Merge pull request #171 from smithlabcode/round-two-silence-more-warnings-on-osx-clang

Silencing warnings (round two)

Author: andrewdavidsmith

src/analysis/hmr-rep.cpp

@@ -105,22 +105,19 @@ get_domain_scores_rep(const vector<bool> &state_ids,
 
 static void
 build_domains(const vector<MSite> &cpgs,
-              const vector<double> &post_scores,
               const vector<size_t> &reset_points,
               const vector<bool> &state_ids,
               vector<GenomicRegion> &domains) {
 
   size_t n_cpgs = 0, n_domains = 0, reset_idx = 1, prev_end = 0;
   bool in_domain = false;
-  double score = 0;
   for (size_t i = 0; i < state_ids.size(); ++i) {
     if (reset_points[reset_idx] == i) {
       if (in_domain) {
         in_domain = false;
         domains.back().set_end(prev_end);
         domains.back().set_score(n_cpgs);
         n_cpgs = 0;
-        score = 0;
       }
       ++reset_idx;
     }
@@ -131,14 +128,12 @@ build_domains(const vector<MSite> &cpgs,
         domains.back().set_name("HYPO" + to_string(n_domains++));
       }
       ++n_cpgs;
-      score += post_scores[i];
     }
     else if (in_domain) {
       in_domain = false;
       domains.back().set_end(prev_end);
       domains.back().set_score(n_cpgs);
       n_cpgs = 0;
-      score = 0;
     }
     prev_end = cpgs[i].pos + 1;
   }
@@ -505,7 +500,7 @@ main_hmr_rep(int argc, const char **argv) {
       fdr_cutoff = get_stepup_cutoff(p_values, 0.01);
 
     vector<GenomicRegion> domains;
-    build_domains(cpgs, posteriors, reset_points, state_ids, domains);
+    build_domains(cpgs, reset_points, state_ids, domains);
 
     std::ofstream of;
     if (!outfile.empty()) of.open(outfile);

src/analysis/hmr.cpp

@@ -108,7 +108,7 @@ get_domain_scores(const vector<bool> &state_ids,
                   const vector<size_t> &reset_points,
                   vector<double> &scores) {
 
-  size_t n_cpgs = 0, reset_idx = 1;
+  size_t reset_idx = 1;
   bool in_domain = false;
   double score = 0;
   for (size_t i = 0; i < state_ids.size(); ++i) {
@@ -123,7 +123,6 @@ get_domain_scores(const vector<bool> &state_ids,
     if (state_ids[i]) {
       in_domain = true;
       score += 1.0 - (meth[i].first/(meth[i].first + meth[i].second));
-      ++n_cpgs;
     }
     else if (in_domain) {
       in_domain = false;
@@ -132,30 +131,26 @@ get_domain_scores(const vector<bool> &state_ids,
     }
   }
 
-  if (in_domain) {
+  if (in_domain)
     scores.push_back(score);
-  }
 }
 
 
 static void
 build_domains(const vector<MSite> &cpgs,
-              const vector<double> &post_scores,
               const vector<size_t> &reset_points,
               const vector<bool> &state_ids,
               vector<GenomicRegion> &domains) {
 
   size_t n_cpgs = 0, reset_idx = 1, prev_end = 0;
   bool in_domain = false;
-  double score = 0;
   for (size_t i = 0; i < state_ids.size(); ++i) {
     if (reset_points[reset_idx] == i) {
       if (in_domain) {
         in_domain = false;
         domains.back().set_end(prev_end);
         domains.back().set_score(n_cpgs);
         n_cpgs = 0;
-        score = 0;
       }
       ++reset_idx;
     }
@@ -166,14 +161,12 @@ build_domains(const vector<MSite> &cpgs,
         domains.back().set_name("HYPO" + to_string(domains.size()));
       }
       ++n_cpgs;
-      score += post_scores[i];
     }
     else if (in_domain) {
       in_domain = false;
       domains.back().set_end(prev_end);
       domains.back().set_score(n_cpgs);
       n_cpgs = 0;
-      score = 0;
     }
     prev_end = cpgs[i].pos + 1;
   }
@@ -556,7 +549,7 @@ main_hmr(int argc, const char **argv) {
                         p_fb, p_bf, domain_score_cutoff);
 
     vector<GenomicRegion> domains;
-    build_domains(cpgs, posteriors, reset_points, state_ids, domains);
+    build_domains(cpgs, reset_points, state_ids, domains);
 
     std::ofstream of;
     if (!outfile.empty()) of.open(outfile.c_str());

src/analysis/levels.cpp

@@ -146,13 +146,10 @@ main_levels(int argc, const char **argv) {
     LevelsCounter cytosines("cytosines");
 
     MSite site, prev_site;
-    size_t chrom_count = 0;
 
     while (read_site(in, site)) {
-      if (site.chrom != prev_site.chrom) {
-        ++chrom_count;
+      if (site.chrom != prev_site.chrom)
         if (VERBOSE) cerr << "processing " << site.chrom << endl;
-      }
 
       cytosines.update(site);
 

src/analysis/metagene.cpp

@@ -169,8 +169,6 @@ metagene(int argc, const char **argv) {
     bamxx::bgzf_file cpgin(cpg_file_name, "r");
     if (!cpgin) throw runtime_error("failed to open file: " + cpg_file_name);
 
-    uint32_t total_features = 0u;
-
     vector<MSite> sites;
     string line;
     chrom_name.clear();
@@ -185,7 +183,6 @@ metagene(int argc, const char **argv) {
           if (show_progress)
             cerr << "[sites=" << sites.size() << " features=" << n_features
                  << "]" << endl;
-          total_features += n_features;
           sites.clear();
         }
         if (show_progress) cerr << "[processing: " << the_site.chrom << "]";
@@ -202,7 +199,6 @@ metagene(int argc, const char **argv) {
       if (show_progress)
         cerr << "[sites=" << sites.size() << " features=" << n_features << "]"
              << endl;
-      total_features += n_features;
     }
 
     collapse_bins(bin_size, levels);

src/analysis/methcounts.cpp

@@ -195,24 +195,6 @@ has_mutated(const char base, const CountSet &cs) {
            : (cs.pG < MUTATION_DEFINING_FRACTION * (cs.pos_total()));
 }
 
-static inline bool
-is_cpg_site(const string &s, const size_t pos) {
-  return is_cytosine(s[pos])
-           ? is_guanine(s[pos + 1])
-           : (is_guanine(s[pos]) ? (pos > 0 && is_cytosine(s[pos - 1]))
-                                 : false);
-}
-
-static inline size_t
-get_chrom_id(const string &chrom_name,
-             const unordered_map<string, size_t> &cl) {
-  auto the_chrom(cl.find(chrom_name));
-  if (the_chrom == end(cl))
-    throw dnmt_error("could not find chrom: " + chrom_name);
-
-  return the_chrom->second;
-}
-
 static const char *tag_values[] = {
   "CpG", // 0
   "CHH", // 1

src/common/EpireadStats.cpp

@@ -57,11 +57,11 @@ get_n_cpgs(const vector<epi_r> &reads) {
   return n_cpgs;
 }
 
-static inline bool
-is_meth(const epi_r &r, const uint32_t pos) {return (r.seq[pos] == 'C');}
+// static inline bool
+// is_meth(const epi_r &r, const uint32_t pos) {return (r.seq[pos] == 'C');}
 
-static inline bool
-un_meth(const epi_r &r, const uint32_t pos) {return (r.seq[pos] == 'T');}
+// static inline bool
+// un_meth(const epi_r &r, const uint32_t pos) {return (r.seq[pos] == 'T');}
 
 inline double
 log_likelihood(const epi_r &r, const vector<double> &a) {

src/common/TwoStateHMM.cpp

@@ -537,7 +537,6 @@ TwoStateHMM::PosteriorScores(const vector<pair<double, double> > &values,
   get_emissions(begin(values), end(values), begin(fg_emit), fg_distro);
   get_emissions(begin(values), end(values), begin(bg_emit), bg_distro);
 
-  double total_loglik = 0;
   for (size_t i = 0; i < reset_points.size() - 1; ++i) {
     const double score =
       forward_algorithm(reset_points[i], reset_points[i + 1],
@@ -552,8 +551,6 @@ TwoStateHMM::PosteriorScores(const vector<pair<double, double> > &values,
                        fg_emit, bg_emit, backward);
 
     assert(fabs(score - backward_score)/max(score, backward_score) < tolerance);
-
-    total_loglik += score;
   }
 
   get_posteriors(forward, backward, posteriors);
@@ -620,7 +617,6 @@ TwoStateHMM::TransitionPosteriors(const vector<pair<double, double> > &values,
   get_emissions(begin(values), end(values), begin(fg_emit), fg_distro);
   get_emissions(begin(values), end(values), begin(bg_emit), bg_distro);
 
-  double total_loglik = 0;
   for (size_t i = 0; i < reset_points.size() - 1; ++i) {
     const double score =
       forward_algorithm(reset_points[i], reset_points[i + 1],
@@ -635,8 +631,6 @@ TwoStateHMM::TransitionPosteriors(const vector<pair<double, double> > &values,
                        fg_emit, bg_emit, backward);
 
     assert(fabs(score - backward_score)/max(score, backward_score) < tolerance);
-
-    total_loglik += score;
   }
 
   scores.clear();
@@ -1074,7 +1068,6 @@ TwoStateHMM::PosteriorScores(const vector<vector<pair<double, double> > > &value
   get_emissions_rep(values, fg_emit, fg_distro);
   get_emissions_rep(values, bg_emit, bg_distro);
 
-  double total_loglik = 0;
   for (size_t i = 0; i < reset_points.size() - 1; ++i) {
     const double score =
       forward_algorithm(reset_points[i], reset_points[i + 1],
@@ -1089,8 +1082,6 @@ TwoStateHMM::PosteriorScores(const vector<vector<pair<double, double> > > &value
                        fg_emit, bg_emit, backward);
 
     assert(fabs(score - backward_score)/max(score, backward_score) < tolerance);
-
-    total_loglik += score;
   }
 
   get_posteriors(forward, backward, posteriors);

src/common/TwoStateHMM_PMD.cpp

@@ -625,7 +625,6 @@ TwoStateHMM::PosteriorScores_rep(
   const vector<unique_ptr<EmissionDistribution>> &fg_distro,
   const vector<unique_ptr<EmissionDistribution>> &bg_distro,
   const vector<bool> &classes, vector<double> &llr_scores) const {
-  double total_score = 0;
 
   const double lp_sf = log(p_sf);
   const double lp_sb = log(p_sb);
@@ -669,8 +668,6 @@ TwoStateHMM::PosteriorScores_rep(
                   max(score, backward_score)) > 1e-10)
       cerr << "fabs(score - backward_score)/"
            << "max(score, backward_score) > 1e-10" << endl;
-
-    total_score += score;
   }
 
   llr_scores.resize(values[0].size());
@@ -737,7 +734,6 @@ TwoStateHMM::TransitionPosteriors_rep(
       const size_t transition,
       vector<double> &scores) const {
 
-  double total_score = 0;
   size_t NREP = values.size();
   const double lp_sf = log(p_sf);
   const double lp_sb = log(p_sb);
@@ -773,9 +769,7 @@ TwoStateHMM::TransitionPosteriors_rep(
     if (DEBUG && (fabs(score - backward_score)/
           max(score, backward_score)) > 1e-10)
       cerr << "fabs(score - backward_score)/"
-       << "max(score, backward_score) > 1e-10" << endl;
-
-    total_score += score;
+           << "max(score, backward_score) > 1e-10" << endl;
   }
   scores.resize(values[0].size());
   size_t j = 0;

src/common/bam_record_utils.cpp

@@ -70,16 +70,16 @@ bam_get_aux(const bam1_t *b) {
          ((b->core.l_qseq + 1) >> 1) + b->core.l_qseq;
 }
 
-static inline int
-bam_get_l_aux(const bam1_t *b) {
-  return b->l_data - (b->core.l_qname + (b->core.n_cigar << 2) +
-                      ((b->core.l_qseq + 1) >> 1) + b->core.l_qseq);
-}
+// static inline int
+// bam_get_l_aux(const bam1_t *b) {
+//   return b->l_data - (b->core.l_qname + (b->core.n_cigar << 2) +
+//                       ((b->core.l_qseq + 1) >> 1) + b->core.l_qseq);
+// }
 
-static inline bool
-bam_same_orientation(const bam1_t *a, const bam1_t *b) {
-  return ((a->core.flag ^ b->core.flag) & BAM_FREVERSE) != 0;
-}
+// static inline bool
+// bam_same_orientation(const bam1_t *a, const bam1_t *b) {
+//   return ((a->core.flag ^ b->core.flag) & BAM_FREVERSE) != 0;
+// }
 
 static void
 roundup_to_power_of_2(uint32_t &x) {
@@ -255,10 +255,10 @@ bam_set1_wrapper(bam1_t *bam, const size_t l_qname, const char *qname,
   return static_cast<int>(data_len);
 }
 
-static inline size_t
-bam_get_n_cigar(const bam1_t *b) {
-  return b->core.n_cigar;
-}
+// static inline size_t
+// bam_get_n_cigar(const bam1_t *b) {
+//   return b->core.n_cigar;
+// }
 
 static inline uint32_t
 to_insertion(const uint32_t x) {
@@ -373,24 +373,24 @@ get_l_qseq(const bam1_t *b) {
   return b->core.l_qseq;
 }
 
-static inline void
-complement_seq(char *first, char *last) {
-  for (; first != last; ++first) {
-    assert(valid_base(*first));
-    *first = complement(*first);
-  }
-}
+// static inline void
+// complement_seq(char *first, char *last) {
+//   for (; first != last; ++first) {
+//     assert(valid_base(*first));
+//     *first = complement(*first);
+//   }
+// }
 
-static inline void
-reverse(char *a, char *b) {
-  char *p1, *p2;
-  for (p1 = a, p2 = b - 1; p2 > p1; ++p1, --p2) {
-    *p1 ^= *p2;
-    *p2 ^= *p1;
-    *p1 ^= *p2;
-    assert(valid_base(*p1) && valid_base(*p2));
-  }
-}
+// static inline void
+// reverse(char *a, char *b) {
+//   char *p1, *p2;
+//   for (p1 = a, p2 = b - 1; p2 > p1; ++p1, --p2) {
+//     *p1 ^= *p2;
+//     *p2 ^= *p1;
+//     *p1 ^= *p2;
+//     assert(valid_base(*p1) && valid_base(*p2));
+//   }
+// }
 
 // return value is the number of cigar ops that are fully consumed in
 // order to read n_ref, while "partial_oplen" is the number of bases
@@ -542,15 +542,15 @@ flip_conversion(bam_rec &aln) {
   flip_conversion(aln.b);
 }
 
-static inline bool
-are_mates(const bam1_t *one, const bam1_t *two) {
-  return one->core.mtid == two->core.tid && one->core.mpos == two->core.pos &&
-         (one->core.flag & BAM_FREVERSE) != (one->core.flag & BAM_FREVERSE);
-  // below is a consistency check and should not be necessary
-  /* &&
-     two->core.mtid == one->core.tid &&
-     two->core.mpos == one->core.pos; */
-}
+// static inline bool
+// are_mates(const bam1_t *one, const bam1_t *two) {
+//   return one->core.mtid == two->core.tid && one->core.mpos == two->core.pos &&
+//          (one->core.flag & BAM_FREVERSE) != (one->core.flag & BAM_FREVERSE);
+//   // below is a consistency check and should not be necessary
+//   /* &&
+//      two->core.mtid == one->core.tid &&
+//      two->core.mpos == one->core.pos; */
+// }
 
 static inline int
 truncate_overlap(const bam1_t *a, const uint32_t overlap, bam1_t *c) {