Add argument to change accuracy percentile of smoothing

Author: ldenti

config.cpp

@@ -42,6 +42,7 @@ Configuration::Configuration()
     ("min-sv-length", "", cxxopts::value<int>())
     ("min-mapq", "", cxxopts::value<int>())
     ("min-cluster-weight", "", cxxopts::value<int>())
+    ("accq", "", cxxopts::value<float>())
     ("clipped", "", cxxopts::value<bool>()->default_value("false"))
     ("noref", "", cxxopts::value<bool>()->default_value("false"))
     ("noht", "", cxxopts::value<bool>()->default_value("false"))
@@ -68,7 +69,8 @@ void Configuration::parse(int argc, char **argv) {
   if (results.count("index"))
     index = results["index"].as<std::string>();
   if (results.count("fastx"))
-    fastq = results["fastx"].as<std::string>(); // FIXME: use fastx here and in pingpong
+    fastq = results["fastx"]
+                .as<std::string>(); // FIXME: use fastx here and in pingpong
   if (results.count("overlap"))
     overlap = results["overlap"].as<int>();
   if (results.count("bsize"))
@@ -87,6 +89,8 @@ void Configuration::parse(int argc, char **argv) {
     min_cluster_weight = results["min-cluster-weight"].as<int>();
   if (results.count("min-mapq"))
     min_mapq = results["min-mapq"].as<int>();
+  if (results.count("accq"))
+    accq = results["accq"].as<float>();
   if (results.count("l"))
     min_ratio = results["l"].as<float>();
   binary = results["binary"].as<bool>();

config.hpp

@@ -24,7 +24,8 @@ static const char INDEX_USAGE_MESSAGE[] =
 
 static const char SMOOTH_USAGE_MESSAGE[] =
   "SVDSS smooth --reference <reference> --bam <bam>\n"
-  "      --min-mapq                       minimum mapping quality (default: 20)\n"
+  "      --min-mapq <INT>                 minimum mapping quality (default: 20)\n"
+  "      --accq <FLOAT>                   accuracy percentile for alignments filtering (default: 0.98)\n"
   "      --threads <INT>                  number of threads to use (default: 4)\n"
   "      --help                           print help message\n";
 
@@ -69,6 +70,9 @@ class Configuration {
   bool verbose = false;
   bool help = false;
 
+  // smoother
+  float accq = 0.98;
+
   // pingpong.index
   bool binary = false;
   // pingpong.search

smoother.cpp

@@ -342,7 +342,7 @@ double Smoother::compute_maxaccuracy() {
   hts_idx_destroy(bam_index);
   sam_close(bam_file);
   std::sort(accuracies.begin(), accuracies.end());
-  return quantile(accuracies, 0.98);
+  return quantile(accuracies, config->accq);
 }
 
 // BAM writing based on https://www.biostars.org/p/181580/