Merge pull request #19 from mourisl/dev

Add "centrifuger-quant" for quantification

BufferManager.hpp

@@ -63,6 +63,11 @@ class BufferManager
     }
     return _buffers[i] ;
   }
+
+  size_t GetBufferSize(int i)
+  {
+    return _bufferSize[i] ;
+  }
 } ;
 
 #endif

CentrifugerQuant.cpp

@@ -0,0 +1,81 @@
+#include <stdio.h>
+#include <time.h>
+#include <getopt.h>
+
+#include "argvdefs.h"
+#include "Taxonomy.hpp"
+#include "Quantifier.hpp"
+
+char usage[] = "./centrifuger-quant [OPTIONS]:\n"
+	"Required:\n"
+  "\t-x FILE: index prefix\n"
+  "\t-c FILE: classification result file\n"
+  //"When not giving "-x"\n"
+  //"\t--taxonomy-tree FILE: taxonomy tree, i.e., nodes.dmp file\n"
+  //"\t--name-table FILE: name table, i.e., names.dmp file\n"
+  //"\t--size-table FILE: size table, table of contig (or genome) sizes\n"
+  //"\t--conversion-table FILE: a table that converts any id to a taxonomy id\n"
+	;
+
+static const char *short_options = "x:c:" ;
+static struct option long_options[] = {
+  { (char *)0, 0, 0, 0} 
+} ;
+
+int main(int argc, char *argv[])
+{
+  if ( argc <= 1 )
+  {
+    fprintf( stderr, "%s", usage ) ;
+    return 0 ;
+  }
+
+  int c, option_index ;
+  option_index = 0 ;
+
+  char *idxPrefix = NULL ; 
+  char *classificationFile = NULL ;
+
+  while (1)
+  {
+    c = getopt_long( argc, argv, short_options, long_options, &option_index ) ;
+
+    if (c == -1)
+      break ;
+
+    if (c == 'x')
+    {
+      idxPrefix = strdup(optarg) ;
+    }
+    else if (c == 'c')
+    {
+      classificationFile = strdup(optarg) ;
+    }
+    else
+    {
+      fprintf(stderr, "Unknown parameter found.\n%s", usage) ;
+      return EXIT_FAILURE ;
+    }
+  }
+
+	Utils::PrintLog("Centrifuger-quant v" CENTRIFUGER_VERSION " starts." ) ;
+  if (idxPrefix == NULL)
+  {
+    Utils::PrintLog("Need to use -x to specify index prefix.") ;
+    return EXIT_FAILURE ;
+  }
+
+  Quantifier quantifier ;
+  quantifier.Init(idxPrefix) ;
+  quantifier.LoadReadAssignments(classificationFile, 0) ;
+
+  quantifier.Quantification() ;
+
+  quantifier.Output(stdout, 0) ;
+
+  free(idxPrefix) ;
+  free(classificationFile) ;
+
+	Utils::PrintLog("Centrifuger-quant finishes." ) ;
+  return 0 ;
+}

Makefile

@@ -11,7 +11,7 @@ ifneq ($(asan),)
 	LDFLAGS+=-fsanitize=address -ldl -g
 endif
 
-all: centrifuger centrifuger-build centrifuger-inspect
+all: centrifuger centrifuger-build centrifuger-inspect centrifuger-quant
 
 centrifuger-build: CentrifugerBuild.o
 	$(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
@@ -22,9 +22,14 @@ centrifuger: CentrifugerClass.o
 centrifuger-inspect: CentrifugerInspect.o
 	$(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
 
+centrifuger-quant: CentrifugerQuant.o
+	$(CXX) -o $@ $(LINKPATH) $(CXXFLAGS) $< $(LINKFLAGS)
+
+
 CentrifugerBuild.o: CentrifugerBuild.cpp Builder.hpp ReadFiles.hpp Taxonomy.hpp defs.h compactds/*.hpp 
 CentrifugerClass.o: CentrifugerClass.cpp Classifier.hpp ReadFiles.hpp Taxonomy.hpp defs.h ResultWriter.hpp ReadPairMerger.hpp ReadFormatter.hpp BarcodeCorrector.hpp BarcodeTranslator.hpp compactds/*.hpp 
 CentrifugerInspect.o: CentrifugerInspect.cpp Taxonomy.hpp defs.h compactds/*.hpp 
+CentrifugerQuant.o: CentrifugerQuant.cpp Quantifier.hpp Taxonomy.hpp compactds/*.hpp
 
 clean:
-	rm -f *.o centrifuger-build centrifuger centrifuger-inspect
+	rm -f *.o centrifuger-build centrifuger centrifuger-inspect centrifuger-quant