Merge branch 'develop' into main

Author: Genevieve Krause

src/Makefile.in

@@ -132,6 +132,7 @@ OBJS =  build.o\
 	p7_pipeline.o\
 	p7_prior.o\
 	p7_profile.o\
+    p7_search_builder.o\
 	p7_spensemble.o\
 	p7_tophits.o\
 	p7_trace.o\

src/bathbuild.c

@@ -395,6 +395,7 @@ apply_fixed_gap_params(P7_HMM *hmm, double popen, double pextend){
 int
 main(int argc, char **argv)
 {
+
   ESL_GETOPTS     *go = NULL;	/* command line processing                 */
   ESL_STOPWATCH   *w  = esl_stopwatch_Create();
   struct cfg_s     cfg;
@@ -416,6 +417,7 @@ main(int argc, char **argv)
   cfg.ofp         = NULL;	           
   cfg.fmt         = eslMSAFILE_UNKNOWN;    /* autodetect alignment format by default. */ 
   cfg.afp         = NULL;	           
+  cfg.sfp         = NULL;
   cfg.abc         = NULL;	           
   cfg.hmmfp       = NULL;	           
   cfg.postmsafile = esl_opt_GetString(go, "-O"); /* NULL by default */
@@ -483,8 +485,10 @@ main(int argc, char **argv)
     if (cfg.abc)   esl_alphabet_Destroy(cfg.abc);
     if (cfg.hmmfp) fclose(cfg.hmmfp);
   }
+  
   esl_getopts_Destroy(go);
   esl_stopwatch_Destroy(w);
+  
   return 0;
 }
 
@@ -499,6 +503,7 @@ main(int argc, char **argv)
 static int
 usual_master(const ESL_GETOPTS *go, struct cfg_s *cfg)
 {
+  
   int              ncpus    = 0;
   int              infocnt  = 0;
   WORKER_INFO     *info     = NULL;
@@ -677,7 +682,7 @@ usual_master(const ESL_GETOPTS *go, struct cfg_s *cfg)
       esl_threads_Destroy(threadObj);
   }
 #endif
-
+  
   free(info);
   return eslOK;
 

src/bathsearch.c

@@ -1925,6 +1925,9 @@ extern int         p7_profile_GetT(const P7_PROFILE *gm, char st1, int k1,
 extern int         p7_profile_Validate(const P7_PROFILE *gm, char *errbuf, float tol);
 extern int         p7_profile_Compare(P7_PROFILE *gm1, P7_PROFILE *gm2, float tol);
 
+/* p7_search_builder.c */
+extern int p7_search_builder(const ESL_GETOPTS *go, ESL_ALPHABET *abc, char *infile, char *hmmfile, int fmt);
+
 /* p7_spensemble.c */
 P7_SPENSEMBLE *p7_spensemble_Create(int init_n, int init_epc, int init_sigc);
 extern int     p7_spensemble_Reuse(P7_SPENSEMBLE *sp);

src/hmmer.h

@@ -490,8 +490,7 @@ p7_alidisplay_fs_Create(const P7_TRACE *tr, int which, const P7_PROFILE *gm, con
   }
 
   if (ad->ppline != NULL) {
-    for (z = z1; z <= z2; z++) 
-	    ad->ppline[z-z1] = ( (tr->st[z] == p7T_D) ? '.' : p7_alidisplay_EncodePostProb(tr->pp[z]));
+    for (z = z1; z <= z2; z++) ad->ppline[z-z1] = ( (tr->st[z] == p7T_D) ? '.' : p7_alidisplay_EncodePostProb(tr->pp[z]));
 
 	    ad->ppline[z-z1] = '\0';
   }