fixed issue for multiple read groups

wwylab · Jun 8, 2023 · afe6322 · afe6322
1 parent 7f42988
commit afe6322
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Showing 2 changed files with 11 additions and 3 deletions.
diff --git a/src/main_muse.cpp b/src/main_muse.cpp
@@ -239,7 +239,7 @@ void get_MuseSumpOpts(int argc, char *argv[]){
         fprintf(stderr, "         -G         input generated from whole genome sequencing data\n");
         fprintf(stderr, "         -E         input generated from whole exome sequencing data\n");
         fprintf(stderr, "         -O STR     output file name (VCF format)\n");
-	fprintf(stderr, "         -n int     number of cores specified (default=1)\n");
+	fprintf(stderr, "         -n INT     number of cores specified (default=1)\n");
         fprintf(stderr, "         -D FILE    dbSNP vcf file that should be bgzip compressed,\n");
         fprintf(stderr, "                    tabix indexed and based on the same reference\n");
         fprintf(stderr, "                    genome used in 'MuSE call'\n");

diff --git a/src/muse_sump.cpp b/src/muse_sump.cpp
@@ -90,7 +90,14 @@ std::string IntToString(int x) {
     return o.str();
 }
 
-void muse_sump(const char *inFile, const char *outFile, const char *dbsnpFile, bool isWGS, bool isWES, int num_threads, int argc, char *argv[]){
+void muse_sump(const char *inFile, 
+               const char *outFile, 
+               const char *dbsnpFile, 
+               bool isWGS, 
+               bool isWES, 
+               int num_threads, 
+               int argc, 
+               char *argv[]){
 
     int        minDepth     = 8;
     double     passVAF      = 0.02;
@@ -290,6 +297,7 @@ void muse_sump(const char *inFile, const char *outFile, const char *dbsnpFile, b
 	}
     }
 
+    buffer = "";
     int dataSize = dataParser.size();
 
     for(int index = 0; index < dataSize; index++){
@@ -644,7 +652,7 @@ void muse_sump(const char *inFile, const char *outFile, const char *dbsnpFile, b
         int    emReplicate  = 50;
         int    maxIteration = 5000;
         int    maxRestarts  = 20;
-
+        int    dataSize     = (int)lnTEVAF.size();
         double epsilon      = 1e-08;
 
         // partition