Add CLI flag to ignore haplotagging information

Author: ldenti

caller.cpp

@@ -104,12 +104,17 @@ vector<Cluster> Caller::split_cluster(const Cluster &cluster) {
   Cluster cluster_2 = cluster;
   cluster_2.clear();
   for (const SubRead &sr : cluster.subreads) {
-    if (sr.htag == 0)
+    if (config->useht) {
+      if (sr.htag == 1)
+        cluster_1.add_subread(sr);
+      else if (sr.htag == 2)
+        cluster_2.add_subread(sr);
+      else
+        // 0 or no tag
+        cluster_0.add_subread(sr);
+    } else {
       cluster_0.add_subread(sr);
-    else if (sr.htag == 1)
-      cluster_1.add_subread(sr);
-    else if (sr.htag == 2)
-      cluster_2.add_subread(sr);
+    }
   }
   cluster_0.cov1 = -1;
   cluster_0.cov2 = -1;
@@ -118,13 +123,6 @@ vector<Cluster> Caller::split_cluster(const Cluster &cluster) {
   cluster_2.cov0 = -1;
   cluster_2.cov1 = -1;
 
-  assert(cluster_0.size() <= cluster_0.cov0 &&
-         cluster_1.size() <= cluster_1.cov1 &&
-         cluster_2.size() <= cluster_2.cov2);
-
-  assert(cluster_1.size() != 0 || cluster_2.size() != 0 ||
-         cluster_0.size() != 0);
-
   vector<Cluster> out_subclusters;
   if (cluster_1.size() == 0 && cluster_2.size() == 0) {
     // no alignment is tagged, use length

config.cpp

@@ -44,6 +44,7 @@ Configuration::Configuration()
     ("min-cluster-weight", "", cxxopts::value<int>())
     ("clipped", "", cxxopts::value<bool>()->default_value("false"))
     ("noref", "", cxxopts::value<bool>()->default_value("false"))
+    ("noht", "", cxxopts::value<bool>()->default_value("false"))
     ("noassemble", "", cxxopts::value<bool>()->default_value("false"))
     ("noputative", "", cxxopts::value<bool>()->default_value("false"))
     ("binary", "", cxxopts::value<bool>()->default_value("false"))
@@ -93,6 +94,7 @@ void Configuration::parse(int argc, char **argv) {
     al_accuracy = results["acc"].as<float>();
   binary = results["binary"].as<bool>();
   clipped = results["clipped"].as<bool>();
+  useht = !results["noht"].as<bool>();
   noref = results["noref"].as<bool>();
   assemble = !(results["noassemble"].as<bool>());
   putative = !(results["noputative"].as<bool>());

config.hpp

@@ -43,6 +43,7 @@ static const char CALL_USAGE_MESSAGE[] =
   "      --clusters <FILE>                store clusters to this file (default: do not store)\n"
   "      --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"
+  "      --noht                           do not use haplotagging information even if present\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"
@@ -86,6 +87,7 @@ class Configuration {
   int min_indel_length = 20;
   uint min_cluster_weight = 2;
   float min_ratio = 0.97; // FIXME: change name
+  bool useht = true;
   bool noref = false;
   bool clipped = false;