/* Function: FM_backtrackSeed()
*
* Synopsis: Find position(s) in the FM index for a diagonal that meets score threshold
*
* Details: Follows the BWT/FM-index until finding an entry of the implicit
* suffix array that is found in the sampled SA.
*
* Args: fmf - FM index for finding matches to the input sequence
* fm_cfg - FM-index meta data
* i - Single position in the BWT
*
* Returns: <eslOK> on success.
*/
static uint32_t
FM_backtrackSeed(const FM_DATA *fmf, const FM_CFG *fm_cfg, int i) {
int j = i;
int len = 0;
int c;
while ( j != fmf->term_loc && (j % fm_cfg->meta->freq_SA)) { //go until we hit a position in the full SA that was sampled during FM index construction
c = fm_getChar( fm_cfg->meta->alph_type, j, fmf->BWT);
j = fm_getOccCount (fmf, fm_cfg, j-1, c);
j += abs(fmf->C[c]);
len++;
}
return len + (j==fmf->term_loc ? 0 : fmf->SA[ j / fm_cfg->meta->freq_SA ]) ; // len is how many backward steps we had to take to find a sampled SA position
}
/* Function: getFMHits()
* Synopsis: For a given interval, identify the position in original text for each element
* of interval
* Purpose: Implement Algorithm 3.7 (p17) of Firth paper (A Comparison of BWT Approaches
* to String Pattern Matching). Most of the meat is in the method of counting
* characters - bwt_getOccCount, which depends on compilation choices.
*/
int
getFMHits( FM_DATA *fm, FM_CFG *cfg, FM_INTERVAL *interval, int block_id, int hit_offset, int hit_length, FM_HIT *hits_ptr, int fm_direction) {
int i, j, len = 0;
int dist_from_end;
for (i = interval->lower; i<= interval->upper; i++) {
j = i;
len = 0;
while ( j != fm->term_loc && (j % cfg->meta->freq_SA)) { //go until we hit a position in the full SA that was sampled during FM index construction
uint8_t c = fm_getChar( cfg->meta->alph_type, j, fm->BWT);
j = fm_getOccCount (fm, cfg, j-1, c);
j += abs(fm->C[c]);
len++;
}
hits_ptr[hit_offset + i - interval->lower].block = block_id;
hits_ptr[hit_offset + i - interval->lower].direction = fm_direction;
hits_ptr[hit_offset + i - interval->lower].length = hit_length;
dist_from_end = 1 + len + (j==fm->term_loc ? 0 : fm->SA[ j / cfg->meta->freq_SA ]) ; // len is how many backward steps we had to take to find a sampled SA position
if (fm_direction == fm_forward)
dist_from_end += hit_length;
else
dist_from_end += 1;
//the SA is on the reversed string. What would be the position in the unreversed string?
hits_ptr[hit_offset + i - interval->lower].start = fm->N - dist_from_end;
//printf ("SA: %d\n", hits_ptr[hit_offset + i - interval->lower].start);
}
return eslOK;
}
