Merge branch 'master' of github.com:zhanxw/rvtests

zhanxw · May 5, 2016 · b2b4760 · b2b4760
2 parents 7f4d2ba + a422487
commit b2b4760
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diff --git a/ChangeLog b/ChangeLog
@@ -1,3 +1,8 @@
+2016-05-04  Xiaowei Zhan  <zhanxw@bunny.swmed.edu>
+
+	* Reduce memory consumption for logistic regression
+	* Clean codes
+
 2016-04-22  Xiaowei Zhan  <zhanxw@fantasia.csgstat.sph.umich.edu>
 
 	* Fix crash when analyzing large samples (>80,000)

diff --git a/Makefile b/Makefile
@@ -15,7 +15,6 @@ $(DIR_EXEC_DBG):
 	mkdir -p $@
 
 .PHONY: release debug profile lib lib-dbg clean tar doc
-
 release: lib
 	$(MAKE) -C $(ROOT)/src release
 	$(MAKE) -C $(ROOT)/vcfUtils release
@@ -29,11 +28,6 @@ debug.vcfUtil: lib-dbg
 profile: lib-dbg
 	$(MAKE) -C $(ROOT)/src profile
 	$(MAKE) -C $(ROOT)/vcfUtils profile
-##################################################
-GitVersion.h: .git/HEAD .git/index
-	-echo "const char *gitVersion = \"$(shell git rev-parse HEAD)\";" > $@
-.git/HEAD .git/index:
-	-echo "const char *gitVersion = \"not-a-git-repo\"" > GitVersion.h 
 
 ##################################################
 ## clean

diff --git a/Makefile.common b/Makefile.common
@@ -55,7 +55,7 @@ GONCALO_LIB_DBG = $(ROOT)/libsrc/lib-dbg-goncalo.a
 ##################################################
 ## Common compiler options
 CXX=g++
-DEFAULT_CXXFLAGS = -D__STDC_LIMIT_MACROS -std=c++0x -Wall -Wno-unused-function $(OPENMP_FLAG)
+DEFAULT_CXXFLAGS = -D__STDC_LIMIT_MACROS -std=c++0x -Wall -Wno-unused-function $(OPENMP_FLAG) -DGIT_VERSION="\"$(GIT_VERSION)\""
 
 INCLUDE = $(THIRD_INC) $(REGRESSION_INC) $(VCF_INC) $(BASE_INC) $(GONCALO_INC)
 LIB = $(REGRESSION_LIB) $(VCF_LIB) $(BASE_LIB) $(GONCALO_LIB) $(THIRD_LIB) 
@@ -88,3 +88,7 @@ lint: *.cpp *.h
 	cpplint.py --filter=-legal/copyright $^
 
 
+##################################################
+## Git version
+##################################################
+GIT_VERSION := $(shell git rev-parse HEAD || echo Unknown)
diff --git a/libVcf/VCFIndividual.h b/libVcf/VCFIndividual.h
@@ -1,9 +1,9 @@
 #ifndef _VCFINDIVIDUAL_H_
 #define _VCFINDIVIDUAL_H_
 
+#include "VCFBuffer.h"
 #include "VCFFunction.h"
 #include "VCFValue.h"
-#include "VCFBuffer.h"
 
 #include <vector>
 
@@ -13,7 +13,7 @@ class VCFIndividual {
   // FUNC parseFunction[4];
   VCFIndividual() {
     this->include();  // by default, enable everyone
-  };
+  }
   /**
    * 0-base index for beg and end, e.g.
    *     0 1 2  3
@@ -50,27 +50,27 @@ class VCFIndividual {
       fprintf(stderr, "Empty individual column - very strange!!\n");
       fprintf(stderr, "vcfValue = %s\n", vcfValue.toStr());
     }
-  };
+  }
 
-  const std::string& getName() const { return this->name; };
-  void setName(std::string& s) { this->name = s; };
-  void include() { this->inUse = true; };
-  void exclude() { this->inUse = false; };
-  bool isInUse() { return this->inUse; };
+  const std::string& getName() const { return this->name; }
+  void setName(std::string& s) { this->name = s; }
+  void include() { this->inUse = true; }
+  void exclude() { this->inUse = false; }
+  bool isInUse() { return this->inUse; }
 
   const VCFValue& operator[](const unsigned int i) const
       __attribute__((deprecated)) {
     if (i >= fd.size()) {
       FATAL("index out of bound!");
     }
     return (this->fd[i]);
-  };
+  }
   VCFValue& operator[](const unsigned int i) __attribute__((deprecated)) {
     if (i >= fd.size()) {
       FATAL("index out of bound!");
     }
     return (this->fd[i]);
-  };
+  }
   /**
    * @param isMissing: index @param i does not exists. Not testing if the value
    * in ith field is missing
@@ -82,7 +82,7 @@ class VCFIndividual {
     }
     *isMissing = this->fd[i].isMissing();
     return (this->fd[i]);
-  };
+  }
   /**
    * @return VCFValue without checking missingness
    */
@@ -91,10 +91,10 @@ class VCFIndividual {
       return VCFIndividual::defaultVCFValue;
     }
     return (this->fd[i]);
-  };
+  }
 
-  VCFValue& getSelf() { return this->self; };
-  const VCFValue& getSelf() const { return this->self; };
+  VCFValue& getSelf() { return this->self; }
+  const VCFValue& getSelf() const { return this->self; }
 
   size_t size() const { return this->fd.size(); }
   /**
@@ -105,7 +105,7 @@ class VCFIndividual {
       if (i) fputc(':', fp);
       this->fd[i].output(fp);
     }
-  };
+  }
 
  private:
   bool inUse;

diff --git a/libVcf/VCFInputFile.cpp b/libVcf/VCFInputFile.cpp
@@ -1,9 +1,10 @@
 #include "VCFInputFile.h"
-#include "Utils.h"
+
 #include "IO.h"
+#include "Utils.h"
 
-#include "TabixReader.h"
 #include "BCFReader.h"
+#include "TabixReader.h"
 
 // use current subset of included people
 // to reconstruct a new VCF header line
@@ -29,7 +30,7 @@ void VCFInputFile::setRangeMode() {
       this->mode = VCFInputFile::VCF_RANGE_MODE;
     }
   } else if (mode == VCF_RANGE_MODE) {
-    // Auto-merge should be handled by VCFInputFile, not in tabixReader    
+    // Auto-merge should be handled by VCFInputFile, not in tabixReader
     // if (this->autoMergeRange) {
     //   this->tabixReader->enableAutoMerge();
     // }
@@ -204,12 +205,11 @@ void VCFInputFile::setRangeList(const RangeList& rl) {
   if (rl.size() == 0) return;
 
   this->setRangeMode();
-  
+
   RangeList l;
   l.setRange(rl);
-  if (this->autoMergeRange)
-    l.sort();
-
+  if (this->autoMergeRange) l.sort();
+
   if (mode == VCF_RANGE_MODE) {
     this->tabixReader->setRange(l);
   } else if (mode == BCF_MODE) {
@@ -243,3 +243,7 @@ int VCFInputFile::setSiteFile(const std::string& fn) {
   }
   return 0;
 }
+
+void VCFInputFile::getIncludedPeopleName(std::vector<std::string>* p) {
+  record.getIncludedPeopleName(p);
+}
diff --git a/libVcf/VCFInputFile.h b/libVcf/VCFInputFile.h
@@ -2,8 +2,8 @@
 #define _VCFINPUTFILE_H_
 
 // #include "tabix.h"
-#include "VCFRecord.h"
 #include "VCFFilter.h"
+#include "VCFRecord.h"
 
 class TabixReader;
 class BCFReader;
@@ -115,9 +115,7 @@ class VCFInputFile {
     r.addRange(chrom, begin, end);
     this->setRange(r);
   }
-  void setRange(const RangeList& rl) {
-    this->setRangeList(rl);
-  }
+  void setRange(const RangeList& rl) { this->setRangeList(rl); }
   void setRangeList(const std::string& l) {
     if (l.empty()) return;
 
@@ -140,6 +138,7 @@ class VCFInputFile {
   VCFRecord& getVCFRecord() { return this->record; };
   const char* getLine() const { return this->line.c_str(); };
   const char* getFileName() const { return this->fileName.c_str(); };
+  void getIncludedPeopleName(std::vector<std::string>* p);
 
  private:
   void setRangeMode();