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Fixes major bug in cm_pipeline.c:pli_p7_filter(), was not updating sc… 

…ore based on viterbi bias. This had the effect that the viterbi bias filter never removed any windows. Noticed this in regression testing on rmark3 against 1.1.1 in release process of 1.1.2. A very important catch that reminds why it's worth it to do the annoying and time consuming regression testing in the release 00CHECKLIST.
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1 parent 9f040a7 commit c1193d68b5192f8b44256f31ec22fbd8f76557ec @nawrockie nawrockie committed Jul 1, 2016
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Showing with 31 additions and 33 deletions.
  1. +31 −33 src/cm_pipeline.c
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64 src/cm_pipeline.c
@@ -24,8 +24,6 @@
#include "infernal.h"
-#define DEBUG_NOW 0
-
static int pli_p7_filter (CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam, P7_SCOREDATA *msvdata, const ESL_SQ *sq, int64_t **ret_ws, int64_t **ret_we, float **ret_wb, int *ret_nwin);
static int pli_p7_env_def (CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam, const ESL_SQ *sq, int64_t *ws, int64_t *we, int nwin, P7_HMM **opt_hmm, P7_PROFILE **opt_gm,
P7_PROFILE **opt_Rgm, P7_PROFILE **opt_Lgm, P7_PROFILE **opt_Tgm, int64_t **ret_es, int64_t **ret_ee, float **ret_eb, int *ret_nenv);
@@ -1325,7 +1323,7 @@ cm_Pipeline(CM_PIPELINE *pli, off_t cm_offset, P7_OPROFILE *om, P7_BG *bg, float
have3term = (sq->end == 1) ? TRUE : FALSE;
}
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
/*printf("\nPIPELINE ENTRANCE %s %s %" PRId64 " residues (pli->maxW: %d om->max_length: %d cm->W: %d)\n", sq->name, sq->desc, sq->n, pli->maxW, om->max_length, (*opt_cm)->W);*/
printf("\nPIPELINE ENTRANCE %-15s %15s (n: %6" PRId64 " start: %6" PRId64 " end: %6" PRId64 " C: %6" PRId64 " W: %6" PRId64 " L: %6" PRId64 " have5term: %d have3term: %d)\n",
sq->name, om->name, sq->n, sq->start, sq->end, sq->C, sq->W, sq->L, have5term, have3term);
@@ -1454,7 +1452,7 @@ cm_Pipeline(CM_PIPELINE *pli, off_t cm_offset, P7_OPROFILE *om, P7_BG *bg, float
* A. pli_p7_filter(): MSV, Viterbi, local Forward filters
* B. pli_final_stage_hmmonly(): use H3 local domain definition to define HMM hits
********************************************************************************************************/
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("\nHMM ONLY PIPELINE calling p7_filter() %s %" PRId64 " residues (pass: %d)\n", sq2search->name, sq2search->n, p);
#endif
if((status = pli_p7_filter(pli, om, bg, p7_evparam, msvdata, sq2search, &ws, &we, &wb, &nwin)) != eslOK) return status;
@@ -1472,7 +1470,7 @@ cm_Pipeline(CM_PIPELINE *pli, off_t cm_offset, P7_OPROFILE *om, P7_BG *bg, float
* A. pli_p7_filter(): SSV, Viterbi, local Forward filters
* B. pli_p7_env_def(): glocal Forward, and glocal (usually) HMM envelope definition, then
*/
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("\nPIPELINE calling p7_filter() %s %" PRId64 " residues (pass: %d)\n", sq2search->name, sq2search->n, p);
#endif
if((status = pli_p7_filter(pli, om, bg, p7_evparam, msvdata, sq2search, &ws, &we, &wb, &nwin)) != eslOK) return status;
@@ -1521,7 +1519,7 @@ cm_Pipeline(CM_PIPELINE *pli, off_t cm_offset, P7_OPROFILE *om, P7_BG *bg, float
}
}
else {
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("\nPIPELINE calling p7_env_def() %s %" PRId64 " residues (pass: %d)\n", sq2search->name, sq2search->n, p);
#endif
if((status = pli_p7_env_def(pli, om, bg, p7_evparam, sq2search, ws, we, nwin, opt_hmm, opt_gm, opt_Rgm, opt_Lgm, opt_Tgm, &(p7esAA[p]), &(p7eeAA[p]), &(p7ebAA[p]), &(np7envA[p]))) != eslOK) return status;
@@ -1597,7 +1595,7 @@ cm_Pipeline(CM_PIPELINE *pli, off_t cm_offset, P7_OPROFILE *om, P7_BG *bg, float
/* 1. Banded CYK on the envelopes defined by the p7 HMM in the pipeline pass above (if pli->do_edef == TRUE) */
if(pli->do_edef) {
if(pli->do_fcyk) {
- #if DEBUG_NOW
+ #if eslDEBUGLEVEL >= 3
printf("\nPIPELINE calling pli_cyk_env_filter() %s %" PRId64 " residues (pass: %d)\n", sq2search->name, sq2search->n, p);
#endif
if((status = pli_cyk_env_filter(pli, cm_offset, sq2search, p7esAA[p], p7eeAA[p], np7envA[p], opt_cm, &es, &ee, &nenv)) != eslOK) return status;
@@ -1613,7 +1611,7 @@ cm_Pipeline(CM_PIPELINE *pli, off_t cm_offset, P7_OPROFILE *om, P7_BG *bg, float
/* 2. Using CYK to define envelopes on full sequences (if pli->do_edef == FALSE && pli->fcyk = TRUE) */
else if((! pli->do_edef) && pli->do_fcyk) {
/* Defining envelopes with CYK */
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("\nPIPELINE calling pli_cyk_seq_filter() %s %" PRId64 " residues (pass: %d)\n", sq2search->name, sq2search->n, p);
#endif
if((status = pli_cyk_seq_filter(pli, cm_offset, sq2search, opt_cm, &es, &ee, &nenv)) != eslOK) return status;
@@ -1628,12 +1626,12 @@ cm_Pipeline(CM_PIPELINE *pli, off_t cm_offset, P7_OPROFILE *om, P7_BG *bg, float
/* Filters are finished. Final stage of pipeline (always run).
*/
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("\nPIPELINE calling FinalStage() %s %" PRId64 " residues model: %s (pass: %d) nhits: %" PRId64 "\n", sq2search->name, sq2search->n, om->name, p, hitlist->N);
#endif
prv_ntophits = hitlist->N;
if((status = pli_final_stage(pli, cm_offset, sq2search, es, ee, nenv, hitlist, opt_cm)) != eslOK) return status;
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("\nPIPELINE back from FinalStage() %s %" PRId64 " residues model: %s (pass: %d) nhits: %" PRId64 "\n", sq2search->name, sq2search->n, om->name, p, hitlist->N);
#endif
@@ -2472,7 +2470,7 @@ pli_p7_filter(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam, P
p7_oprofile_ReconfigMSVLength(om, pli->maxW);
om->max_length = pli->maxW;
- #if DEBUG_NOW
+ #if eslDEBUGLEVEL >= 3
printf("\nPIPELINE pli_p7_filter() %s %" PRId64 " residues\n", sq->name, sq->n);
#endif
@@ -2589,7 +2587,7 @@ pli_p7_filter(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam, P
p7_bg_SetLength(bg, wlen);
p7_bg_NullOne (bg, subdsq, wlen, &nullsc);
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
if(cur_do_msv) printf("SURVIVOR window %5d [%10" PRId64 "..%10" PRId64 "] survived SSV ? bits ? P\n", i, ws[i], we[i]);
#endif
survAA[p7_SURV_F1][i] = TRUE;
@@ -2617,7 +2615,7 @@ pli_p7_filter(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam, P
pli->acct[pli->cur_pass_idx].n_past_msvbias++;
survAA[p7_SURV_F1b][i] = TRUE;
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
if(cur_do_msv && cur_do_msvbias) printf("SURVIVOR window %5d [%10" PRId64 "..%10" PRId64 "] survived MSV-Bias ? bits P ?\n", i, ws[i], we[i]);
#endif
if(pli->do_time_F1) return eslOK;
@@ -2652,7 +2650,7 @@ pli_p7_filter(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam, P
pli->acct[pli->cur_pass_idx].n_past_vit++;
survAA[p7_SURV_F2][i] = TRUE;
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
if (cur_do_vit) printf("SURVIVOR window %5d [%10" PRId64 "..%10" PRId64 "] survived Vit %6.2f bits P %g\n", i, ws[i], we[i], wb[i], wp[i]);
#endif
@@ -2663,7 +2661,7 @@ pli_p7_filter(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam, P
}
have_filtersc = TRUE;
wsc = (vfsc - filtersc) / eslCONST_LOG2;
- P = esl_gumbel_surv(wb[i], p7_evparam[CM_p7_LVMU], p7_evparam[CM_p7_LVLAMBDA]);
+ P = esl_gumbel_surv(wsc, p7_evparam[CM_p7_LVMU], p7_evparam[CM_p7_LVLAMBDA]);
wp[i] = P;
wb[i] = wsc;
if (P > cur_F2b) continue;
@@ -2672,7 +2670,7 @@ pli_p7_filter(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam, P
pli->acct[pli->cur_pass_idx].n_past_vitbias++;
survAA[p7_SURV_F2b][i] = TRUE;
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
if (cur_do_vit && cur_do_vitbias) printf("SURVIVOR window %5d [%10" PRId64 "..%10" PRId64 "] survived Vit-Bias %6.2f bits P %g\n", i, ws[i], we[i], wb[i], wp[i]);
#endif
if(pli->do_time_F2) continue;
@@ -2693,7 +2691,7 @@ pli_p7_filter(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam, P
pli->acct[pli->cur_pass_idx].n_past_fwd++;
survAA[p7_SURV_F3][i] = TRUE;
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
if(cur_do_fwd) printf("SURVIVOR window %5d [%10" PRId64 "..%10" PRId64 "] survived Fwd %6.2f bits P %g\n", i, ws[i], we[i], wb[i], wp[i]);
#endif
@@ -2713,7 +2711,7 @@ pli_p7_filter(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam, P
nsurv_fwd++;
survAA[p7_SURV_F3b][i] = TRUE;
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
if(cur_do_fwd && cur_do_fwdbias) printf("SURVIVOR window %5d [%10" PRId64 "..%10" PRId64 "] survived Fwd-Bias %6.2f bits P %g\n", i, ws[i], we[i], wb[i], wp[i]);
#endif
}
@@ -2916,7 +2914,7 @@ pli_p7_env_def(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam,
nenv = 0;
seq = esl_sq_CreateDigital(sq->abc);
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("\nPIPELINE p7EnvelopeDef() %s %" PRId64 " residues\n", sq->name, sq->n);
#endif
@@ -2971,7 +2969,7 @@ pli_p7_env_def(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam,
Tgm = *opt_Tgm;
for (i = 0; i < nwin; i++) {
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("p7 envdef win: %4d of %4d [%6" PRId64 "..%6" PRId64 "] pass: %" PRId64 "\n", i, nwin, ws[i], we[i], pli->cur_pass_idx);
#endif
/* if we require first or final residue, and don't have it, then
@@ -3062,7 +3060,7 @@ pli_p7_env_def(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam,
P = esl_exp_surv (sc_for_pvalue, p7_evparam[CM_p7_GFMU], p7_evparam[CM_p7_GFLAMBDA]);
}
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
if(P > pli->F4) {
printf("KILLED window %5d [%10" PRId64 "..%10" PRId64 "] gFwd %6.2f bits P %g\n", i, ws[i], we[i], sc_for_pvalue, P);
}
@@ -3073,7 +3071,7 @@ pli_p7_env_def(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam,
pli->acct[pli->cur_pass_idx].n_past_gfwd++;
pli->acct[pli->cur_pass_idx].pos_past_gfwd += wlen;
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("SURVIVOR window %5d [%10" PRId64 "..%10" PRId64 "] survived gFwd %6.2f bits P %g\n", i, ws[i], we[i], sc_for_pvalue, P);
#endif
@@ -3096,7 +3094,7 @@ pli_p7_env_def(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam,
P = esl_exp_surv (sc_for_pvalue, p7_evparam[CM_p7_GFMU], p7_evparam[CM_p7_GFLAMBDA]);
}
if(P > pli->F4b) continue;
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("SURVIVOR window %5d [%10" PRId64 "..%10" PRId64 "] survived gFwdBias %6.2f bits P %g\n", i, ws[i], we[i], sc_for_pvalue, P);
#endif
pli->acct[pli->cur_pass_idx].n_past_gfwdbias++;
@@ -3180,7 +3178,7 @@ pli_p7_env_def(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam,
continue;
}
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("SURVIVOR envelope [%10" PRId64 "..%10" PRId64 "] survived F5 %6.2f bits P %g\n", pli->ddef->dcl[d].ienv + ws[i] - 1, pli->ddef->dcl[d].jenv + ws[i] - 1, env_sc_for_pvalue, P);
#endif
pli->acct[pli->cur_pass_idx].n_past_edef++;
@@ -3204,7 +3202,7 @@ pli_p7_env_def(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam,
continue;
}
}
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("SURVIVOR envelope [%10" PRId64 "..%10" PRId64 "] survived F5-bias %6.2f bits P %g\n", pli->ddef->dcl[d].ienv + ws[i] - 1, pli->ddef->dcl[d].jenv + ws[i] - 1, env_sc_for_pvalue, P);
#endif
pli->acct[pli->cur_pass_idx].n_past_edefbias++;
@@ -3320,12 +3318,12 @@ pli_cyk_env_filter(CM_PIPELINE *pli, off_t cm_offset, const ESL_SQ *sq, int64_t
*/
cyk_env_cutoff = cm->expA[pli->fcyk_cm_exp_mode]->mu_extrap + (log(pli->F6env) / (-1 * cm->expA[pli->fcyk_cm_exp_mode]->lambda));
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("\nPIPELINE EnvCYKFilter() %s %" PRId64 " residues\n", sq->name, sq->n);
#endif
for (i = 0; i < np7env; i++) {
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("\nSURVIVOR Envelope %5d [%10ld..%10ld] being passed to EnvCYKFilter pass: %" PRId64 "\n", i, p7es[i], p7ee[i], pli->cur_pass_idx);
#endif
cm->search_opts = pli->fcyk_cm_search_opts;
@@ -3353,7 +3351,7 @@ pli_cyk_env_filter(CM_PIPELINE *pli, off_t cm_offset, const ESL_SQ *sq, int64_t
p7ee[i] = cyk_envj;
}
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("SURVIVOR envelope [%10" PRId64 "..%10" PRId64 "] survived EnvCYKFilter %6.2f bits P %g\n", p7es[i], p7ee[i], sc, P);
#endif
}
@@ -3498,7 +3496,7 @@ pli_cyk_seq_filter(CM_PIPELINE *pli, off_t cm_offset, const ESL_SQ *sq, CM_t **o
iwin = ESL_MAX(1, sq_hitlist->hit[h]->stop - (cm->W-1));
jwin = ESL_MIN(sq->n, sq_hitlist->hit[h]->start + (cm->W-1));
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
double P = esl_exp_surv(sq_hitlist->hit[h]->score, cm->expA[pli->fcyk_cm_exp_mode]->mu_extrap, cm->expA[pli->fcyk_cm_exp_mode]->lambda);
printf("SURVIVOR window [%10" PRId64 "..%10" PRId64 "] survived SeqCYKFilter %6.2f bits P %g\n", iwin, jwin, sq_hitlist->hit[h]->score, P);
#endif
@@ -3601,7 +3599,7 @@ pli_final_stage(CM_PIPELINE *pli, off_t cm_offset, const ESL_SQ *sq, int64_t *es
save_tau = cm->tau;
for (i = 0; i < nenv; i++) {
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("\nSURVIVOR Envelope %5d [%10ld..%10ld] being passed to Final stage pass: %" PRId64 "\n", i, es[i], ee[i], pli->cur_pass_idx);
#endif
nhit = hitlist->N;
@@ -3658,7 +3656,7 @@ pli_final_stage(CM_PIPELINE *pli, off_t cm_offset, const ESL_SQ *sq, int64_t *es
if ((status = esl_strdup(cm->acc, -1, &(hit->acc))) != eslOK) ESL_FAIL(eslEMEM, pli->errbuf, "allocation failure");
if ((status = esl_strdup(cm->desc, -1, &(hit->desc))) != eslOK) ESL_FAIL(eslEMEM, pli->errbuf, "allocation failure");
}
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("SURVIVOR envelope [%10ld..%10ld] survived Inside %6.2f bits P %g\n", hit->start, hit->stop, hit->score, hit->pvalue);
#endif
/* Get an alignment of the hit.
@@ -3812,7 +3810,7 @@ pli_final_stage_hmmonly(CM_PIPELINE *pli, off_t cm_offset, P7_OPROFILE *om, P7_B
nullsc2 = (float)loc_window_length * log((float)loc_window_length/(loc_window_length+1)) + log(1./(loc_window_length+1));
for (i = 0; i < nwin; i++) {
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("p7 final stage win: %4d of %4d [%6" PRId64 "..%6" PRId64 "] pass: %" PRId64 "\n", i, nwin, ws[i], we[i], pli->cur_pass_idx);
#endif
@@ -3906,7 +3904,7 @@ pli_final_stage_hmmonly(CM_PIPELINE *pli, off_t cm_offset, P7_OPROFILE *om, P7_B
p7_alidisplay_Destroy(pli->ddef->dcl[d].ad);
pli->ddef->dcl[d].ad = NULL;
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("SURVIVOR envelope [%10ld..%10ld] survived Final HMM ONLY stage %6.2f bits P %g\n", hit->start, hit->stop, hit->score, hit->pvalue);
#endif

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