Add mapq filter in caller

clusterer.cpp

@@ -120,6 +120,8 @@ bool Clusterer::load_batch(int p) {
       spdlog::warn("Non primary alignment.. Is bam file smoothed?");
       continue;
     }
+    if (aln->core.qual < config->min_mapq)
+      continue;
     char *qname = bam_get_qname(aln);
     if (SFSs->find(qname) == SFSs->end())
       continue;
@@ -527,6 +529,8 @@ void Clusterer::fill_clusters() {
       if (aln->core.flag & BAM_FUNMAP || aln->core.flag & BAM_FSUPPLEMENTARY ||
           aln->core.flag & BAM_FSECONDARY)
         continue;
+      if (aln->core.qual < config->min_mapq)
+        continue;
       int hp_t = bam_aux_get(aln, "HP") != NULL
                      ? bam_aux2i(bam_aux_get(aln, "HP"))
                      : 0;

config.cpp

@@ -40,6 +40,7 @@ Configuration::Configuration()
     ("bsize", "", cxxopts::value<int>())
     ("omax", "", cxxopts::value<int>())
     ("min-sv-length", "", cxxopts::value<int>())
+    ("min-mapq", "", cxxopts::value<int>())
     ("min-cluster-weight", "", cxxopts::value<int>())
     ("clipped", "", cxxopts::value<bool>()->default_value("false"))
     ("noref", "", cxxopts::value<bool>()->default_value("false"))
@@ -84,6 +85,8 @@ void Configuration::parse(int argc, char **argv) {
     min_sv_length = max(25, results["min-sv-length"].as<int>());
   if (results.count("min-cluster-weight"))
     min_cluster_weight = results["min-cluster-weight"].as<int>();
+  if (results.count("min-mapq"))
+    min_mapq = results["min-mapq"].as<int>();
   if (results.count("l"))
     min_ratio = results["l"].as<float>();
   if (results.count("acc"))

config.hpp

@@ -42,6 +42,7 @@ static const char CALL_USAGE_MESSAGE[] =
   "      --min-cluster-weight <INT>       minimum number of supporting superstrings for a call to be reported (default: 2)\n"
   "      --min-sv-length <INT>            minimum length of reported SVs (default: 25)\n"
   "      --noref                          do not report 0/0 calls\n"
+  "      --min-mapq                       minimum mapping quality (default: 20)\n"
   "      --clipped                        calls SVs from clipped SFS (EXPERIMENTAL)\n"
   "      --threads <INT>                  number of threads to use (default: 4)\n"
   "      --help                           print help message\n";
@@ -79,6 +80,7 @@ class Configuration {
   uint flank = 100;
   uint ksize = 7;
   uint min_sv_length = 25;
+  uint min_mapq = 20;
   int min_indel_length = 20;
   uint min_cluster_weight = 2;
   float min_ratio = 0.97; // FIXME: change name