fix siteFile flag

ChangeLog

@@ -1,6 +1,7 @@
 2017-04-14  Xiaowei Zhan  <zhanxw@bunny.swmed.edu>
 
 	* Fix a critical bug related to AF calculation (issue 15)
+	* Fix siteFile flag and provide prompt when it's used
 
 2017-04-12  Xiaowei Zhan  <zhanxw@fantasia.csgstat.sph.umich.edu>
 

src/GenotypeExtractor.cpp

@@ -338,6 +338,10 @@ void GenotypeExtractor::setGQmax(int m) {
   this->GQmax = m;
 }
 
+void GenotypeExtractor::setSiteFile(const std::string& fn) {
+  this->vin->setSiteFile(fn);
+}
+
 void GenotypeExtractor::setSiteQualMin(int q) { this->vin->setSiteQualMin(q); }
 void GenotypeExtractor::setSiteMACMin(int n) { this->vin->setSiteMACMin(n); }
 int GenotypeExtractor::setAnnoType(const std::string& s) {

src/GenotypeExtractor.h

@@ -61,6 +61,7 @@ class GenotypeExtractor {
   void setGQmin(int m);
   void setGQmax(int m);
 
+  void setSiteFile(const std::string& fn);
   void setSiteQualMin(int q);
   void setSiteMACMin(int n);
   int setAnnoType(const std::string& s);
@@ -149,8 +150,8 @@ class GenotypeExtractor {
   const std::vector<int>* sex;  // external sex information
   // bool claytonCoding;  // code male hemi region genotype from 0/1 to 0/2
   std::vector<double> genotype;          // store extracted genotypes
-  std::vector<std::string> variantName;  // store extract variant names
-  int sampleSize;                        // number of extract vcf samples
+  std::vector<std::string> variantName;  // store extracted variant names
+  int sampleSize;                        // number of extracted vcf samples
   // for multiallelic
   bool multiAllelicMode;               // default is false
   std::vector<std::string> altAllele;  // store alt alleles

src/Main.cpp

@@ -30,7 +30,7 @@
 
 Logger* logger = NULL;
 
-const char* VERSION = "20170414";
+const char* VERSION = "20170418";
 
 void banner(FILE* fp) {
   const char* string =
@@ -224,6 +224,9 @@ void welcome() {
   fprintf(stdout,
           "  For questions and comments, send to Xiaowei Zhan "
           "<zhanxw@umich.edu>\n");
+  fprintf(stdout,
+          "  For bugs and feature requests, please submit at: "
+          "https://github.com/zhanxw/rvtests/issues\n");
   fprintf(stdout, "\n");
 }
 
@@ -492,6 +495,11 @@ int main(int argc, char** argv) {
   ge.excludePeople(FLAG_peopleExcludeID.c_str());
   ge.excludePeopleFromFile(FLAG_peopleExcludeFile.c_str());
 
+  if (!FLAG_siteFile.empty()) {
+    ge.setSiteFile(FLAG_siteFile);
+    logger->info("Restrict analysis based on specified site file [ %s ]",
+                 FLAG_siteFile.c_str());
+  }
   if (FLAG_siteDepthMin > 0) {
     ge.setSiteDepthMin(FLAG_siteDepthMin);
     logger->info("Set site depth minimum to %d", FLAG_siteDepthMin);