fix wrong position in the JSON report

OpenGene · Sep 26, 2018 · c366103 · c366103
1 parent 7999ce9
commit c366103
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Showing 4 changed files with 11 additions and 3 deletions.
diff --git a/src/common.h b/src/common.h
@@ -1,7 +1,7 @@
 #ifndef COMMON_H
 #define COMMON_H
 
-#define FUSIONSCAN_VER "0.6.0"
+#define FUSIONSCAN_VER "0.6.1"
 
 #define _DEBUG true
 

diff --git a/src/gene.cpp b/src/gene.cpp
@@ -86,6 +86,13 @@ Gene Gene::parse(string linestr) {
 
 }
 
+int Gene::genePos2ChrPos(int genepos) {
+    int chrpos = abs(genepos) + mStart;
+    if(genepos <0)
+        chrpos *= -1;
+    return chrpos;
+}
+
 string Gene::pos2str(int pos) {
     int pp = abs(pos) + mStart;
     stringstream ss;

diff --git a/src/gene.h b/src/gene.h
@@ -31,6 +31,7 @@ class Gene{
     void print();
     static Gene parse(string linestr);
     string pos2str(int pos);
+    int genePos2ChrPos(int genepos);
     void getExonIntron(int pos, bool& isExon, int& number);
 
 public:

diff --git a/src/jsonreporter.cpp b/src/jsonreporter.cpp
@@ -46,7 +46,7 @@ void JsonReporter::run() {
             mFile << "\t\t\t\"" <<  "left" << "\":{" << endl;
                 mFile << "\t\t\t\t\"" <<  "gene_name" << "\":" << "\"" << fusion.mLeftGene.mName << "\"," << endl;
                 mFile << "\t\t\t\t\"" <<  "gene_chr" << "\":" << "\"" << fusion.mLeftGene.mChr << "\"," << endl;
-                mFile << "\t\t\t\t\"" <<  "position" << "\":" << fusion.mLeftGP.position << "," << endl;
+                mFile << "\t\t\t\t\"" <<  "position" << "\":" <<  fusion.mLeftGene.genePos2ChrPos(fusion.mLeftGP.position) << "," << endl;
                 mFile << "\t\t\t\t\"" <<  "reference" << "\":" << "\"" << fusion.mLeftRef << "\"," << endl;
                 mFile << "\t\t\t\t\"" <<  "ref_ext" << "\":" << "\"" << fusion.mLeftRefExt << "\"," << endl;
                 mFile << "\t\t\t\t\"" <<  "pos_str" << "\":" << "\"" << fusion.mLeftPos << "\"," << endl;
@@ -57,7 +57,7 @@ void JsonReporter::run() {
             mFile << "\t\t\t\"" <<  "right" << "\":{" << endl;
                 mFile << "\t\t\t\t\"" <<  "gene_name" << "\":" << "\"" << fusion.mRightGene.mName << "\"," << endl;
                 mFile << "\t\t\t\t\"" <<  "gene_chr" << "\":" << "\"" << fusion.mRightGene.mChr << "\"," << endl;
-                mFile << "\t\t\t\t\"" <<  "position" << "\":" << fusion.mRightGP.position << "," << endl;
+                mFile << "\t\t\t\t\"" <<  "position" << "\":" << fusion.mRightGene.genePos2ChrPos(fusion.mRightGP.position) << "," << endl;
                 mFile << "\t\t\t\t\"" <<  "reference" << "\":" << "\"" << fusion.mRightRef << "\"," << endl;
                 mFile << "\t\t\t\t\"" <<  "ref_ext" << "\":" << "\"" << fusion.mRightRefExt << "\"," << endl;
                 mFile << "\t\t\t\t\"" <<  "pos_str" << "\":" << "\"" << fusion.mRightPos << "\"," << endl;