added a module fusion to prepare contigs for scaffolding

Makefile

@@ -1,12 +1,13 @@
+MAKEFLAGS += --no-print-directory
 CC = g++
 ifdef debug
 CFLAGS=         -O0 -g -fomit-frame-pointer
 else
-CFLAGS=         -O4 -fomit-frame-pointer
+CFLAGS=         -O3 -fomit-frame-pointer
 endif
 
-SUBDIRS = sparsePregraph standardPregraph
-PROG=       SOAPdenovo-63mer SOAPdenovo-127mer
+SUBDIRS = sparsePregraph standardPregraph fusion
+PROG=       SOAPdenovo-63mer SOAPdenovo-127mer SOAPdenovo-fusion
 INCLUDES=   -I./sparsePregraph/inc -I./standardPregraph/inc
 
 LIBPATH=    -L/lib64 -L/usr/lib64 -L./sparsePregraph/inc -L./standardPregraph/inc
@@ -23,15 +24,6 @@ EXTRA_FLAGS += -Wl,--hash-style=both
 LIBS += -lbam -lrt
 endif
 
-ifneq (,$(findstring Unix,$(shell uname)))
-EXTRA_FLAGS += -Wl,--hash-style=both
-LIBS += -lbam -lrt
-endif
-
-ifneq (,$(findstring Darwin,$(shell uname)))
-LIBS += -lbammac
-endif
-
 ifneq (,$(findstring $(shell uname -m), x86_64))
 CFLAGS += -m64
 endif
@@ -45,7 +37,10 @@ CFLAGS += -mpowerpc64
 endif
 
 
-all: SOAPdenovo-63mer SOAPdenovo-127mer
+all: SOAPdenovo-63mer SOAPdenovo-127mer SOAPdenovo-fusion 
+
+SOAPdenovo-fusion:
+	@cd fusion;make;cp SOAPdenovo-fusion ../;cd ..;
 
 ifdef debug
 SOAPdenovo-63mer:
@@ -56,10 +51,6 @@ SOAPdenovo-127mer:
 	@cd sparsePregraph;make 127mer=1 debug=1;cd ..;
 	@cd standardPregraph;make 127mer=1 debug=1;cd ..;
 	@$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
-clean:
-	@cd sparsePregraph;make clean;cd ..;
-	@cd standardPregraph;make clean;cd ..;
-	@rm SOAPdenovo-63mer SOAPdenovo-127mer -f
 else
 SOAPdenovo-63mer:
 	@cd sparsePregraph;make 63mer=1;cd ..;
@@ -69,8 +60,10 @@ SOAPdenovo-127mer:
 	@cd sparsePregraph;make 127mer=1;cd ..;
 	@cd standardPregraph;make 127mer=1;cd ..;
 	@$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
+endif
+
 clean:
 	@cd sparsePregraph;make clean;cd ..;
 	@cd standardPregraph;make clean;cd ..;
-	@rm SOAPdenovo-63mer SOAPdenovo-127mer -f
-endif
+	@cd fusion;make clean;cd ..;
+	@rm -f SOAPdenovo-63mer SOAPdenovo-127mer SOAPdenovo-fusion

README.md

@@ -1,12 +1,19 @@
 # Manual of SOAPdenovo2
 
-## What's next of SOAPdenovo2
+## About MEGAHIT
 
-MEGAHIT is the formal successor of SOAPdenovo2
+MEGAHIT works with single-cell sequencing data and metagenomcis data. Compare to SOAPdenovo, it generates longer contigs and consumes less memory.
 
+To scaffold the contigs generated by MEGAHIT, please use SOAPdenovo-fusion. It is a preparation module that takes contigs as input and generates files that could be used consecutively by SOAPdenovo's map and scaff module.
+
+Reference:
 MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
-http://www.ncbi.nlm.nih.gov/pubmed/25609793
-https://github.com/voutcn/megahit
+<a href="http://www.ncbi.nlm.nih.gov/pubmed/25609793">Manuscript</a>
+<a href="https://github.com/voutcn/megahit">Github</a>
+
+## For MAC users
+
+Please use <a href="http://brew.sh">brew</a> to install SOAPdenovo. SOAPdenovo's package in Homebrew-science is managed by Shaun Jackman. 
 
 ## Introduction
 

fusion/Makefile

@@ -0,0 +1,46 @@
+# Generated automatically from Makefile.in by configure.
+SHELL = /bin/sh
+
+exec_prefix = .
+bindir = $(exec_prefix)/bin
+libdir = 
+mandir = 
+
+CC = gcc
+CCOPT = -O3 -fprefetch-loop-arrays -funroll-loops -fomit-frame-pointer -w 
+LIBS = -lm -lpthread
+INCDIRS = -Iinc/
+CFLAGS = ${CCOPT} ${INCDIRS}
+
+all: clean SOAPdenovo-fusion
+SRCS1 = searchPath.c scaffold.c check.c seq.c bundle.c potential.c\
+	loadGraph.c mem_manager.c attachPEinfo.c newhash.c\
+	output_scaffold.c orderContig.c connect.c hashFunction.c\
+	readseq1by1.c fib.c fibHeap.c stack.c kmer.c prepare.c
+OBJS1 = searchPath.o scaffold.o check.o seq.o bundle.o potential.o\
+	loadGraph.o mem_manager.o attachPEinfo.o newhash.o\
+	output_scaffold.o orderContig.o connect.o hashFunction.o\
+	readseq1by1.o fib.o fibHeap.o stack.o kmer.o prepare.o
+
+SRCS2 = prlHashCtg.c prlRead2Ctg.c map.c localAsm.c\
+	lib.c darray.c prlReadFillGap.c read2scaf.c
+OBJS2 = prlHashCtg.o prlRead2Ctg.o map.o localAsm.o\
+	lib.o darray.o prlReadFillGap.o read2scaf.o
+
+
+SRCS3 = main.c 
+OBJS3 = main.o
+
+.c.o :
+	@printf "Compiling $<...                              \r"
+	@$(CC) $(CFLAGS) -c $< 
+
+SOAPdenovo-fusion:  $(OBJS1) $(OBJS2) $(OBJS3)
+	@printf "Making $@...                                 \r"
+	@$(CC) $(CCOPT) -o $@ $^ $(LIBS)
+	@printf "$@ compilation done.\n";
+
+clean:
+	@/bin/rm -f *.o SOAPdenovo-fusion
+	@printf "SOAPdenovo-fusion cleaning done.             \n"
+