/*

Date : 19th June 2011

Author : Edward MK Wu

Change : Packaging 2BWT library as a separate product.

Enhancing the 2BWT library with interface functions

for basic BWT search.

*/

#include "2BWT-Interface.h"

Idx2BWT * BWTLoad2BWT(const char * indexFilePrefix, const char * saFileNameExtension) {

Idx2BWT * idx2BWT = malloc(sizeof(Idx2BWT));

BWT * bwt;

BWT * rev_bwt;

HSP * hsp;

char bwtFilename[MAX_INDEX_FILENAME_LENGTH];

char bwtOccFilename[MAX_INDEX_FILENAME_LENGTH];

char saFilename[MAX_INDEX_FILENAME_LENGTH];

char rev_bwtFilename[MAX_INDEX_FILENAME_LENGTH];

char rev_bwtOccFilename[MAX_INDEX_FILENAME_LENGTH];

char packedDnaFilename[MAX_INDEX_FILENAME_LENGTH];

char annotationFilename[MAX_INDEX_FILENAME_LENGTH];

char ambiguityFilename[MAX_INDEX_FILENAME_LENGTH];

char translateFilename[MAX_INDEX_FILENAME_LENGTH];

strcpy(bwtFilename,indexFilePrefix);

strcpy(bwtOccFilename,indexFilePrefix);

strcpy(saFilename,indexFilePrefix);

strcpy(rev_bwtFilename,indexFilePrefix);

strcpy(rev_bwtOccFilename,indexFilePrefix);

strcpy(packedDnaFilename,indexFilePrefix);

strcpy(annotationFilename,indexFilePrefix);

strcpy(ambiguityFilename,indexFilePrefix);

strcpy(translateFilename,indexFilePrefix);

strcat(bwtFilename,".bwt");

strcat(bwtOccFilename,".fmv");

strcat(saFilename,saFileNameExtension);

strcat(rev_bwtFilename,".rev.bwt");

strcat(rev_bwtOccFilename,".rev.fmv");

strcat(packedDnaFilename,".pac");

strcat(annotationFilename,".ann");

strcat(ambiguityFilename,".amb");

strcat(translateFilename,".tra");

MMMasterInitialize(3, 0, FALSE, NULL);

MMPool * mmPool = MMPoolCreate(2097152);

bwt = BWTLoad(mmPool, bwtFilename, bwtOccFilename, saFilename, NULL, NULL, NULL);

rev_bwt = BWTLoad(mmPool, rev_bwtFilename, rev_bwtOccFilename, NULL, NULL, NULL, NULL);

hsp = HSPLoad(mmPool, packedDnaFilename, annotationFilename, ambiguityFilename,translateFilename, 1);

HSPFillCharMap(idx2BWT->charMap);

HSPFillComplementMap(idx2BWT->complementMap);

idx2BWT->bwt = bwt;

idx2BWT->rev_bwt = rev_bwt;

idx2BWT->hsp = hsp;

idx2BWT->mmPool = mmPool;

return idx2BWT;

}

void BWTFree2BWT(Idx2BWT * idx2BWT) {

BWT * bwt = idx2BWT->bwt;

BWT * rev_bwt = idx2BWT->rev_bwt;

HSP * hsp = idx2BWT->hsp;

MMPool * mmPool = idx2BWT->mmPool;

HSPFree(mmPool, hsp, 1);

BWTFree(mmPool, bwt);

BWTFree(mmPool, rev_bwt);

MMPoolFree(mmPool);

free(idx2BWT);

}

void BWTConvertPattern(Idx2BWT * idx2BWT, const char * patternSource, int patternLength, unsigned char * patternDestination) {

int i;

for (i=0;i<patternLength;i++) {

patternDestination[i] = idx2BWT->charMap[patternSource[i]];

}

patternDestination[i]='\0';

}

void BWTSARangeInitial(Idx2BWT * idx2BWT, const unsigned char c,

unsigned int *saIndexLeft, unsigned int *saIndexRight) {

BWT * bwt = idx2BWT->bwt;

BWT * rev_bwt = idx2BWT->rev_bwt;

//TODO I guess saIndex is start from 1, and cumulativeFreq is from 0

(*saIndexLeft) = bwt->cumulativeFreq[c]+1;

(*saIndexRight) = bwt->cumulativeFreq[c+1];

}

//给出saIndex, backward 算出 saIndex

void BWTSARangeBackward(Idx2BWT * idx2BWT, const unsigned char c,

unsigned int *saIndexLeft, unsigned int *saIndexRight) {

BWT * bwt = idx2BWT->bwt;

BWT * rev_bwt = idx2BWT->rev_bwt;

unsigned int l = (*saIndexLeft);

unsigned int r = (*saIndexRight);

(*saIndexLeft) = bwt->cumulativeFreq[c] + BWTOccValue(bwt, l, c) + 1;

(*saIndexRight) = bwt->cumulativeFreq[c] + BWTOccValue(bwt, r + 1, c);

}

//给出saIndex, foreward 算出 saIndex

void BWTSARangeForeward(Idx2BWT * idx2BWT, const unsigned char c,

unsigned int *saIndexLeft, unsigned int *saIndexRight) {

BWT * rev_bwt = idx2BWT->rev_bwt;

BWT *bwt = idx2BWT->bwt;

unsigned int l = (*saIndexLeft);

unsigned int r = (*saIndexRight);

(*saIndexLeft) = bwt->cumulativeFreq[c] + BWTOccValue(rev_bwt, l, c) + 1;

(*saIndexRight) = bwt->cumulativeFreq[c] + BWTOccValue(rev_bwt, r + 1, c);

}

//给出saIndex,rev_saIndex backward算出saIndex 和 rev_saIndex

void BWTSARangeBackward_Bidirection(Idx2BWT * idx2BWT, const unsigned char c,

unsigned int *saIndexLeft, unsigned int *saIndexRight,

unsigned int *rev_saIndexLeft, unsigned int *rev_saIndexRight) {

BWT * bwt = idx2BWT->bwt;

BWT * rev_bwt = idx2BWT->rev_bwt;

unsigned int oL[ALPHABET_SIZE];

unsigned int oR[ALPHABET_SIZE];

unsigned int oCount[ALPHABET_SIZE];

unsigned int l = (*saIndexLeft);

unsigned int r = (*saIndexRight);

unsigned int rev_l = (*rev_saIndexLeft);

unsigned int rev_r = (*rev_saIndexRight);

int k;

BWTAllOccValue(bwt,l,oL);

BWTAllOccValue(bwt,r + 1,oR); //TODO why r need plus 1

oCount[ALPHABET_SIZE-1]=0;

for (k=ALPHABET_SIZE-2;k>=0;k--) {

oCount[k]=oCount[k+1]+oR[k+1]-oL[k+1];

}

l = bwt->cumulativeFreq[c] + oL[c] + 1;

r = bwt->cumulativeFreq[c] + oR[c];

rev_r = rev_r - oCount[c];

rev_l = rev_r - (r-l);

(*saIndexLeft) = l;

(*saIndexRight) = r;

(*rev_saIndexLeft) = rev_l;

(*rev_saIndexRight) = rev_r;

}

//根据rev_saIndex saIndex, forward算出rev_saIndex and saIndex

void BWTSARangeForward_Bidirection(Idx2BWT * idx2BWT, const unsigned char c,

unsigned int *saIndexLeft, unsigned int *saIndexRight,

unsigned int *rev_saIndexLeft, unsigned int *rev_saIndexRight) {

BWT * bwt = idx2BWT->bwt;

BWT * rev_bwt = idx2BWT->rev_bwt;

unsigned int oL[ALPHABET_SIZE];

unsigned int oR[ALPHABET_SIZE];

unsigned int oCount[ALPHABET_SIZE];

unsigned int l = (*saIndexLeft);

unsigned int r = (*saIndexRight);

unsigned int rev_l = (*rev_saIndexLeft);

unsigned int rev_r = (*rev_saIndexRight);

int k;

BWTAllOccValue(rev_bwt,rev_l,oL);

BWTAllOccValue(rev_bwt,rev_r + 1,oR);

oCount[ALPHABET_SIZE-1]=0;

for (k=ALPHABET_SIZE-2;k>=0;k--) {

oCount[k]=oCount[k+1]+oR[k+1]-oL[k+1];

}

rev_l = bwt->cumulativeFreq[c] + oL[c] + 1;

rev_r = bwt->cumulativeFreq[c] + oR[c];

r = r - oCount[c];

l = r - (rev_r-rev_l);

(*saIndexLeft) = l;

(*saIndexRight) = r;

(*rev_saIndexLeft) = rev_l;

(*rev_saIndexRight) = rev_r;

}

//根据给出的saIndex, backward算出所有字符的saIndex

void BWTAllSARangesBackward(Idx2BWT * idx2BWT, const unsigned int saIndexLeft,

const unsigned int saIndexRight,unsigned int *resultSaIndexesLeft,

unsigned int *resultSaIndexesRight)

{

BWT * bwt = idx2BWT->bwt;

BWT * rev_bwt = idx2BWT->rev_bwt;

unsigned int oL[ALPHABET_SIZE];

unsigned int oR[ALPHABET_SIZE];

unsigned int oCount[ALPHABET_SIZE];

unsigned int l = saIndexLeft;

unsigned int r = saIndexRight;

int k;

BWTAllOccValue(bwt,l,oL);

BWTAllOccValue(bwt,r + 1,oR);

for (k=0;k<ALPHABET_SIZE;k++) {

resultSaIndexesLeft[k] = bwt->cumulativeFreq[k] + oL[k] + 1;

resultSaIndexesRight[k] = bwt->cumulativeFreq[k] + oR[k];

}

}

//根据给出的saIndex rev_saIndex, backward算出所有char的saIndex 和 rev_saIndex

void BWTAllSARangesBackward_Bidirection(Idx2BWT * idx2BWT, const unsigned int saIndexLeft,

unsigned int *rev_resultSaIndexRight)

{

BWT * bwt = idx2BWT->bwt;

BWT * rev_bwt = idx2BWT->rev_bwt;

unsigned int oL[ALPHABET_SIZE];

unsigned int oR[ALPHABET_SIZE];

unsigned int oCount[ALPHABET_SIZE];

unsigned int l = saIndexLeft;

unsigned int r = saIndexRight;

unsigned int rev_l = rev_saIndexLeft;

unsigned int rev_r = rev_saIndexRight;

int k;

BWTAllOccValue(bwt,l,oL);

BWTAllOccValue(bwt,r + 1,oR);

oCount[ALPHABET_SIZE-1]=0;

for (k=ALPHABET_SIZE-2;k>=0;k--) {

oCount[k]=oCount[k+1]+oR[k+1]-oL[k+1];

}

for (k=0;k<ALPHABET_SIZE;k++) {

resultSaIndexLeft[k] = bwt->cumulativeFreq[k] + oL[k] + 1;

resultSaIndexRight[k] = bwt->cumulativeFreq[k] + oR[k];

rev_resultSaIndexRight[k] = rev_r - oCount[k];

rev_resultSaIndexLeft[k] = rev_resultSaIndexRight[k] -

(resultSaIndexRight[k]-resultSaIndexLeft[k]);

}

}

//根据rev_saIndex saIndex, forward算出所有char的saIndex and rev_saIndex

void BWTAllSARangesForward_Bidirection(Idx2BWT * idx2BWT, const unsigned int saIndexLeft,

unsigned int *rev_resultSaIndexRight)

{

BWT * bwt = idx2BWT->bwt;

BWT * rev_bwt = idx2BWT->rev_bwt;

unsigned int oL[ALPHABET_SIZE];

unsigned int oR[ALPHABET_SIZE];

unsigned int oCount[ALPHABET_SIZE];

unsigned int l = saIndexLeft;

unsigned int r = saIndexRight;

unsigned int rev_l = rev_saIndexLeft;

unsigned int rev_r = rev_saIndexRight;

int k;

BWTAllOccValue(rev_bwt,rev_l,oL);

BWTAllOccValue(rev_bwt,rev_r + 1,oR);

oCount[ALPHABET_SIZE-1]=0;

for (k=ALPHABET_SIZE-2;k>=0;k--) {

oCount[k]=oCount[k+1]+oR[k+1]-oL[k+1];

}

for (k=0;k<ALPHABET_SIZE;k++) {

rev_resultSaIndexLeft[k] = bwt->cumulativeFreq[k] + oL[k] + 1;

rev_resultSaIndexRight[k] = bwt->cumulativeFreq[k] + oR[k];

resultSaIndexRight[k] = r - oCount[k];

resultSaIndexLeft[k] = resultSaIndexRight[k] - (rev_resultSaIndexRight[k]-rev_resultSaIndexLeft[k]);

}

}

//根据saIndex还原出seq在ref中的位置

void BWTRetrievePositionFromSAIndex(Idx2BWT * idx2BWT, unsigned int saIndex,

unsigned int * sequenceId, unsigned int * offset)

{

BWT * bwt = idx2BWT->bwt;

BWT * rev_bwt = idx2BWT->rev_bwt;

HSP * hsp = idx2BWT->hsp;

unsigned short * ambiguityMap = hsp->ambiguityMap;

Translate * translate = hsp->translate;

unsigned int ambPosition = BWTSaValue(bwt,saIndex);

unsigned int approxIndex = ambPosition>>GRID_SAMPLING_FACTOR_2_POWER;

unsigned int approxValue = ambiguityMap[approxIndex];

while (translate[approxValue].startPos>ambPosition) {

approxValue--;

}

ambPosition-=translate[approxValue].correction;

(*sequenceId) = translate[approxValue].chrID;

(*offset) = ambPosition;

}

//exact match seq to ref

int bwt_match_exact(Idx2BWT *bi_bwt, ubyte_t *seq, int len, bwtint_t *sa_begin,

bwtint_t *sa_end, bwtint_t *rev_sa_begin, bwtint_t *rev_sa_end)

{

bwtint_t l, k, rev_l, rev_k;

int i;

k = *sa_begin;

l = *sa_end;

rev_k = *rev_sa_begin;

rev_l = *rev_sa_end;

for (i = len - 1; i >= 0; i--) {

if(seq[i]>3)

return 0;

BWTSARangeBackward_Bidirection(bi_bwt, seq[i], &k, &l, &rev_k, &rev_l);

if(k > l)

break; //no match

}

if (k > l)

return 0;

if(*sa_begin) *sa_begin = k;

if(*sa_end) *sa_end = l;

if(*rev_sa_begin) *rev_sa_begin = rev_k;

if(*rev_sa_end) *rev_sa_end = rev_l;

return l - k + 1;

}

// exact extend

// leav_len: leaving length to extend

// type: 1 - backward, 0 - forward

int bwt_extend_exact(const Idx2BWT *bi_bwt, ubyte_t *seq, int len, int *leav_len, int type,

bwtint_t *sa_begin, bwtint_t *sa_end, bwtint_t *rev_sa_begin, bwtint_t *rev_sa_end)

{

bwtint_t k, l, rev_k, rev_l;

int i;

k = *sa_begin;

l = *sa_end;

rev_k = *rev_sa_begin;

rev_l = *rev_sa_end;

if(type == 1){

for(i = *leav_len; i > 0; --i){

if(seq[i - 1] > 3)

break;

BWTSARangeBackward_Bidirection(bi_bwt, seq[i], &k, &l, &rev_k, &rev_l);

if(k > l)

break;

else{

*sa_begin = k;

*sa_end = l;

*rev_sa_begin = rev_k;

*rev_sa_end = rev_l;

}

}

} else {

for(i = (*leav_len); i > 0; --i){

if(seq[len-i] > 3)

break;

BWTSARangeForward_Bidirection(bi_bwt, seq[len-i], &k, &l, &rev_k, &rev_l);

if(k > l)

break;

else{

*sa_begin = k;

*sa_end = l;

*rev_sa_begin = rev_k;

*rev_sa_end = rev_l;

}

}

}

*leav_len = i;

return *sa_end - (*sa_begin) + 1;

}