/* Function: p7_SSVFilter_longtarget()
* Synopsis: Finds windows with SSV scores above some threshold (vewy vewy fast, in limited precision)
*
* Purpose: Calculates an approximation of the SSV (single ungapped diagonal)
* score for regions of sequence <dsq> of length <L> residues, using
* optimized profile <om>, and a preallocated one-row DP matrix <ox>,
* and captures the positions at which such regions exceed the score
* required to be significant in the eyes of the calling function,
* which depends on the <bg> and <p> (usually p=0.02 for nhmmer).
* Note that this variant performs only SSV computations, never
* passing through the J state - the score required to pass SSV at
* the default threshold (or less restrictive) is sufficient to
* pass MSV in essentially all DNA models we've tested.
*
* Above-threshold diagonals are captured into a preallocated list
* <windowlist>. Rather than simply capturing positions at which a
* score threshold is reached, this function establishes windows
* around those high-scoring positions, using scores in <msvdata>.
* These windows can be merged by the calling function.
*
*
* Args: dsq - digital target sequence, 1..L
* L - length of dsq in residues
* om - optimized profile
* ox - DP matrix
* msvdata - compact representation of substitution scores, for backtracking diagonals
* bg - the background model, required for translating a P-value threshold into a score threshold
* P - p-value below which a region is captured as being above threshold
* windowlist - preallocated container for all hits (resized if necessary)
*
*
* Note: We misuse the matrix <ox> here, using only a third of the
* first dp row, accessing it as <dp[0..Q-1]> rather than
* in triplets via <{MDI}MX(q)> macros, since we only need
* to store M state values. We know that if <ox> was big
* enough for normal DP calculations, it must be big enough
* to hold the MSVFilter calculation.
*
* Returns: <eslOK> on success.
*
* Throws: <eslEINVAL> if <ox> allocation is too small.
*/
int
p7_SSVFilter_longtarget(const ESL_DSQ *dsq, int L, P7_OPROFILE *om, P7_OMX *ox, const P7_SCOREDATA *msvdata,
P7_BG *bg, double P, P7_HMM_WINDOWLIST *windowlist)
{
register __m128i mpv; /* previous row values */
register __m128i xEv; /* E state: keeps max for Mk->E for a single iteration */
register __m128i xBv; /* B state: splatted vector of B[i-1] for B->Mk calculations */
register __m128i sv; /* temp storage of 1 curr row value in progress */
register __m128i biasv; /* emission bias in a vector */
uint8_t xJ; /* special states' scores */
int i; /* counter over sequence positions 1..L */
int q; /* counter over vectors 0..nq-1 */
int Q = p7O_NQB(om->M); /* segment length: # of vectors */
__m128i *dp = ox->dpb[0]; /* we're going to use dp[0][0..q..Q-1], not {MDI}MX(q) macros*/
__m128i *rsc; /* will point at om->rbv[x] for residue x[i] */
__m128i tecv; /* vector for E->C cost */
__m128i tjbmv; /* vector for J->B move cost + B->M move costs */
__m128i basev; /* offset for scores */
__m128i ceilingv; /* saturated simd value used to test for overflow */
__m128i tempv; /* work vector */
int cmp;
int k;
int n;
int end;
int rem_sc;
int start;
int target_end;
int target_start;
int max_end;
int max_sc;
int sc;
int pos_since_max;
float ret_sc;
union { __m128i v; uint8_t b[16]; } u;
/*
* Computing the score required to let P meet the F1 prob threshold
* In original code, converting from a scaled int MSV
* score S (the score getting to state E) to a probability goes like this:
* usc = S - om->tec_b - om->tjb_b - om->base_b;
* usc /= om->scale_b;
* usc -= 3.0;
* P = f ( (usc - nullsc) / eslCONST_LOG2 , mu, lambda)
* and we're computing the threshold usc, so reverse it:
* (usc - nullsc) / eslCONST_LOG2 = inv_f( P, mu, lambda)
* usc = nullsc + eslCONST_LOG2 * inv_f( P, mu, lambda)
* usc += 3
* usc *= om->scale_b
* S = usc + om->tec_b + om->tjb_b + om->base_b
*
* Here, I compute threshold with length model based on max_length. Doesn't
* matter much - in any case, both the bg and om models will change with roughly
* 1 bit for each doubling of the length model, so they offset.
*/
float nullsc;
__m128i sc_threshv;
uint8_t sc_thresh;
float invP = esl_gumbel_invsurv(P, om->evparam[p7_MMU], om->evparam[p7_MLAMBDA]);
/* Check that the DP matrix is ok for us. */
if (Q > ox->allocQ16) ESL_EXCEPTION(eslEINVAL, "DP matrix allocated too small");
ox->M = om->M;
p7_bg_SetLength(bg, om->max_length);
p7_oprofile_ReconfigMSVLength(om, om->max_length);
p7_bg_NullOne (bg, dsq, om->max_length, &nullsc);
sc_thresh = (int) ceil( ( ( nullsc + (invP * eslCONST_LOG2) + 3.0 ) * om->scale_b ) + om->base_b + om->tec_b + om->tjb_b );
sc_threshv = _mm_set1_epi8((int8_t) 255 - sc_thresh);
/* Initialization. In offset unsigned arithmetic, -infinity is 0, and 0 is om->base.
*/
biasv = _mm_set1_epi8((int8_t) om->bias_b); /* yes, you can set1() an unsigned char vector this way */
ceilingv = _mm_cmpeq_epi8(biasv, biasv);
for (q = 0; q < Q; q++) dp[q] = _mm_setzero_si128();
xJ = 0;
basev = _mm_set1_epi8((int8_t) om->base_b);
tecv = _mm_set1_epi8((int8_t) om->tec_b);
tjbmv = _mm_set1_epi8((int8_t) om->tjb_b + (int8_t) om->tbm_b);
xBv = _mm_subs_epu8(basev, tjbmv);
for (i = 1; i <= L; i++) {
rsc = om->rbv[dsq[i]];
xEv = _mm_setzero_si128();
/* Right shifts by 1 byte. 4,8,12,x becomes x,4,8,12.
* Because ia32 is littlendian, this means a left bit shift.
* Zeros shift on automatically, which is our -infinity.
*/
mpv = _mm_slli_si128(dp[Q-1], 1);
for (q = 0; q < Q; q++) {
/* Calculate new MMXo(i,q); don't store it yet, hold it in sv. */
sv = _mm_max_epu8(mpv, xBv);
sv = _mm_adds_epu8(sv, biasv);
sv = _mm_subs_epu8(sv, *rsc); rsc++;
xEv = _mm_max_epu8(xEv, sv);
mpv = dp[q]; /* Load {MDI}(i-1,q) into mpv */
dp[q] = sv; /* Do delayed store of M(i,q) now that memory is usable */
}
/* test if the pthresh significance threshold has been reached;
* note: don't use _mm_cmpgt_epi8, because it's a signed comparison, which won't work on uint8s */
tempv = _mm_adds_epu8(xEv, sc_threshv);
tempv = _mm_cmpeq_epi8(tempv, ceilingv);
cmp = _mm_movemask_epi8(tempv);
if (cmp != 0) { //hit pthresh, so add position to list and reset values
//figure out which model state hit threshold
end = -1;
rem_sc = -1;
for (q = 0; q < Q; q++) { /// Unpack and unstripe, so we can find the state that exceeded pthresh
u.v = dp[q];
for (k = 0; k < 16; k++) { // unstripe
//(q+Q*k+1) is the model position k at which the xE score is found
if (u.b[k] >= sc_thresh && u.b[k] > rem_sc && (q+Q*k+1) <= om->M) {
end = (q+Q*k+1);
rem_sc = u.b[k];
}
}
dp[q] = _mm_set1_epi8(0); // while we're here ... this will cause values to get reset to xB in next dp iteration
}
//recover the diagonal that hit threshold
start = end;
target_end = target_start = i;
sc = rem_sc;
while (rem_sc > om->base_b - om->tjb_b - om->tbm_b) {
rem_sc -= om->bias_b - msvdata->msv_scores[start*om->abc->Kp + dsq[target_start]];
--start;
--target_start;
}
start++;
target_start++;
//extend diagonal further with single diagonal extension
k = end+1;
n = target_end+1;
max_end = target_end;
max_sc = sc;
pos_since_max = 0;
while (k<om->M && n<=L) {
sc += om->bias_b - msvdata->msv_scores[k*om->abc->Kp + dsq[n]];
if (sc >= max_sc) {
max_sc = sc;
max_end = n;
pos_since_max=0;
} else {
pos_since_max++;
if (pos_since_max == 5)
break;
}
k++;
n++;
}
end += (max_end - target_end);
k += (max_end - target_end);
target_end = max_end;
ret_sc = ((float) (max_sc - om->tjb_b) - (float) om->base_b);
ret_sc /= om->scale_b;
ret_sc -= 3.0; // that's ~ L \log \frac{L}{L+3}, for our NN,CC,JJ
p7_hmmwindow_new(windowlist, 0, target_start, k, end, end-start+1 , ret_sc, p7_NOCOMPLEMENT );
i = target_end; // skip forward
}
} /* end loop over sequence residues 1..L */
return eslOK;
}
/* Function: p7_SSVFM_longlarget()
* Synopsis: Finds windows with SSV scores above given threshold, using FM-index
*
* Details: Uses FM-index to find high-scoring diagonals (seeds), then extends those
* seeds to maximal scoring diagonals (no gaps). Windows meeting the SSV
* scoring threshold (usually score s.t. p=0.02) are captured, and passed
* on to the Viterbi and Forward stages of the pipeline.
*
* Args: om - optimized profile
* nu - configuration: expected number of hits (use 2.0 as a default)
* bg - the background model, required for translating a P-value threshold into a score threshold
* F1 - p-value below which a window is captured as being above threshold
* fmf - data for forward traversal of the FM-index
* fmb - data for backward traversal of the FM-index
* fm_cfg - FM-index meta data
* ssvdata - compact data required for computing SSV scores
* windowlist - RETURN: collection of SSV-passing windows, with meta data required for downstream stages.
*
* Returns: <eslOK> on success.
*
* Throws: <eslEMEM> if trouble allocating memory for seeds
*/
int
p7_SSVFM_longlarget( P7_OPROFILE *om, float nu, P7_BG *bg, double F1,
const FM_DATA *fmf, const FM_DATA *fmb, FM_CFG *fm_cfg, const P7_SCOREDATA *ssvdata,
P7_HMM_WINDOWLIST *windowlist)
{
float sc_thresh, sc_threshFM;
float invP, invP_FM;
float nullsc;
int i;
float tloop = logf((float) om->max_length / (float) (om->max_length+3));
float tloop_total = tloop * om->max_length;
float tmove = logf( 3.0f / (float) (om->max_length+3));
float tbmk = logf( 2.0f / ((float) om->M * (float) (om->M+1)));
float tec = logf(1.0f / nu);
FM_DIAG *diag;
ESL_SQ *tmp_sq;
FM_DIAGLIST seeds;
int status;
status = fm_initSeeds(&seeds);
if (status != eslOK)
ESL_EXCEPTION(eslEMEM, "Error allocating memory for seed list\n");
/* Set false target length. This is a conservative estimate of the length of window that'll
* soon be passed on to later phases of the pipeline; used to recover some bits of the score
* that we would miss if we left length parameters set to the full target length */
p7_oprofile_ReconfigMSVLength(om, om->max_length);
p7_bg_SetLength(bg, om->max_length);
p7_bg_NullOne (bg, NULL, om->max_length, &nullsc);
tmp_sq = esl_sq_CreateDigital(om->abc);
/*
* Computing the score required to let P meet the F1 prob threshold
* In original code, converting from an SSV score S (the score getting
* to state C) to a probability goes like this:
* S = XMX(L,p7G_C)
* usc = S + tmove + tloop_total
* P = f ( (usc - nullsc) / eslCONST_LOG2 , mu, lambda)
* and XMX(C) was the diagonal score + tmove + tbmk + tec
* and we're computing the threshold score S, so reverse it:
* (usc - nullsc) / eslCONST_LOG2 = inv_f( P, mu, lambda)
* usc = nullsc + eslCONST_LOG2 * inv_f( P, mu, lambda)
* S = usc - tmove - tloop_total - tmove - tbmk - tec
*
*
* Here, I compute threshold with length model based on max_length. Usually, the
* length of a window returned by this scan will be 2*max_length-1 or longer. Doesn't
* really matter - in any case, both the bg and om models will change with roughly
* 1 bit for each doubling of the length model, so they offset.
*/
invP = esl_gumbel_invsurv(F1, om->evparam[p7_MMU], om->evparam[p7_MLAMBDA]);
sc_thresh = (invP * eslCONST_LOG2) + nullsc - (tmove + tloop_total + tmove + tbmk + tec);
invP_FM = esl_gumbel_invsurv(0.5, om->evparam[p7_MMU], om->evparam[p7_MLAMBDA]);
sc_threshFM = ESL_MAX(fm_cfg->scthreshFM, (invP_FM * eslCONST_LOG2) + nullsc - (tmove + tloop_total + tmove + tbmk + tec) ) ;
sc_threshFM *= fm_cfg->info_deficit_ratio;
sc_threshFM = ESL_MAX(7.0, sc_threshFM);
//get diagonals that score above sc_threshFM
status = FM_getSeeds(fmf, fmb, fm_cfg, ssvdata, om->abc->Kp, sc_threshFM, &seeds );
if (status != eslOK)
ESL_EXCEPTION(eslEMEM, "Error allocating memory for seed computation\n");
//now extend those diagonals to find ones scoring above sc_thresh
for(i=0; i<seeds.count; i++) {
FM_extendSeed( seeds.diags+i, fmf, ssvdata, fm_cfg, tmp_sq);
}
for(i=0; i<seeds.count; i++) {
diag = seeds.diags+i;
if (diag->score >= sc_thresh)
FM_window_from_diag(diag, fmf, fm_cfg->meta, windowlist );
}
esl_sq_Destroy(tmp_sq);
free(seeds.diags);
return eslEOF;
//ERROR:
// ESL_EXCEPTION(eslEMEM, "Error allocating memory for hit list\n");
}
