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test.c
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test.c
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/*
* Copyright (c) <2008 - 2020>, University of Washington, Simon Fraser University, Bilkent 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,
* 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
Faraz Hach
Can Alkan
Emails:
farhadh AT uw DOT edu
fhach AT cs DOT sfu DOT ca
calkan AT cs DOT bilkent DOT edu DOT tr
*/
#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 "SirFAST.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))))
#define MAX_REF_SIZE 18
#define KEY_LENGTH 10 // sirfast
#define KEY_LENGTH0 5 // sirfast
#define INDEL_GAP 3 // sirfast
#define EXPECTED_GAP 2 // sirfast
#define INITIAL_GAP01 -1 // sirfast
#define INITIAL_GAP12 0 // sirfast
#define INITIAL_GAP23 5 // sirfast
#define DEBUG 2
double binomial_coefficient(int n, int k);
float calculateScore(int index, char *seq, char *qual, char *md);
unsigned char mrFAST = 1;
char *versionNumberF = "0.1";
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;
ReadCG *_msf_seqListCG; // sirFAST
int _msf_seqListSize;
Pair *_msf_sort_seqList = NULL;
int *_msf_map_sort_seqList;
ReadIndexTable *_msf_rIndex = NULL;
int _msf_rIndexSize;
int _msf_rIndexMax;
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 counter = 0;
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]);
}
char fastEditDistance(int per1, int per2)
{
int i = 0;
int j = 0;
char str1[7];
char str2[7];
int val1 = per1;
int val2 = per2;
int index = 0;
int mod = 0;
int matrix[7][7];
int min = 20;
while(index < 6)
{
mod = val1 % 5;
str1[5-index] = (mod==0 ? 'A':(mod==1?'C':mod==2?'G':(mod==3)?'T':'N'));
val1 = val1 / 5;
index++;
}
str1[6] = '\0';
index = 0;
while(index < 6)
{
mod = val2 % 5;
str2[5-index] = (mod==0 ? 'A':(mod==1?'C':mod==2?'G':(mod==3)?'T':'N'));
val2 = val2 / 5;
index++;
}
str2[6] = '\0';
for(i = 0; i < 7; i++)
{
matrix[0][i] = i;
matrix[i][0] = i;
}
for(i = 1; i < 7; i++)
{
for(j = 1; j < 7; j++)
{
matrix[i][j] = min3(matrix[i-1][j-1]+ (str1[i-1] != str2[j-1]),matrix[i][j-1]+1 ,matrix[i-1][j]+1);
}
}
for(i = 0; i < 7; i++)
{
if (matrix[i][6] < min)
min = matrix[i][6];
}
for(i = 0; i < 7; i++)
{
if (matrix[6][i] < min)
min = matrix[6][i];
}
return min;
}
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;
}
}
int backwardEditDistanceSSE2Odd(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 e = errThreshold;
char flag = 0;
int minError = 2 * e;
__m128i R0, R1;
__m128i Diag;
__m128i Side1, Side2;
__m128i Down1, Down2;
__m128i Error;
__m128i tmp;
/* 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();
Error = _mm_setzero_si128();
tmp = _mm_setzero_si128();
/* end initialize */
if(lenb <= e)
{
return smallEditDistanceB(a, lena, b, lenb);
}
R1 = _mm_xor_si128(R1, R1);
R0 = _mm_xor_si128(R0, R0);
Diag = _mm_xor_si128(Diag, Diag);
Side1 = _mm_xor_si128(Side1, Side1);
Down1 = _mm_xor_si128(Down1, Down1);
Diag = _mm_insert_epi16(Diag,2*e,0);
Side1 = _mm_insert_epi16(Side1,1,0);
Side1 = _mm_insert_epi16(Side1,2*e,1);
Down1 = _mm_insert_epi16(Down1,2*e,0);
Down1 = _mm_insert_epi16(Down1,1,1);
Down1 = _mm_insert_epi16(Down1,2*e,2);
R0 = _mm_insert_epi16(R0,0,0);
R1 = _mm_insert_epi16(R1,1,0);
R1 = _mm_insert_epi16(R1,1,1);
for(i = 2; i <= e; i++)
{
//set side
Side1 = _mm_slli_si128(Side1,2);
Side1 = _mm_insert_epi16(Side1,1,0);
Down1 = _mm_insert_epi16(Down1,1,0);
Down1 = _mm_slli_si128(Down1,2);
Down1 = _mm_insert_epi16(Down1,2*e,0);
Diag = _mm_xor_si128(Diag, Diag);
if (i % 2 == 0) {
Diag = _mm_insert_epi16(Diag,2*e,0);
for (j = 1; j <= i - 1; j++) {
Diag = _mm_slli_si128(Diag, 2);
Diag =
_mm_insert_epi16(Diag, *(b-(i/2-1+(i/2-j))) != *(a-(i/2-1-(i/2-j))),0);
}
Diag = _mm_slli_si128(Diag, 2);
Diag = _mm_insert_epi16(Diag, 2*e,0);
R0 = _mm_min_epi16(R1 + Side1, _mm_slli_si128(R0,2) + Diag);
R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2) + Down1);
}
else {
Diag = _mm_insert_epi16(Diag,2*e,0);
for (j = i / 2 - 1; j >= -i / 2; j--) {
Diag = _mm_slli_si128(Diag, 2);
Diag =
_mm_insert_epi16(Diag, *(b-((i+1)/2+j-1)) != *(a-((i-1)/2-j-1)),0);
}
Diag = _mm_slli_si128(Diag, 2);
Diag = _mm_insert_epi16(Diag, 2*e,0);
R1 = _mm_min_epi16(R0 + Side1, _mm_slli_si128(R1,2) + Diag);
R1 = _mm_min_epi16(R1, _mm_slli_si128(R0,2) + Down1);
}
}
Error = _mm_xor_si128(Error, Error);
Side2 = _mm_xor_si128(Side2, Side2);
Down2 = _mm_xor_si128(Down2, Down2);
Down1 = _mm_xor_si128(Down1, Down1);
Error = _mm_insert_epi16(Error,e,0);
Side1 = _mm_insert_epi16(Side2,2*e,0);
Side2 = _mm_insert_epi16(Side2,2*e,0);
Down1 = _mm_insert_epi16(Down1,2*e,0);
for (j = 0; j < e; j++) {
Side2 = _mm_slli_si128(Side2, 2);
Side2 = _mm_insert_epi16(Side2,1,0);
Side1 = _mm_slli_si128(Side1, 2);
Side1 = _mm_insert_epi16(Side1,1,0);
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);
Error = _mm_slli_si128(Error, 2);
Error = _mm_insert_epi16(Error, e, 0);
}
Down2 = _mm_slli_si128(Down2, 2);
Down2 = _mm_insert_epi16(Down2,2*e,0);
for (; i <= 2 * lenb - (e - 1); i++) {
flag = 0;
Diag = _mm_xor_si128(Diag, Diag);
if (i % 2 == 0) {
for (j = e / 2; j >= -e / 2; j--) {
Diag = _mm_slli_si128(Diag, 2);
Diag =
_mm_insert_epi16(Diag, *(b-(i/2-1+j)) != *(a-(i/2-1-j)),0);
}
R0 = _mm_min_epi16(_mm_srli_si128(R1,2) + Side1, R0 + Diag);
R0 = _mm_min_epi16(R0, R1 + Down1);
if (_mm_extract_epi16(R0,0) <= e)
flag = 1;
tmp = _mm_srli_si128(R0,2);
for (j = 0; j <= e; j++) {
if (_mm_extract_epi16(tmp,0) <= e)
flag = 1;
tmp = _mm_srli_si128(tmp,2);
}
if (_mm_extract_epi16(R1,1) <= e)
flag = 1;
tmp = _mm_srli_si128(R1,2);
for (j = 0; j < e-1; j++) {
if (_mm_extract_epi16(tmp,0) <= e)
flag = 1;
tmp = _mm_srli_si128(tmp,2);
}
if (flag == 0)
return -1;
/* farhad: lenb1 */
if (i == 2 * lenb - (e - 1)) {
tmp = _mm_srli_si128(R0,2);
for (k = 0; k < e - 2; k++)
tmp = _mm_srli_si128(tmp,2);
minError = _mm_extract_epi16(tmp,0);
}
}
else {
for (j = e / 2; j >= -e / 2 - 1; j--) {
Diag = _mm_slli_si128(Diag, 2);
Diag =
_mm_insert_epi16(Diag, *(b-((i+1)/2+j-1)) != *(a-((i)/2-j-1)),0);
}
R1 = _mm_min_epi16(R0 + Side2, R1 + Diag);
R1 = _mm_min_epi16(R1, _mm_slli_si128(R0,2) + Down2);
/* farhad: lenb2 */
if (i >= 2 * lenb - e) {
tmp = _mm_srli_si128(R1,2);
for (k = 0; k < e - 1; k++)
tmp = _mm_srli_si128(tmp,2);
minError = min(minError, _mm_extract_epi16(tmp,0));
}
}
}
//first cell
Diag = _mm_xor_si128(Diag, Diag);
Diag = _mm_insert_epi16(Diag, *(b-(lenb-3)) != *(a-lena), 0);
Diag = _mm_insert_epi16(Diag, *(b-(lenb-2)) != *(a-(lena-1)), 1);
Diag = _mm_insert_epi16(Diag, *(b-(lenb-1)) != *(a-(lena-2)), 2);
Diag = _mm_insert_epi16(Diag, 2*e, 3);
R1 = _mm_min_epi16(R0 + Side2, R1 + Diag);
R1 = _mm_min_epi16(R1, _mm_slli_si128(R0,2) + Down2);
minError = min(minError, _mm_extract_epi16(R1,2));
//second cell
Diag = _mm_xor_si128(Diag, Diag);
Diag = _mm_insert_epi16(Diag, *(b-(lenb-2)) != *(a-(lena)), 0);
Diag = _mm_insert_epi16(Diag, *(b-(lenb-1)) != *(a-(lena-1)), 1);
Diag = _mm_insert_epi16(Diag, 2*e, 2);
R0 = _mm_min_epi16(_mm_srli_si128(R1,2) + Side1, R0 + Diag);
R0 = _mm_min_epi16(R0, R1 + Down1);
minError = min(minError, _mm_extract_epi16(R0,1));
//third cell
Diag = _mm_xor_si128(Diag, Diag);
Diag = _mm_insert_epi16(Diag, *(b-(lenb-2)) != *(a-(lena+1)), 0);
Diag = _mm_insert_epi16(Diag, *(b-(lenb-1)) != *(a-(lena)), 1);
Diag = _mm_insert_epi16(Diag, 2*e, 2);
R1 = _mm_min_epi16(R0 + Side2, R1 + Diag);
R1 = _mm_min_epi16(R1, _mm_slli_si128(R0,2) + Down2);
minError = min(minError, _mm_extract_epi16(R1,1));
//forth
Diag = _mm_xor_si128(Diag, Diag);
Diag = _mm_insert_epi16(Diag, *(b-(lenb-1)) != *(a-(lena+1)), 0);
Diag = _mm_insert_epi16(Diag, 2*e, 1);
R0 = _mm_min_epi16(_mm_srli_si128(R1,2) + Side1, R0 + Diag);
R0 = _mm_min_epi16(R0, R1 + Down1);
minError = min(minError, _mm_extract_epi16(R0,0));
//fifth
Diag = _mm_xor_si128(Diag, Diag);
Diag = _mm_insert_epi16(Diag, *(b-(lenb-1)) != *(a-(lena+2)), 0);
Diag = _mm_insert_epi16(Diag, 2*e, 1);
R1 = _mm_min_epi16(R0 + Side2, R1 + Diag);
R1 = _mm_min_epi16(R1, _mm_slli_si128(R0,2) + Down2);
minError = min(minError, _mm_extract_epi16(R0,0));
if (minError > e)
return -1;
return minError;
}
int backwardEditDistanceSSE2G(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 e = errThreshold;
char flag = 0;
int minError = 2 * e;
__m128i R0, R1;
__m128i Diag;
__m128i Side1, Side2;
__m128i Down1, Down2;
__m128i Error;
__m128i tmp;
/* 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();
Error = _mm_setzero_si128();
tmp = _mm_setzero_si128();
/* end initialize */
if (lenb <= e) {
return smallEditDistanceB(a, lena, b, lenb);
}
R1 = _mm_xor_si128(R1, R1);
R0 = _mm_xor_si128(R0, R0);
Diag = _mm_xor_si128(Diag, Diag);
Side1 = _mm_xor_si128(Side1, Side1);
Down1 = _mm_xor_si128(Down1, Down1);
Diag = _mm_insert_epi16(Diag,2*e,0);
Side1 = _mm_insert_epi16(Side1,1,0);
Side1 = _mm_insert_epi16(Side1,2*e,1);
Down1 = _mm_insert_epi16(Down1,2*e,0);
Down1 = _mm_insert_epi16(Down1,1,1);
Down1 = _mm_insert_epi16(Down1,2*e,2);
R0 = _mm_insert_epi16(R0,0,0);
R1 = _mm_insert_epi16(R1,1,0);
R1 = _mm_insert_epi16(R1,1,1);
for (i = 2; i <= e; i++) {
//set side
Side1 = _mm_slli_si128(Side1,2);
Side1 = _mm_insert_epi16(Side1,1,0);
Down1 = _mm_insert_epi16(Down1,1,0);
Down1 = _mm_slli_si128(Down1,2);
Down1 = _mm_insert_epi16(Down1,2*e,0);
Diag = _mm_xor_si128(Diag, Diag);
if (i % 2 == 0) {
Diag = _mm_insert_epi16(Diag,2*e,0);
for (j = 1; j <= i - 1; j++) {
Diag = _mm_slli_si128(Diag, 2);
Diag =
_mm_insert_epi16(Diag, *(b-(i/2-1+(i/2-j))) != *(a-(i/2-1-(i/2-j))),0);
}
Diag = _mm_slli_si128(Diag, 2);
Diag = _mm_insert_epi16(Diag, 2*e,0);
R0 = _mm_min_epi16(R1 + Side1, _mm_slli_si128(R0,2) + Diag);
R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2) + Down1);
}
else {
Diag = _mm_insert_epi16(Diag,2*e,0);
for (j = i / 2 - 1; j >= -i / 2; j--) {
Diag = _mm_slli_si128(Diag, 2);
Diag =
_mm_insert_epi16(Diag, *(b-((i+1)/2+j-1)) != *(a-((i-1)/2-j-1)),0);
}
Diag = _mm_slli_si128(Diag, 2);
Diag = _mm_insert_epi16(Diag, 2*e,0);
R1 = _mm_min_epi16(R0 + Side1, _mm_slli_si128(R1,2) + Diag);
R1 = _mm_min_epi16(R1, _mm_slli_si128(R0,2) + Down1);
}
}
Error = _mm_xor_si128(Error, Error);
Side2 = _mm_xor_si128(Side2, Side2);
Down2 = _mm_xor_si128(Down2, Down2);
Down1 = _mm_xor_si128(Down1, Down1);
Error = _mm_insert_epi16(Error,e,0);
Side2 = _mm_insert_epi16(Side2,2*e,0);
Down1 = _mm_insert_epi16(Down1,2*e,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);
Error = _mm_slli_si128(Error, 2);
Error = _mm_insert_epi16(Error, e, 0);
}
Down2 = _mm_slli_si128(Down2, 2);
Down2 = _mm_insert_epi16(Down2,2*e,0);
for (; i <= 2 * lenb - (e - 1); i++) {
flag = 0;
Diag = _mm_xor_si128(Diag, Diag);
if (i % 2 == 0) {
for (j = e / 2; j >= -e / 2; j--) {
Diag = _mm_slli_si128(Diag, 2);
Diag =
_mm_insert_epi16(Diag, *(b-(i/2-1+j)) != *(a-(i/2-1-j)),0);
}
R0 = _mm_min_epi16(R1 + Side2, R0 + Diag);
R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2) + Down2);
if (_mm_extract_epi16(R0,0) <= e)
flag = 1;
tmp = _mm_srli_si128(R0,2);
for (j = 0; j <= e; j++) {
if (_mm_extract_epi16(tmp,0) <= e)
flag = 1;
tmp = _mm_srli_si128(tmp,2);
}
if (flag == 0)
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 {
for (j = -e / 2 + 1; j <= e / 2; j++) {
Diag = _mm_slli_si128(Diag, 2);
Diag =
_mm_insert_epi16(Diag, *(b-((i+1)/2-j-1)) != *(a-((i-1)/2+j-1)),0);
}
R1 = _mm_min_epi16(_mm_srli_si128(R0,2) + Side1, R1 + Diag);
R1 = _mm_min_epi16(R1, 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(R1 + Side2, R0 + Diag);
R0 = _mm_min_epi16(R0, _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(R1 + Side2, R0 + Diag);
R0 = _mm_min_epi16(R0, _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_srli_si128(R0,2) + Side1, R1 + Diag);
R1 = _mm_min_epi16(R1, 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*e, 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*e, 0);
Down1 = _mm_insert_epi16(Down1, 1, 1);
R1 = _mm_min_epi16(R0 + Side1, _mm_slli_si128(R1,2) + Diag);
R1 = _mm_min_epi16(R1, _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(R1 + Down1, R0 + Diag);
R0 = _mm_min_epi16(R0, _mm_srli_si128(R1,2) + Side1);
minError = min(minError, _mm_extract_epi16(R0,0));
if (minError > e)
return -1;
return minError;
}
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(R1 + Side2, R0 + Diag);
R0 = _mm_min_epi16(R0, _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_srli_si128(R0,2) + Side1, R1 + Diag);
R1 = _mm_min_epi16(R1, 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(R1 + Side2, R0 + Diag);
R0 = _mm_min_epi16(R0, _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);