
for (int32_t i=0; i<commonData::d; i++) {
if(QueryFile.readChunks()){
reportMEM(refHash, RefFile.totalBases-1, QueryFile.totalBases-1, RefFile, QueryFile, arrayTmpFile, revComplement);
QueryFile.setCurrPos();
QueryFile.clearMapForNs();
}
else
break;
}
QueryFile.clearTmpString();
}
void processReference(seqFileReadInfo &RefFile, seqFileReadInfo &QueryFile, tmpFilesInfo &arrayTmpFile, uint32_t &revComplement)
{
uint64_t numberOfKmers=0,n=0;
int hashTableSizeIndex=0;
Knode *refHash;
numberOfKmers = ceil((RefFile.totalBases-commonData::kmerSize/2+1)/((commonData::minMemLen/2-commonData::kmerSize/2 + 1)) + 1);
/* Set the size of the hash table to the numberofKmers. */
for (n=0; n<450; ++n)
{
if (hashTableSize[n] > 1.75*numberOfKmers)
{
hashTableSizeIndex = n;
break;
}
}
Knode::currHashTabSize = hashTableSize[hashTableSizeIndex]; //Store the size of the hash table.
if (hashTableSizeIndex)
Knode::prevHashTabSize = hashTableSize[hashTableSizeIndex-1];
else
Knode::prevHashTabSize = 3;
/* Create the refHash for K-mers. */
refHash = new Knode[Knode::currHashTabSize];
buildRefHash(refHash, CHARS2BITS(RefFile.totalBases-1), RefFile);
processQuery(refHash, RefFile, QueryFile, arrayTmpFile, revComplement);
delete [] refHash;
}
bool is_numeric(const string &str)
{
return all_of(str.begin(), str.end(), ::isdigit);
}
void checkCommandLineOptions(uint32_t &options)
{
if (!IS_REF_FILE_DEF(options)){
cout << "ERROR: reference file must be passed!" << endl;
exit(EXIT_FAILURE);
}
if (!IS_QUERY_FILE_DEF(options)){
cout << "ERROR: query file must be passed!" << endl;
exit(EXIT_FAILURE);
}
if (IS_SPLIT_SIZE_DEF(options)){
if (commonData::d <= 0){
cout << "ERROR: -d cannot be less than or equal to zero!" << endl;
exit(EXIT_FAILURE);
}
}
if (IS_NUM_THREADS_DEF(options)){
if (commonData::numThreads <= 0){
cout << "ERROR: -t cannot be less than or equal to zero!" << endl;
exit(EXIT_FAILURE);
}
}
if (IS_LENGTH_DEF(options)){
if (commonData::minMemLen <= 2){
cout << "ERROR: -l cannot be less than or equal to one!" << endl;
exit(EXIT_FAILURE);
}
if ((commonData::minMemLen - commonData::kmerSize) < 0)
{
if (IS_KMER_SIZE_DEF(options)){
cout << "ERROR: kmer-size cannot be larger than min mem length!" << endl;
exit( EXIT_FAILURE );
}else {
commonData::kmerSize = commonData::minMemLen;
}
}
}
if (IS_KMER_SIZE_DEF(options)){
if (commonData::kmerSize <= 0){
cout << "ERROR: -k cannot be less than or equal to zero!" << endl;
exit(EXIT_FAILURE);
}
if (commonData::kmerSize > CHARS2BITS(28))
{
cout << "ERROR: kmer-size cannot be greater than 28" << endl;
exit( EXIT_FAILURE );
}
}
if (IS_MATCH_REV_DEF(options) && IS_MATCH_BOTH_DEF(options)) {
cout << "ERROR: option -b and option -r exclude each other!" << endl;
exit(EXIT_FAILURE);
}
if(IS_RELREV_QUEPOS_DEF(options)) {
if (!IS_MATCH_REV_DEF(options) && !IS_MATCH_BOTH_DEF(options)) {
cout << "ERROR: option -c requires either option -r or - b" << endl;
exit( EXIT_FAILURE );
}
}
}
void print_help_msg()
{
cout << endl;
cout << "E-MEM Version 1.0.2, Dec. 12, 2017" << endl;
cout << "© 2014 Nilesh Khiste, Lucian Ilie" << endl;
cout << endl;
cout << "E-MEM finds and outputs the position and length of all maximal" << endl;
cout << "exact matches (MEMs) between <query-file> and <reference-file>" << endl;
cout << endl;
cout << "Usage: ../e-mem [options] <reference-file> <query-file>" << endl;
cout << endl;
cout << "Options:" << endl;
cout << "-n\t" << "match only the characters a, c, g, or t" << endl;
cout << " \tthey can be in upper or in lower case" << endl;
cout << "-l\t" << "set the minimum length of a match. The default length" << endl;
cout << " \tis 50" << endl;
cout << "-b\t" << "compute forward and reverse complement matches" << endl;
cout << "-r\t" << "only compute reverse complement matches" << endl;
cout << "-c\t" << "report the query-position of a reverse complement match" << endl;
cout << " \trelative to the original query sequence" << endl;
cout << "-F\t" << "force 4 column output format regardless of the number of" << endl;
cout << " \treference sequence input" << endl;
cout << "-L\t" << "show the length of the query sequences on the header line" << endl;
cout << "-d\t" << "set the split size. The default value is 1" << endl;
cout << "-t\t" << "number of threads. The default is 1 thread" << endl;
cout << "-h\t" << "show possible options" << endl;
}
int main (int argc, char *argv[])
{
int32_t i=0, n=1;
uint32_t options=0, revComplement=0;
seqFileReadInfo RefFile, QueryFile;
// Check Arguments
if (argc==1 || argc==2){
print_help_msg();
exit(EXIT_SUCCESS);
}
while(argv[n]) {
if(boost::equals(argv[n],"-l")){
if (IS_LENGTH_DEF(options)) {
cout << "ERROR: Length argument passed multiple times!" << endl;
exit(EXIT_FAILURE);
}
SET_LENGTH(options);
if (!argv[n+1] || !is_numeric(argv[n+1])){
cout << "ERROR: Invalid value for -l option!" << endl;
exit(EXIT_FAILURE);
}
commonData::minMemLen = 2*std::stoi(argv[n+1]);
n+=2;
}else if (boost::equals(argv[n],"-d")){
if (IS_SPLIT_SIZE_DEF(options)) {
cout << "ERROR: Split size argument passed multiple times!" << endl;
exit(EXIT_FAILURE);
}
if (!argv[n+1] || !is_numeric(argv[n+1])){
cout << "ERROR: Invalid value for -d option!" << endl;
exit(EXIT_FAILURE);
}
SET_SPLIT_SIZE(options);
commonData::d = std::stoi(argv[n+1]);
n+=2;
}else if (boost::equals(argv[n],"-t")){
if (IS_NUM_THREADS_DEF(options)) {
cout << "ERROR: Number of threads argument passed multiple times!" << endl;
exit(EXIT_FAILURE);
}
if (!argv[n+1] || !is_numeric(argv[n+1])){
cout << "ERROR: Invalid value for -t option!" << endl;
exit(EXIT_FAILURE);
}
SET_NUM_THREADS(options);
commonData::numThreads = std::stoi(argv[n+1]);
n+=2;
}else if (boost::equals(argv[n],"-k")){
if (IS_KMER_SIZE_DEF(options)) {
cout << "ERROR: Kmer size argument passed multiple times!" << endl;
exit(EXIT_FAILURE);
}
if (!argv[n+1] || !is_numeric(argv[n+1])){
cout << "ERROR: Invalid value for -k option!" << endl;
exit(EXIT_FAILURE);
}
SET_KMER_SIZE(options);
commonData::kmerSize = 2*std::stoi(argv[n+1]);
n+=2;
}else if (argv[n][0] != '-'){
/* These are files */
if (!IS_REF_FILE_DEF(options)) {
/* Open referencead file provided by the user. */
SET_REF_FILE(options);
RefFile.openFile(argv[n]);
n+=1;
continue;
}
if (!IS_QUERY_FILE_DEF(options)) {
/* Open query file provided by the user. */
SET_QUERY_FILE(options);
QueryFile.openFile(argv[n]);
n+=1;
continue;
}
cout << "ERROR: More input files than expected!" << endl;
exit(EXIT_FAILURE);
}else if (boost::equals(argv[n],"-r")){
if (IS_MATCH_REV_DEF(options)) {
cout << "ERROR: Reverse match argument passed multiple times!" << endl;
exit(EXIT_FAILURE);
}
SET_MATCH_REV(options);
n+=1;
}else if (boost::equals(argv[n],"-b")){
if (IS_MATCH_BOTH_DEF(options)) {
cout << "ERROR: option -b passed multiple times!" << endl;
exit(EXIT_FAILURE);
}
SET_MATCH_BOTH(options);
n+=1;
}else if (boost::equals(argv[n],"-n")){
if (IS_IGNORE_N_DEF(options)) {
cout << "ERROR: Ignore N's argument passed multiple times!" << endl;
exit(EXIT_FAILURE);
}
SET_IGNORE_N(options);
commonData::ignoreN = 1;
n+=1;
}else if (boost::equals(argv[n],"-c")){
if (IS_RELREV_QUEPOS_DEF(options)) {
cout << "ERROR: option -c passed multiple times!" << endl;
exit(EXIT_FAILURE);
}
SET_RELREV_QUEPOS(options);
n+=1;
commonData::relQueryPos = 1;
}else if (boost::equals(argv[n],"-F")){
if (IS_FCOL_OUTPUT_DEF(options)) {
cout << "ERROR: option -F passed multiple times!" << endl;
exit(EXIT_FAILURE);
}
SET_FCOL_OUTPUT(options);
n+=1;
commonData::fourColOutput = 1;
}else if (boost::equals(argv[n],"-L")){
if (IS_LEN_IN_HEADER_DEF(options)) {
cout << "ERROR: option -L passed multiple times!" << endl;
exit(EXIT_FAILURE);
}
SET_LEN_IN_HEADER(options);
n+=1;
commonData::lenInHeader = 1;
}else if (boost::equals(argv[n],"-mum")){
/* Ignore this option and continue */
n+=1;
}else if (boost::equals(argv[n],"-mumcand")){
/* Ignore this option and continue */
n+=1;
}else if (boost::equals(argv[n],"-mumreference")){
/* Ignore this option and continue */
n+=1;
}else if (boost::equals(argv[n],"-maxmatch")){
/* Ignore this option and continue */
n+=1;
}else if (boost::equals(argv[n],"-s")){
/* Ignore this option and continue */
n+=1;
}else if (boost::equals(argv[n],"-h")){
print_help_msg();
exit(EXIT_SUCCESS);
}else {
cout << "ERROR: Invalid option." << endl << flush;
print_help_msg();
exit( EXIT_FAILURE );
}
}
checkCommandLineOptions(options);
/*
* Check if e-mem if being run from QUAST
*/
sprintf(commonData::nucmer_path, "%s/%d_tmp", getenv("NUCMER_E_MEM_OUTPUT_DIRPATH")?getenv("NUCMER_E_MEM_OUTPUT_DIRPATH"):".",getpid());
tmpFilesInfo arrayTmpFile(IS_MATCH_BOTH_DEF(options)?(2*NUM_TMP_FILES+2):NUM_TMP_FILES+2);
arrayTmpFile.openFiles(ios::out|ios::binary, IS_MATCH_BOTH_DEF(options)?(2*NUM_TMP_FILES+2):NUM_TMP_FILES+2);
RefFile.generateRevComplement(0); // This routine also computers size and num sequences
QueryFile.generateRevComplement((IS_MATCH_REV_DEF(options) || IS_MATCH_BOTH_DEF(options))); // Reverse complement only for query
/* Only reverse complement matches */
if (IS_MATCH_REV_DEF(options)){
QueryFile.setReverseFile();
SET_MATCH_REV(revComplement);
}
arrayTmpFile.setNumMemsInFile(QueryFile.allocBinArray(), QueryFile.getNumSequences());
RefFile.allocBinArray();
RefFile.clearFileFlag();
while (true)
{
for (i=0; i<commonData::d; i++) {
if(RefFile.readChunks()){
processReference(RefFile, QueryFile, arrayTmpFile, revComplement);
RefFile.setCurrPos();
RefFile.clearMapForNs();
}
else
break;
}
/*
* Process MemExt list
*/
arrayTmpFile.mergeMemExtVector(revComplement);
if (revComplement)
break;
if (IS_MATCH_BOTH_DEF(options)){
SET_MATCH_BOTH(revComplement);
//revComplement=1;
RefFile.clearFileFlag();
RefFile.resetCurrPos();
RefFile.totalBases=0;
QueryFile.setReverseFile();
QueryFile.totalBases=0;
}
else
break;
}
/*
* Free up the allocated arrays
*/
arrayTmpFile.closeFiles(IS_MATCH_BOTH_DEF(options)?(2*NUM_TMP_FILES):NUM_TMP_FILES);
RefFile.destroy();
QueryFile.destroy();
/*
* Populate sequence information in vectors. Use this to get MEM
* positions relative to the original sequences.
*/
vector<seqData> refSeqInfo;
vector<seqData> querySeqInfo;
refSeqInfo.reserve(RefFile.getNumSequences());
querySeqInfo.reserve(QueryFile.getNumSequences());
RefFile.generateSeqPos(refSeqInfo);
QueryFile.generateSeqPos(querySeqInfo);
RefFile.closeFile();
QueryFile.closeFile();
arrayTmpFile.removeDuplicates(refSeqInfo, querySeqInfo, revComplement);
fflush(0);
return 0;
}