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MrFAST.c
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MrFAST.c
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/*
* Copyright (c) <2008 - 2020>, University of Washington, Simon Fraser University,
* Bilkent University and Carnegie Mellon University
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification,
* are permitted provided that the following conditions are met:
*
* Redistributions of source code must retain the above copyright notice, this list
* of conditions and the following disclaimer.
* - Redistributions in binary form must reproduce the above copyright notice, this
* list of conditions and the following disclaimer in the documentation and/or other
* materials provided with the distribution.
* - Neither the names of the University of Washington, Simon Fraser University,
* Bilkent University, Carnegie Mellon University,
* nor the names of its contributors may be
* used to endorse or promote products derived from this software without specific
* prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
* CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
* EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
* PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
* PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
* LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
* NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Authors:
Farhad Hormozdiari
farhadh AT uw DOT edu
Faraz Hach
fhach AT cs DOT sfu DOT ca
Can Alkan
calkan AT gmail DOT com
Hongyi Xin
gohongyi AT gmail DOT com
Donghyuk Lee
bleups AT gmail DOT com
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <dirent.h>
#include <xmmintrin.h>
#include <emmintrin.h>
#include <mmintrin.h>
#include "Common.h"
#include "Reads.h"
#include "HashTable.h"
#include "Output.h"
#include "MrFAST.h"
#include "RefGenome.h"
#define min(a,b) ((a)>(b)?(b):(a))
#define min3(a,b,c) ((a)>(b)?(b>c?c:b):(a>c?c:a))
#define CHARCODE(a) (a=='A' ? 0 : (a=='C' ? 1 : (a=='G' ? 2 : (a=='T' ? 3 : 4))))
double binomial_coefficient(int n, int k);
float calculateScore(int index, char *seq, char *qual, char *md);
unsigned char mrFAST = 1;
char *versionNumberF = "1.0";
long long verificationCnt = 0;
long long mappingCnt = 0;
long long mappedSeqCnt = 0;
long long completedSeqCnt = 0;
char *mappingOutput;
/**********************************************/
char *_msf_refGen = NULL;
int _msf_refGenLength = 0;
int _msf_refGenOffset = 0;
char *_msf_refGenName = NULL;
int _msf_refGenBeg;
int _msf_refGenEnd;
IHashTable *_msf_hashTable = NULL;
int *_msf_samplingLocs;
int *_msf_samplingLocsEnds;
int _msf_samplingLocsSize;
Read *_msf_seqList;
int _msf_seqListSize;
Pair *_msf_sort_seqList = NULL;
SAM _msf_output;
OPT_FIELDS *_msf_optionalFields;
char *_msf_op;
int *_msf_verifiedLocs = NULL;
char _msf_numbers[200][3];
char _msf_cigar[5];
MappingInfo *_msf_mappingInfo;
int *_msf_seqHits;
int _msf_openFiles = 0;
int _msf_maxLSize = 0;
int _msf_maxRSize = 0;
BestFullMappingInfo *bestHitMappingInfo;
/*************************/
int _msf_maxFile = 0;
char _msf_fileName[4000][200][2][FILE_NAME_LENGTH];
int _msf_fileCount[4000];
char *_msf_readHasConcordantMapping; //boolean if a read has concordant mapping
int *_msf_oeaMapping;
int *_msf_discordantMapping;
int scoreF[SEQ_MAX_LENGTH][SEQ_MAX_LENGTH];
int scoreB[SEQ_MAX_LENGTH][SEQ_MAX_LENGTH];
int score[SEQ_MAX_LENGTH][SEQ_MAX_LENGTH];
int direction1[SEQ_MAX_LENGTH][SEQ_MAX_LENGTH];
int direction2[SEQ_MAX_LENGTH][SEQ_MAX_LENGTH];
__m128i MASK;
/**************************************************Methods***************************************************/
int smallEditDistanceF(char *a, int lena, char *b, int lenb)
{
int matrix[20][20];
int i = 0;
int j = 0;
for(i = 0; i <= lena; i++)
{
matrix[0][i] = i;
}
for(i = 0; i <= lenb; i++)
{
matrix[i][0] = i;
}
for(i = 1; i <= lenb; i++)
{
for(j = 1; j <= lena; j++)
{
matrix[i][j] = min3(matrix[i-1][j-1]+ (a[j-1] != b[i-1]),matrix[i][j-1]+1 ,matrix[i-1][j]+1);
}
}
return (matrix[lenb][lena] > errThreshold ? -1 : matrix[lenb][lena]);
}
int smallEditDistanceB(char *a, int lena, char *b, int lenb)
{
int matrix[20][20];
int i = 0;
int j = 0;
for(i = 0; i <= lena; i++)
{
matrix[0][i] = i;
}
for(i = 0; i <= lenb; i++)
{
matrix[i][0] = i;
}
for(i = 1; i <= lenb; i++)
{
for(j = 1; j <= lena; j++)
{
matrix[i][j] = min3(matrix[i-1][j-1]+ (*(a-j+1) != *(b-i+1)),matrix[i][j-1]+1 ,matrix[i-1][j]+1);
}
}
return (matrix[lenb][lena] > errThreshold ? -1 : matrix[lenb][lena]);
}
void initLookUpTable()
{
int i = 0;
MASK = _mm_insert_epi16(MASK,1,0);
MASK = _mm_insert_epi16(MASK,1,1);
MASK = _mm_insert_epi16(MASK,1,2);
MASK = _mm_insert_epi16(MASK,1,3);
MASK = _mm_insert_epi16(MASK,1,4);
MASK = _mm_insert_epi16(MASK,0,5);
MASK = _mm_insert_epi16(MASK,0,6);
MASK = _mm_insert_epi16(MASK,0,7);
for(i = 0; i < errThreshold + 1; i++)
{
scoreF[0][i] = i;
scoreF[i][0] = i;
}
for(i = 0 ; i < errThreshold + 1; i++)
{
scoreB[0][i] = i;
scoreB[i][0] = i;
}
}
inline int backwardEditDistanceSSE2Extension(char *a, int lena, char *b,
int lenb) {
if (lenb == 0 || lena == 0)
return 0;
int i = 0;
int j = 0;
int k = 0;
int i0;
int i1;
int i2;
int i4;
int i5;
int e = 4;
int mismatch = errThreshold;
int minError = 2 * errThreshold;
int index = 0;
int tmpValue = 0;
if (lenb <= e) {
return smallEditDistanceB(a, lena, b, lenb);
}
__m128i R0, R1;
__m128i Diag;
__m128i Side1, Side2;
__m128i Down1, Down2;
__m128i tmp;
__m128i SeqA, SeqB;
__m128i Result;
/* initialize */
R0 = _mm_setzero_si128();
R1 = _mm_setzero_si128();
Diag = _mm_setzero_si128();
Side1 = _mm_setzero_si128();
Side2 = _mm_setzero_si128();
Down1 = _mm_setzero_si128();
Down2 = _mm_setzero_si128();
SeqA = _mm_setzero_si128();
SeqB = _mm_setzero_si128();
Result = _mm_setzero_si128();
/* end initialize */
R1 = _mm_xor_si128(R1, R1);
R0 = _mm_xor_si128(R0, R0);
Diag = _mm_xor_si128(Diag, Diag);
Diag = _mm_insert_epi16(Diag,minError,0);
i0 = (a[0] != b[0]);
i1 = min(i0, ( *(a-1)!=*b) ) + 1;
i2 = min(i0,( a[0] != *(b-1) ) ) + 1;
i0 = min3( i0+ ( *(a-1)!=*(b-1) ),i1+1,i2+1);
i4 = min(i1, ( *(a-2)!=b[0] )+1) + 1;
i5 = min(i2, (a[0] != *(b-2))+1) + 1;
R1 = _mm_insert_epi16(R1, 3, 0);
R1 = _mm_insert_epi16(R1, i1, 1);
R1 = _mm_insert_epi16(R1, i2, 2);
R1 = _mm_insert_epi16(R1, 3, 3);
R0 = _mm_insert_epi16(R0, 4, 0);
R0 = _mm_insert_epi16(R0, i4, 1);
R0 = _mm_insert_epi16(R0, i0, 2);
R0 = _mm_insert_epi16(R0, i5, 3);
R0 = _mm_insert_epi16(R0, 4, 4);
Side2 = _mm_xor_si128(Side2, Side2);
Down2 = _mm_xor_si128(Down2, Down2);
Down1 = _mm_xor_si128(Down1, Down1);
Side1 = _mm_xor_si128(Side1, Side1);
Side2 = _mm_insert_epi16(Side2,minError,0);
Down1 = _mm_insert_epi16(Down1,minError,0);
Side1 = _mm_insert_epi16(Side1,1,0);
index = 0;
for (j = 0; j < e; j++) {
Side2 = _mm_slli_si128(Side2, 2);
Side2 = _mm_insert_epi16(Side2,1,0);
Down1 = _mm_slli_si128(Down1, 2);
Down1 = _mm_insert_epi16(Down1,1,0);
Down2 = _mm_slli_si128(Down2, 2);
Down2 = _mm_insert_epi16(Down2,1,0);
Side1 = _mm_slli_si128(Side1, 2);
Side1 = _mm_insert_epi16(Side1,1,0);
SeqA = _mm_slli_si128(SeqA, 2);
SeqB = _mm_slli_si128(SeqB, 2);
SeqA = _mm_insert_epi16(SeqA,*(a-index),0);
SeqB = _mm_insert_epi16(SeqB,*(b-index),0);
index++;
}
Down2 = _mm_slli_si128(Down2, 2);
Down2 = _mm_insert_epi16(Down2,minError,0);
index = 4;
i = 5;
int loopEnd = 2 * lenb - (e - 1);
for (; i <= loopEnd; i++) {
Diag = _mm_xor_si128(Diag, Diag);
if (i % 2 == 0) {
SeqA = _mm_slli_si128(SeqA, 2);
SeqB = _mm_slli_si128(SeqB, 2);
SeqA = _mm_insert_epi16(SeqA,*(a-(index)),0);
SeqB = _mm_insert_epi16(SeqB,*(b-(index)),0);
index++;
tmp = _mm_shufflelo_epi16(SeqB,27);
tmp = _mm_slli_si128(tmp, 2);
tmpValue = _mm_extract_epi16(tmp, 5);
tmp = _mm_insert_epi16(tmp, tmpValue, 0);
Result = _mm_cmpeq_epi16(SeqA, tmp);
Diag = _mm_andnot_si128(Result, MASK);
R0 = _mm_min_epi16(_mm_add_epi16(R1,Side2), _mm_add_epi16(R0,Diag));
R0 = _mm_min_epi16(R0, _mm_add_epi16(_mm_slli_si128(R1,2) ,Down2));
if (_mm_extract_epi16(R0, 0) > errThreshold
&& _mm_extract_epi16(R0, 1) > errThreshold
&& _mm_extract_epi16(R0, 2) > errThreshold
&& _mm_extract_epi16(R0, 3) > errThreshold
&& _mm_extract_epi16(R0, 4) > errThreshold
&& _mm_extract_epi16(R1, 0) > errThreshold
&& _mm_extract_epi16(R1, 1) > errThreshold
&& _mm_extract_epi16(R1, 2) > errThreshold
&& _mm_extract_epi16(R1, 3) > errThreshold)
return -1;
if (i == 2 * lenb - e) {
tmp = _mm_srli_si128(R0,2);
for (k = 0; k < e - 1; k++)
tmp = _mm_srli_si128(tmp,2);
minError = _mm_extract_epi16(tmp,0);
}
}
else {
Result = _mm_cmpeq_epi16(SeqA, _mm_shufflelo_epi16(SeqB,27));
Diag = _mm_andnot_si128(Result, MASK);
R1 = _mm_min_epi16(_mm_add_epi16(_mm_srli_si128(R0,2),Side1), _mm_add_epi16(R1,Diag));
R1 = _mm_min_epi16(R1, _mm_add_epi16(R0 ,Down1));
if (i >= 2 * lenb - e) {
tmp = _mm_srli_si128(R1,2);
for (k = 0; k < e - 2; k++)
tmp = _mm_srli_si128(tmp,2);
minError = min(minError, _mm_extract_epi16(tmp,0));
}
}
}
j = 0;
int tmpE = e;
for (; j < 2 * (e - 2) + 1; j++) {
Diag = _mm_xor_si128(Diag, Diag);
//set the first element
if (j == 0) {
for (k = 0; k <= e - 1; k++) {
Diag = _mm_slli_si128(Diag, 2);
Diag =
_mm_insert_epi16(Diag, *(b-(lenb-1-k)) != *(a-((i-lenb)-1+k)),0);
}
R0 = _mm_min_epi16(_mm_add_epi16(R1,Side2), _mm_add_epi16(R0,Diag));
R0 = _mm_min_epi16(R0, _mm_add_epi16(_mm_slli_si128(R1,2) ,Down2));
tmpE--;
tmp = _mm_srli_si128(R0,2);
for (k = 0; k < e - 2; k++)
tmp = _mm_srli_si128(tmp,2);
minError = min(minError, _mm_extract_epi16(tmp,0));
} else if (j % 2 == 0) {
for (k = 0; k < tmpE; k++) {
Diag = _mm_slli_si128(Diag, 2);
Diag =
_mm_insert_epi16(Diag, *(b-(lenb-1-k)) != *(a-((i-lenb)-1+k)),0);
}
R0 = _mm_min_epi16(_mm_add_epi16(R1,Side2), _mm_add_epi16(R0,Diag));
R0 = _mm_min_epi16(R0, _mm_add_epi16(_mm_slli_si128(R1,2) ,Down2));
tmpE--;
tmp = _mm_srli_si128(R0,2);
for (k = 0; k < tmpE - 1; k++)
tmp = _mm_srli_si128(tmp,2);
minError = min(minError, _mm_extract_epi16(tmp,0));
}
else {
for (k = 0; k < tmpE; k++) {
Diag = _mm_slli_si128(Diag, 2);
Diag =
_mm_insert_epi16(Diag, *(b-(lenb-1-k)) != *(a-((i-lenb)-1+k)),0);
}
R1 = _mm_min_epi16(_mm_add_epi16(_mm_srli_si128(R0,2),Side1), _mm_add_epi16(R1,Diag));
R1 = _mm_min_epi16(R1, _mm_add_epi16(R0 ,Down1));
tmp = _mm_srli_si128(R1,2);
for (k = 0; k < tmpE - 2; k++)
tmp = _mm_srli_si128(tmp,2);
minError = min(minError, _mm_extract_epi16(tmp,0));
}
i++;
}
//Diag
Diag = _mm_xor_si128(Diag, Diag);
Diag = _mm_insert_epi16(Diag, 2*errThreshold, 0);
Diag = _mm_insert_epi16(Diag, *(a-(lenb+e-2)) != *(b-(lenb-1)), 1);
Side1 = _mm_insert_epi16(Side1,1,0);
Side1 = _mm_insert_epi16(Side1,1,1);
Down1 = _mm_insert_epi16(Down1, 2*errThreshold, 0);
Down1 = _mm_insert_epi16(Down1, 1, 1);
R1 = _mm_min_epi16(_mm_add_epi16(R0,Side1), _mm_add_epi16(_mm_slli_si128(R1,2),Diag));
R1 = _mm_min_epi16(R1, _mm_add_epi16(_mm_slli_si128(R0,2),Down1));
minError = min(minError, _mm_extract_epi16(R1,1));
Diag = _mm_insert_epi16(Diag, *(a-(lenb+e-1)) != *(b-(lenb-1)), 0);
Down1 = _mm_insert_epi16(Down1, 1, 0);
R0 = _mm_min_epi16(_mm_add_epi16(R1,Down1), _mm_add_epi16(R0,Diag));
R0 = _mm_min_epi16(R0, _mm_add_epi16(_mm_srli_si128(R1,2) ,Side1));
minError = min(minError, _mm_extract_epi16(R0,0));
if (minError > mismatch)
return -1;
return minError;
}
inline int forwardEditDistanceSSE2Extension(char *a, int lena, char *b,
int lenb) {
if (lenb == 0 || lena == 0)
return 0;
int i = 0;
int j = 0;
int k = 0;
int i0 = 0;
int i1 = 0;
int i2 = 0;
int i4 = 0;
int i5 = 0;
int mismatch = errThreshold;
int e = 4;
int minError = 4 * mismatch + 1;
int index = 0;
int tmpValue = 0;
if (lenb <= e) {
return smallEditDistanceF(a, lena, b, lenb);
}
register __m128i R0, R1;
__m128i Diag;
__m128i Side1, Side2;
__m128i Down1, Down2;
__m128i tmp;
register __m128i SeqA, SeqB;
__m128i Result;
__m128i tmpSeqA;
__m128i tmpSeqB;
/* initialize */
R0 = _mm_setzero_si128();
R1 = _mm_setzero_si128();
Diag = _mm_setzero_si128();
Side1 = _mm_setzero_si128();
Side2 = _mm_setzero_si128();
Down1 = _mm_setzero_si128();
Down2 = _mm_setzero_si128();
SeqA = _mm_setzero_si128();
SeqB = _mm_setzero_si128();
Result = _mm_setzero_si128();
/* end initialize */
R1 = _mm_xor_si128(R1, R1);
R0 = _mm_xor_si128(R0, R0);
Diag = _mm_xor_si128(Diag, Diag);
Diag = _mm_insert_epi16(Diag,minError,0);
i0 = (a[0] != b[0]);
i1 = min(i0, (a[1]!=b[0])) + 1;
i2 = min(i0,(a[0]!=b[1])) + 1;
i0 = min3(i0+(a[1]!=b[1]),i1+1,i2+1);
i4 = min(i1, (a[2]!=b[0])+1) + 1;
i5 = min(i2, (a[0]!=b[2])+1) + 1;
R1 = _mm_insert_epi16(R1, 3, 0);
R1 = _mm_insert_epi16(R1, i1, 1);
R1 = _mm_insert_epi16(R1, i2, 2);
R1 = _mm_insert_epi16(R1, 3, 3);
R0 = _mm_insert_epi16(R0, 4, 0);
R0 = _mm_insert_epi16(R0, i4, 1);
R0 = _mm_insert_epi16(R0, i0, 2);
R0 = _mm_insert_epi16(R0, i5, 3);
R0 = _mm_insert_epi16(R0, 4, 4);
Side2 = _mm_xor_si128(Side2, Side2);
Down2 = _mm_xor_si128(Down2, Down2);
Down1 = _mm_xor_si128(Down1, Down1);
Side1 = _mm_xor_si128(Side1, Side1);
Side2 = _mm_insert_epi16(Side2,minError,0);
Down1 = _mm_insert_epi16(Down1,minError,0);
Side1 = _mm_insert_epi16(Side1,1,0);
index = 0;
for (j = 0; j < e; j++) {
Side2 = _mm_slli_si128(Side2, 2);
Side2 = _mm_insert_epi16(Side2,1,0);
Down1 = _mm_slli_si128(Down1, 2);
Down1 = _mm_insert_epi16(Down1,1,0);
Down2 = _mm_slli_si128(Down2, 2);
Down2 = _mm_insert_epi16(Down2,1,0);
Side1 = _mm_slli_si128(Side1, 2);
Side1 = _mm_insert_epi16(Side1,1,0);
SeqA = _mm_slli_si128(SeqA, 2);
SeqB = _mm_slli_si128(SeqB, 2);
SeqA = _mm_insert_epi16(SeqA,a[index],0);
SeqB = _mm_insert_epi16(SeqB,b[index],0);
index++;
}
Down2 = _mm_slli_si128(Down2, 2);
Down2 = _mm_insert_epi16(Down2,minError,0);
index = 4;
i = 5;
int loopEnd = 2 * lenb - (e - 1);
for (; i <= loopEnd; i++) {
if (i % 2 == 0) {
tmpSeqA = _mm_slli_si128(SeqA, 2);
tmpSeqB = _mm_slli_si128(SeqB, 2);
SeqA = _mm_insert_epi16(tmpSeqA,a[index],0);
SeqB = _mm_insert_epi16(tmpSeqB,b[index],0);
index++;
tmp = _mm_shufflelo_epi16(SeqB,27);
tmp = _mm_slli_si128(tmp, 2);
tmpValue = _mm_extract_epi16(tmp, 5);
tmp = _mm_insert_epi16(tmp, tmpValue, 0);
Result = _mm_cmpeq_epi16(SeqA, tmp);
Diag = _mm_andnot_si128(Result, MASK);
R0 = _mm_min_epi16(_mm_add_epi16(R1,Side2), _mm_add_epi16(R0,Diag));
R0 = _mm_min_epi16(R0, _mm_add_epi16(_mm_slli_si128(R1,2) ,Down2));
if (_mm_extract_epi16(R0, 0) > errThreshold
&& _mm_extract_epi16(R0, 1) > errThreshold
&& _mm_extract_epi16(R0, 2) > errThreshold
&& _mm_extract_epi16(R0, 3) > errThreshold
&& _mm_extract_epi16(R0, 4) > errThreshold
&& _mm_extract_epi16(R1, 0) > errThreshold
&& _mm_extract_epi16(R1, 1) > errThreshold
&& _mm_extract_epi16(R1, 2) > errThreshold
&& _mm_extract_epi16(R1, 3) > errThreshold)
return -1;
if (i == 2 * lenb - e) {
tmp = _mm_srli_si128(R0,2);
for (k = 0; k < e - 1; k++)
tmp = _mm_srli_si128(tmp,2);
minError = _mm_extract_epi16(tmp,0);
}
}
else {
Result = _mm_cmpeq_epi16(SeqA, _mm_shufflelo_epi16(SeqB,27));
Diag = _mm_andnot_si128(Result, MASK);
R1 = _mm_min_epi16(_mm_add_epi16(_mm_srli_si128(R0,2),Side1), _mm_add_epi16(R1,Diag));
R1 = _mm_min_epi16(R1, _mm_add_epi16(R0 ,Down1));
if (i >= 2 * lenb - e) {
tmp = _mm_srli_si128(R1,2);
for (k = 0; k < e - 2; k++)
tmp = _mm_srli_si128(tmp,2);
minError = min(minError, _mm_extract_epi16(tmp,0));
}
}
}
j = 0;
int tmpE = e;
for (; j < 2 * (e - 2) + 1; j++) {
Diag = _mm_xor_si128(Diag, Diag);
//set the first element
if (j == 0) {
for (k = 0; k <= e - 1; k++) {
Diag = _mm_slli_si128(Diag, 2);
Diag = _mm_insert_epi16(Diag, b[lenb-1-k] != a[(i-lenb)-1+k],0);
}
R0 = _mm_min_epi16(_mm_add_epi16(R1,Side2), _mm_add_epi16(R0,Diag));
R0 = _mm_min_epi16(R0, _mm_add_epi16(_mm_slli_si128(R1,2) ,Down2));
tmpE--;
tmp = _mm_srli_si128(R0,2);
for (k = 0; k < e - 2; k++)
tmp = _mm_srli_si128(tmp,2);
minError = min(minError, _mm_extract_epi16(tmp,0));
} else if (j % 2 == 0) {
for (k = 0; k < tmpE; k++) {
Diag = _mm_slli_si128(Diag, 2);
Diag = _mm_insert_epi16(Diag, b[lenb-1-k] != a[(i-lenb)-1+k],0);
}
R0 = _mm_min_epi16(_mm_add_epi16(R1,Side2), _mm_add_epi16(R0,Diag));
R0 = _mm_min_epi16(R0, _mm_add_epi16(_mm_slli_si128(R1,2) ,Down2));
tmpE--;
tmp = _mm_srli_si128(R0,2);
for (k = 0; k < tmpE - 1; k++)
tmp = _mm_srli_si128(tmp,2);
minError = min(minError, _mm_extract_epi16(tmp,0));
}
else {
for (k = 0; k < tmpE; k++) {
Diag = _mm_slli_si128(Diag, 2);
Diag = _mm_insert_epi16(Diag, b[lenb-1-k] != a[(i-lenb)-1+k],0);
}
R1 = _mm_min_epi16(_mm_add_epi16(_mm_srli_si128(R0,2),Side1), _mm_add_epi16(R1,Diag));
R1 = _mm_min_epi16(R1, _mm_add_epi16(R0 ,Down1));
tmp = _mm_srli_si128(R1,2);
for (k = 0; k < tmpE - 2; k++)
tmp = _mm_srli_si128(tmp,2);
minError = min(minError, _mm_extract_epi16(tmp,0));
}
i++;
}
//Diag
Diag = _mm_xor_si128(Diag, Diag);
Diag = _mm_insert_epi16(Diag, minError, 0);
Diag = _mm_insert_epi16(Diag, a[lenb+e-2] != b[lenb-1], 1);
Side1 = _mm_insert_epi16(Side1,1,0);
Side1 = _mm_insert_epi16(Side1,1,1);
Down1 = _mm_insert_epi16(Down1, minError, 0);
Down1 = _mm_insert_epi16(Down1, 1, 1);
R1 = _mm_min_epi16(_mm_add_epi16(R0,Side1), _mm_add_epi16(_mm_slli_si128(R1,2),Diag));
R1 = _mm_min_epi16(R1, _mm_add_epi16(_mm_slli_si128(R0,2),Down1));
minError = min(minError, _mm_extract_epi16(R1,1));
Diag = _mm_insert_epi16(Diag, a[lenb+e-1] != b[lenb-1], 0);
Down1 = _mm_insert_epi16(Down1, 1, 0);
R0 = _mm_min_epi16(_mm_add_epi16(R1,Down1), _mm_add_epi16(R0,Diag));
R0 = _mm_min_epi16(R0, _mm_add_epi16(_mm_srli_si128(R1,2) ,Side1));
minError = min(minError, _mm_extract_epi16(R0,0));
if (minError > mismatch)
return -1;
return minError;
}
void initBestMapping(int totalReadNumber)
{
int i = 0;
bestHitMappingInfo = getMem(totalReadNumber * sizeof(BestFullMappingInfo));
for (i = 0; i < totalReadNumber; i++) {
bestHitMappingInfo[i].loc = -1;
bestHitMappingInfo[i].tprob = 0.0;
}
}
void finalizeBestSingleMapping()
{
int i = 0;
char *_tmpQual, *_tmpSeq;
char rqual[SEQ_LENGTH + 1];
rqual[SEQ_LENGTH] = '\0';
for(i = 0; i < _msf_seqListSize; i++)
{
if(_msf_seqList[i].hits[0] != 0)
{
if (bestHitMappingInfo[i].dir)
{
reverse(_msf_seqList[i].qual, rqual, SEQ_LENGTH);
_tmpQual = rqual;
_tmpSeq = _msf_seqList[i].rseq;
}
else
{
_tmpQual = _msf_seqList[i].qual;
_tmpSeq = _msf_seqList[i].seq;
}
_msf_output.QNAME = _msf_seqList[i].name;
_msf_output.FLAG = 16 * bestHitMappingInfo[i].dir;
_msf_output.RNAME = bestHitMappingInfo[i].chr;
_msf_output.POS = bestHitMappingInfo[i].loc;
if (seqFastq)
_msf_output.MAPQ = mapQ(i);
else
_msf_output.MAPQ = 255;
_msf_output.CIGAR = bestHitMappingInfo[i].cigar;
_msf_output.MRNAME = "*";
_msf_output.MPOS = 0;
_msf_output.ISIZE = 0;
_msf_output.SEQ = _tmpSeq;
_msf_output.QUAL = _tmpQual;
_msf_output.optSize = 2;
_msf_output.optFields = _msf_optionalFields;
_msf_optionalFields[0].tag = "NM";
_msf_optionalFields[0].type = 'i';
_msf_optionalFields[0].iVal = bestHitMappingInfo[i].err;
_msf_optionalFields[1].tag = "MD";
_msf_optionalFields[1].type = 'Z';
_msf_optionalFields[1].sVal = bestHitMappingInfo[i].md;
output(_msf_output);
}
}
freeMem(bestHitMappingInfo, _msf_seqListSize * sizeof(FullMappingInfo));
}
/**********************************************/
int compare(const void *a, const void *b) {
return ((Pair *) a)->hv - ((Pair *) b)->hv;
}
/**********************************************/
void preProcessReads() {
int i = 0;
_msf_sort_seqList = getMem(_msf_seqListSize * sizeof(Pair));
for (i = 0; i < _msf_seqListSize; i++) {
_msf_sort_seqList[i].hv = hashVal(_msf_seqList[i].seq);
_msf_sort_seqList[i].readNumber = i;
}
qsort(_msf_sort_seqList, _msf_seqListSize, sizeof(Pair), compare);
}
/**********************************************/
int verifySingleEnd(int index, char* seq, int offset) {
int curOff = 0;
int i;
char *ref;
int err;
int errCnt = 0;
int errCntOff = 0;
int NCntOff = 0;
ref = _msf_refGen + index - 1;
verificationCnt++;
for (i = 0; i < SEQ_LENGTH; i++) {
err = *ref != *seq;
errCnt += err;
if (errCnt > errThreshold) {
return -1;
}
if (i >= _msf_samplingLocs[curOff]
&& i <= _msf_samplingLocsEnds[curOff]) {
errCntOff += err;
NCntOff += (*seq == 'N');
} else if (curOff < _msf_samplingLocsSize
&& i >= _msf_samplingLocs[curOff + 1]) {
if (errCntOff == 0 && NCntOff == 0 && offset > curOff) {
return -1;
}
errCntOff = 0;
NCntOff = 0;
curOff++;
if (i >= _msf_samplingLocs[curOff]) {
errCntOff += err;
NCntOff += (*seq == 'N');
}
}
ref++;
seq++;
}
return errCnt;
}
/*********************************************/
void initFAST(Read *seqList, int seqListSize, int *samplingLocs,
int samplingLocsSize, char *genFileName) {
int i;
if (_msf_optionalFields == NULL) {
_msf_op = getMem(SEQ_LENGTH);
if (pairedEndMode) {
_msf_optionalFields = getMem(8 * sizeof(OPT_FIELDS));
} else {
_msf_optionalFields = getMem(2 * sizeof(OPT_FIELDS));
}
for (i = 0; i < 200; i++) {
sprintf(_msf_numbers[i], "%d%c", i, '\0');
}
sprintf(_msf_cigar, "%dM", SEQ_LENGTH);
}
if (_msf_samplingLocsEnds == NULL) {
_msf_samplingLocs = samplingLocs;
_msf_samplingLocsSize = samplingLocsSize;
_msf_samplingLocsEnds = getMem(sizeof(int) * _msf_samplingLocsSize);
for (i = 0; i < _msf_samplingLocsSize; i++) {
_msf_samplingLocsEnds[i] = _msf_samplingLocs[i] + WINDOW_SIZE - 1;
}
_msf_seqList = seqList;
_msf_seqListSize = seqListSize;
preProcessReads();
_msf_oeaMapping = getMem(_msf_seqListSize * sizeof(int));
for (i = 0; i < _msf_seqListSize; i++) {
_msf_oeaMapping[i] = 0;
}
_msf_discordantMapping = getMem(_msf_seqListSize * sizeof(int));
for (i = 0; i < _msf_seqListSize; i++) {
_msf_discordantMapping[i] = 0;
}
}
if (_msf_refGenName == NULL) {
_msf_refGenName = getMem(4 * SEQ_LENGTH);
}
_msf_refGen = getRefGenome();
_msf_refGenLength = strlen(_msf_refGen);
_msf_refGenOffset = getRefGenomeOffset();
snprintf(_msf_refGenName, 4 * SEQ_LENGTH, "%s%c", getRefGenomeName(), '\0');
_msf_refGenName[strlen(getRefGenomeName())] = '\0';
if (_msf_verifiedLocs != NULL) {
freeMem(_msf_verifiedLocs, sizeof(int) * (_msf_refGenLength + 1));
}
_msf_verifiedLocs = (int *) getMem(sizeof(int) * (_msf_refGenLength + 1));
for (i = 0; i <= _msf_refGenLength; i++)
_msf_verifiedLocs[i] = _msf_seqListSize * 10 + 1;
if (pairedEndMode && _msf_seqHits == NULL) {
_msf_mappingInfo = getMem(seqListSize * sizeof(MappingInfo));
for (i = 0; i < seqListSize; i++) {
_msf_mappingInfo[i].next = NULL;
_msf_mappingInfo[i].size = 0;
}
_msf_seqHits = getMem((_msf_seqListSize) * sizeof(int));
for (i = 0; i < _msf_seqListSize; i++) {
_msf_seqHits[i] = 0;
}
_msf_readHasConcordantMapping = getMem(
_msf_seqListSize / 2 * sizeof(char));
for (i = 0; i < _msf_seqListSize / 2; i++) {
_msf_readHasConcordantMapping[i] = 0;
}
initLoadingRefGenome(genFileName);
}
if (_msf_refGenOffset == 0) {
_msf_refGenBeg = 1;
} else {
_msf_refGenBeg = CONTIG_OVERLAP - SEQ_LENGTH + 2 + errThreshold;
}
_msf_refGenEnd = _msf_refGenLength - SEQ_LENGTH + 1;
}
/**********************************************/
void finalizeFAST() {
freeMem(_msf_seqHits, (_msf_seqListSize) * sizeof(int));
freeMem(_msf_refGenName, 4 * SEQ_LENGTH);
freeMem(_msf_sort_seqList, sizeof(int) * _msf_seqListSize);
}
int verifySingleEndEditDistanceExtension(int refIndex, char *lSeq,
int lSeqLength, char *rSeq, int rSeqLength, int segLength, char *matrix,
int *map_location) {
int i = 0;
char * ref;
char * tempref;
int rIndex = 0; //reference Index
int error = 0;
int error1 = 0;
int error2 = 0;
int error3 = 0;
int totalError = 0;
//int errorSegment = 0;
int ERROR_BOUND = min(4, errThreshold);
/*
1: Up
2: Side
3: Diagonal Match