From 42a0d7d279a6670d627e43bc1695cb7fdbb5d826 Mon Sep 17 00:00:00 2001
From: Andrej Fischer <af7@sanger.ac.uk>
Date: Wed, 26 Feb 2014 15:27:26 +0000
Subject: [PATCH] changed BIC complexity to be less conservative

---
 run-example.sh | 2 +-
 src/clone.cpp  | 7 ++++---
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/run-example.sh b/run-example.sh
index 0e176e5..1e63093 100644
--- a/run-example.sh
+++ b/run-example.sh
@@ -56,7 +56,7 @@ then
 ### cloneHD ###
     echo "*** cloneHD ***"
     echo
-    cmd="$cloneHD --cna $tumorCNA --baf $tumorBAF --pre ${results}/tumor --bias $bias --seed 123 --trials 1\
+    cmd="$cloneHD --cna $tumorCNA --baf $tumorBAF --pre ${results}/tumor --bias $bias --seed 123 --trials 3\
  --nmax 3 --force --max-tcn 4 --cna-jumps $tumorCNAjumps --baf-jumps $tumorBAFjumps --min-jump 0.01 --restarts 20"    
     echo $cmd
     $cmd
diff --git a/src/clone.cpp b/src/clone.cpp
index c0203fb..9786731 100755
--- a/src/clone.cpp
+++ b/src/clone.cpp
@@ -540,6 +540,7 @@ void Clone::get_complexity(){
     for (int j=0; j<nClones; j++){
       val *= (double) maxtcn_per_clone[chr][j] + 1;
     }
+    val -= 1.0;
     if (cnaEmit->is_set && cnaEmit->chrs.count(chr)==1){
       cnaC += val*double(cnaEmit->nSites[cnaEmit->idx_of[chr]]);
       cnaN += double(cnaEmit->nSites[cnaEmit->idx_of[chr]]);      
@@ -559,11 +560,11 @@ void Clone::get_complexity(){
     complexity += cnaC / cnaN;
     size += cnaN;
   }
-  if (bafEmit->is_set){
+  /*if (bafEmit->is_set){
     complexity += bafC / bafN;
     size += bafN;
-  }
-  if (snvEmit->is_set){
+    }*/
+  else if (snvEmit->is_set){
     complexity += snvC / snvN;
     size += snvN;
     if (learn_priors){