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127 lines
8.7 KiB
127 lines
8.7 KiB
Debundle zlib, fixes parallel build, respect user FLAGS
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--- src/readSet.c
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+++ src/readSet.c
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@@ -23,18 +23,13 @@
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#include <string.h>
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#include <math.h>
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#include <time.h>
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+#include <zlib.h>
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#include "globals.h"
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#include "tightString.h"
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#include "readSet.h"
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#include "utility.h"
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-#if defined(_WIN32) || defined(__WIN32__) || defined(WIN32)
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-#include "../third-party/zlib-1.2.3/Win32/include/zlib.h"
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-#else
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-#include "../third-party/zlib-1.2.3/zlib.h"
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-#endif
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-
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#if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__)
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# include <fcntl.h>
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# include <io.h>
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--- Makefile
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+++ Makefile
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@@ -1,77 +1,62 @@
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-CC = gcc
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-CFLAGS = -Wall
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-DEBUG = -g
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-LDFLAGS = -lm
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-OPT = -O3
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+LIBS = -lm -lz
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MAXKMERLENGTH=31
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CATEGORIES=2
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DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)
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-Z_LIB_DIR=third-party/zlib-1.2.3
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-Z_LIB_FILES=$(Z_LIB_DIR)/*.o
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-
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-# Mac OS users: uncomment the following lines
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-# Z_LIB_FILES=
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-# LDFLAGS = -lm -lz
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-# CFLAGS = -Wall -m64
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-
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-# Sparc/Solaris users: uncomment the following line
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-# CFLAGS = -Wall -m64
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-
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OBJ = obj/tightString.o obj/run.o obj/splay.o obj/splayTable.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/crc.o obj/utility.o obj/kmer.o obj/scaffold.o
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OBJDBG = $(subst obj,obj/dbg,$(OBJ))
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+OBJDE = $(subst obj,objde,$(OBJ))
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-default : cleanobj zlib obj velveth velvetg doc
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+default : cleanobj obj velveth velvetg
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clean :
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- -rm obj/*.o obj/dbg/*.o ./velvet*
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- cd $(Z_LIB_DIR) && make clean
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+ -rm -f obj/*.o obj/dbg/*.o ./velvet* objde/*.o
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-rm -f doc/manual_src/Manual.toc doc/manual_src/Manual.aux doc/manual_src/Manual.out doc/manual_src/Manual.log
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cleanobj:
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- -rm obj/*.o obj/dbg/*.o
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-
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-zlib :
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- cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o
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+ -rm -f obj/*.o obj/dbg/*.o objde/*.o
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velveth : obj
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- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o $(Z_LIB_FILES)
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+ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o $(LIBS)
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velvetg : obj
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- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o $(Z_LIB_FILES)
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+ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o $(LIBS)
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debug : cleanobj obj/dbg
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- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o $(Z_LIB_FILES)
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- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o $(Z_LIB_FILES)
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+ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o $(LIBS)
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+ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o $(LIBS)
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color : cleanobj obj_de
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- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o $(Z_LIB_FILES)
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- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o $(Z_LIB_FILES)
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+ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de objde/tightString.o objde/run.o objde/recycleBin.o objde/splay.o objde/splayTable.o objde/readSet.o objde/crc.o objde/utility.o objde/kmer.o $(LIBS)
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+ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de objde/tightString.o objde/graph.o objde/run2.o objde/fibHeap.o objde/fib.o objde/concatenatedGraph.o objde/passageMarker.o objde/graphStats.o objde/correctedGraph.o objde/dfib.o objde/dfibHeap.o objde/recycleBin.o objde/readSet.o objde/shortReadPairs.o objde/scaffold.o objde/locallyCorrectedGraph.o objde/graphReConstruction.o objde/roadMap.o objde/preGraph.o objde/preGraphConstruction.o objde/concatenatedPreGraph.o objde/readCoherentGraph.o objde/utility.o objde/kmer.o $(LIBS)
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colordebug : cleanobj obj/dbg_de
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- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o $(Z_LIB_FILES)
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- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o $(Z_LIB_FILES)
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+ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de objde/dbg/tightString.o objde/dbg/run.o objde/dbg/recycleBin.o objde/dbg/splay.o objde/dbg/splayTable.o objde/dbg/readSet.o objde/dbg/crc.o objde/dbg/utility.o objde/dbg/kmer.o $(LIBS)
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+ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de objde/dbg/tightString.o objde/dbg/graph.o objde/dbg/run2.o objde/dbg/fibHeap.o objde/dbg/fib.o objde/dbg/concatenatedGraph.o objde/dbg/passageMarker.o objde/dbg/graphStats.o objde/dbg/correctedGraph.o objde/dbg/dfib.o objde/dbg/dfibHeap.o objde/dbg/recycleBin.o objde/dbg/readSet.o objde/dbg/shortReadPairs.o objde/dbg/scaffold.o objde/dbg/locallyCorrectedGraph.o objde/dbg/graphReConstruction.o objde/dbg/roadMap.o objde/dbg/preGraph.o objde/dbg/preGraphConstruction.o objde/dbg/concatenatedPreGraph.o objde/dbg/readCoherentGraph.o objde/dbg/utility.o objde/dbg/kmer.o $(LIBS)
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objdir:
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mkdir -p obj
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+ mkdir -p objde
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-obj: zlib objdir $(OBJ)
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+obj: objdir $(OBJ)
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-obj_de: override DEF := $(DEF) -D COLOR
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-obj_de: zlib cleanobj objdir $(OBJ)
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+obj_de: cleanobj objdir $(OBJDE)
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obj/dbgdir:
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mkdir -p obj/dbg
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-obj/dbg: zlib obj/dbgdir $(OBJDBG)
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+obj/dbg: obj/dbgdir $(OBJDBG)
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obj/dbg_de: override DEF := $(DEF) -D COLOR
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-obj/dbg_de: zlib cleanobj obj/dbgdir $(OBJDBG)
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+obj/dbg_de: cleanobj obj/dbgdir $(OBJDBG)
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obj/%.o: src/%.c
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$(CC) $(CFLAGS) $(OPT) $(DEF) -c $? -o $@
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+objde/%.o: src/%.c
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+ $(CC) $(CFLAGS) $(OPT) $(DEF) -D COLOR -c $? -o $@
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+
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obj/dbg/%.o: src/%.c
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$(CC) $(CFLAGS) $(DEBUG) $(DEF) -c $? -o $@
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