From 7999ce920fd3b3307e3b05797259701fe51d705d Mon Sep 17 00:00:00 2001
From: Shifu Chen <chen@haplox.com>
Date: Thu, 14 Jun 2018 16:40:40 +0800
Subject: [PATCH] dont output deletion and untranslated fusions by default

---
 src/common.h           |  2 +-
 src/fusionmapper.cpp   |  6 ++++++
 src/globalsettings.cpp |  4 +++-
 src/globalsettings.h   |  8 ++++++++
 src/htmlreporter.cpp   | 10 +++++++++-
 src/jsonreporter.cpp   |  6 ++++++
 src/main.cpp           |  8 +++++++-
 7 files changed, 40 insertions(+), 4 deletions(-)

diff --git a/src/common.h b/src/common.h
index 790abfb..ab94349 100644
--- a/src/common.h
+++ b/src/common.h
@@ -1,7 +1,7 @@
 #ifndef COMMON_H
 #define COMMON_H
 
-#define FUSIONSCAN_VER "0.5.0"
+#define FUSIONSCAN_VER "0.6.0"
 
 #define _DEBUG true
 
diff --git a/src/fusionmapper.cpp b/src/fusionmapper.cpp
index 870cfad..eea535a 100644
--- a/src/fusionmapper.cpp
+++ b/src/fusionmapper.cpp
@@ -303,6 +303,12 @@ void FusionMapper::clusterMatches() {
             frs[f].calcUnique();
             frs[f].updateInfo(fusionList);
             if(frs[f].isQualified()) {
+                if(!GlobalSettings::outputDeletions && frs[f].isDeletion())
+                    continue;
+                if(frs[f].isLeftProteinForward() != frs[f].isRightProteinForward()) {
+                    if(!GlobalSettings::outputUntranslated)
+                        continue;
+                }
                 frs[f].print(fusionList);
                 mFusionResults.push_back(frs[f]);
             }
diff --git a/src/globalsettings.cpp b/src/globalsettings.cpp
index 3710706..3d35309 100644
--- a/src/globalsettings.cpp
+++ b/src/globalsettings.cpp
@@ -2,4 +2,6 @@
 
 bool GlobalSettings::markedOnlyForVCF = false;
 int GlobalSettings::uniqueRequirement = 2;
-int GlobalSettings::deletionThreshold = 50;
\ No newline at end of file
+int GlobalSettings::deletionThreshold = 50;
+bool GlobalSettings::outputDeletions = false;
+bool GlobalSettings::outputUntranslated = false;
\ No newline at end of file
diff --git a/src/globalsettings.h b/src/globalsettings.h
index 3e83bb6..1591e2e 100644
--- a/src/globalsettings.h
+++ b/src/globalsettings.h
@@ -21,11 +21,19 @@ class GlobalSettings{
     inline static void setDeletionThreshold(int val){
         deletionThreshold = val;
     }
+    inline static void setOutputDeletions(bool flag){
+        outputDeletions = flag;
+    }
+    inline static void setOutputUntranslated(bool flag){
+        outputUntranslated = flag;
+    }
 
 public:
     static bool markedOnlyForVCF;
     static int uniqueRequirement;
     static int deletionThreshold;
+    static bool outputDeletions;
+    static bool outputUntranslated;
 };
 
 
diff --git a/src/htmlreporter.cpp b/src/htmlreporter.cpp
index 0e0d18b..d52ed9b 100644
--- a/src/htmlreporter.cpp
+++ b/src/htmlreporter.cpp
@@ -1,6 +1,7 @@
 #include "htmlreporter.h"
 #include "common.h"
 #include <chrono>
+#include "globalsettings.h"
 
 const std::string getCurrentSystemTime()
 {
@@ -62,8 +63,15 @@ void HtmlReporter::printFusions() {
     mFile<<"</ul></div>";
     id=0;
     for(int i=0;i<mFusionResults.size();i++){
+        FusionResult fusion = mFusionResults[i];
+        if(!GlobalSettings::outputDeletions && fusion.isDeletion())
+            continue;
+        if(fusion.isLeftProteinForward() != fusion.isRightProteinForward()) {
+            if(!GlobalSettings::outputUntranslated)
+                continue;
+        }
         id++;
-        printFusion(id, mFusionResults[i]);
+        printFusion(id, fusion);
     }
 }
 
diff --git a/src/jsonreporter.cpp b/src/jsonreporter.cpp
index b018527..337caa0 100644
--- a/src/jsonreporter.cpp
+++ b/src/jsonreporter.cpp
@@ -28,6 +28,12 @@ void JsonReporter::run() {
     for(int i=0;i<mFusionResults.size();i++){
         FusionResult fusion = mFusionResults[i];
         vector<Match*> matches = fusion.mMatches;
+        if(!GlobalSettings::outputDeletions && fusion.isDeletion())
+            continue;
+        if(fusion.isLeftProteinForward() != fusion.isRightProteinForward()) {
+            if(!GlobalSettings::outputUntranslated)
+                continue;
+        }
         
         if(isFirstMut) {
             mFile << endl;
diff --git a/src/main.cpp b/src/main.cpp
index 1ba8225..ddaed98 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -22,10 +22,12 @@ int main(int argc, char* argv[]){
     cmd.add<string>("fusion", 'f', "fusion file name, in CSV format", true, "");
     cmd.add<string>("ref", 'r', "reference fasta file name", true, "");
     cmd.add<int>("unique", 'u', "specify the least supporting read number is required to report a fusion, default is 2", false, 2);
-    cmd.add<int>("deletion", 'd', "specify the least deletion length of a intra-gene deletion to report, default is 50", false, 50);
     cmd.add<string>("html", 'h', "file name to store HTML report, default is genefuse.html", false, "genefuse.html");
     cmd.add<string>("json", 'j', "file name to store JSON report, default is genefuse.json", false, "genefuse.json");
     cmd.add<int>("thread", 't', "worker thread number, default is 4", false, 4);
+    cmd.add<int>("deletion", 'd', "specify the least deletion length of a intra-gene deletion to report, default is 50", false, 50);
+    cmd.add("output_deletions", 'D', "long deletions are not output by default, enable this option to output them");
+    cmd.add("output_untranslated_fusions", 'U', "the fusions that cannot be transcribed or translated are not output by default, enable this option to output them");
     cmd.parse_check(argc, argv);
     string r1file = cmd.get<string>("read1");
     string r2file = cmd.get<string>("read2");
@@ -36,9 +38,13 @@ int main(int argc, char* argv[]){
     int threadNum = cmd.get<int>("thread");
     int unique = cmd.get<int>("unique");
     int deletion = cmd.get<int>("deletion");
+    bool outputDeletion = cmd.exist("output_deletions");
+    bool outputUntranslated = cmd.exist("output_untranslated_fusions");
 
     GlobalSettings::setUniqueRequirement(unique);
     GlobalSettings::setDeletionThreshold(deletion);
+    GlobalSettings::setOutputDeletions(outputDeletion);
+    GlobalSettings::setOutputUntranslated(outputUntranslated);
 
 
     if(ends_with(refFile, ".gz") || ends_with(refFile, ".gz")) {