From b5169f8a9e0b0d56232fcbbf4260858070d2a903 Mon Sep 17 00:00:00 2001
From: zhanxw <zhanxw@gmail.com>
Date: Tue, 18 Apr 2017 02:59:23 -0500
Subject: [PATCH] fix siteFile flag

---
 ChangeLog                 |  1 +
 src/GenotypeExtractor.cpp |  4 ++++
 src/GenotypeExtractor.h   |  5 +++--
 src/Main.cpp              | 10 +++++++++-
 4 files changed, 17 insertions(+), 3 deletions(-)

diff --git a/ChangeLog b/ChangeLog
index 06e60bc..bb03f0b 100644
--- a/ChangeLog
+++ b/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>
 
diff --git a/src/GenotypeExtractor.cpp b/src/GenotypeExtractor.cpp
index 6878d95..d85c3c5 100644
--- a/src/GenotypeExtractor.cpp
+++ b/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) {
diff --git a/src/GenotypeExtractor.h b/src/GenotypeExtractor.h
index 237338f..7bff904 100644
--- a/src/GenotypeExtractor.h
+++ b/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
diff --git a/src/Main.cpp b/src/Main.cpp
index 5c29a3f..989ac83 100644
--- a/src/Main.cpp
+++ b/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);