Added GTC to VCF converter.

Author: kjsanger

Makefile

@@ -41,7 +41,7 @@ INSTALL_INC=$(PREFIX)/include
 INSTALL_LIB=$(PREFIX)/lib
 INSTALL_BIN=$(PREFIX)/bin
 
-EXECUTABLES=gtc g2i gtc_process sim simtools normalize_manifest
+EXECUTABLES=gtc g2i g2v gtc_process sim simtools normalize_manifest
 INCLUDES=Sim.h Gtc.h Manifest.h win2unix.h
 LIBS=libsimtools.so libsimtools.a
 PERL_MODULES=Gtc.pm Sim.pm
@@ -120,6 +120,9 @@ simtools: simtools.o commands.o libsimtools.a
 g2i: g2i.o libsimtools.a
 	$(CXX) $< $(LDFLAGS) -o $@ -lm -Wl,-Bstatic -lsimtools -Wl,-Bdynamic
 
+g2v: g2v.o libsimtools.a
+	$(CXX) $< $(LDFLAGS) -o $@ -pthread -lm -Wl,-Bstatic -lsimtools -Wl,-Bdynamic
+
 gtc_process: gtc_process.o libsimtools.a
 	$(CXX) $< $(LDFLAGS) -o $@ -lm -Wl,-Bstatic -lsimtools -Wl,-Bdynamic
 

Manifest.cpp

@@ -31,6 +31,7 @@
 // THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 
+#include <algorithm>
 #include <iostream>
 #include <fstream>
 #include <map>
@@ -765,8 +766,6 @@ void Manifest::write(string outPath) {
 
 }
 
-
-
 ///////////////////////////////////////////////
 //
 // void Manifest::order_by_position()
@@ -812,12 +811,24 @@ void Manifest::order_by_position() {
 	snps.push_back(s);
   }
 
-
   populate_hashmap();
-
 }
 
-
+///////////////////////////////////////////////
+//
+// void Manifest::order_by_locus()
+//
+// Re-order the vector of snpClass objects such that
+// they are stored in the order first of lexically sorted
+// chromosome name and then chromosomal position.
+//
+// Must be called after Manifest::open().
+//
+///////////////////////////////////////////////
+void Manifest::order_by_locus() {
+  sort(snps.begin(), snps.end());
+  return;
+}
 
 ///////////////////////////////////////////////
 //
@@ -945,6 +956,7 @@ int Manifest::get_map_value (map<string, int>& mymap, const char* const treasure
 }
 
 
+
 ///////////////////////////////////////////////
 //
 // string snpClass::toString()

Manifest.h

@@ -80,6 +80,16 @@ class snpClass {
 
   bool converted; // has SNP been converted from original to ILMN top strand?
   // converted=true changes output of toString(), but not the iStrand and cStrand variables (which represent the original values)
+
+  bool operator<(snpClass other) const {
+    if (chromosome.compare(other.chromosome)) {
+      return (chromosome.compare(other.chromosome) < 0);
+    }
+	if (position != other.position) {
+      return (position < other.position);
+    }
+	return (name.compare(other.name) < 0);
+  }
 };
 
 
@@ -100,6 +110,7 @@ class Manifest {
 	void open (string filename, string chromosome, bool wide = false);
 
 	void order_by_position();
+    void order_by_locus();
 
 	string filename;