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121 lines
6.1 KiB
121 lines
6.1 KiB
--- a/Makefile
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+++ b/Makefile
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@@ -1,5 +1,8 @@
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all:
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- (cd src; $(MAKE))
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+ $(MAKE) -C src
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clean:
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rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay
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- (cd src; $(MAKE) clean)
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+ $(MAKE) -C src clean
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+
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+check: all
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+ (LAGAN_DIR="." ./mlagan -h || true) | grep -q version && echo "[ok]" || echo "[fail]"
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--- a/src/glocal/Makefile
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+++ b/src/glocal/Makefile
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@@ -1,19 +1,13 @@
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-CC = g++
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-OPTFLAGS =
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-CFLAGS = $(OPTFLAGS) -O3
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-CLINKER = g++
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-# LIBDIR = -L/usr/local/lib
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+CXXFLAGS += -Wno-deprecated
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+CPPFLAGS += -I./
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+
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MLIB = -lm
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-INCDIR = -I./
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TRGT_DIR = ../..
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TRGT = glocal
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OBJECTS = glocal.o io.o rightinfluence.o leftinfluence.o score.o
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-.cpp.o:
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- $(CC) -Wno-deprecated $(CFLAGS) $(INCDIR) -c $*.cpp
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-
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$(TRGT): $(OBJECTS)
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- $(CLINKER) $(OPTFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
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+ $(CXX) $(CXXFLAGS) $(LDFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
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clean :
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rm -f *.o ./*~ *~ core
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--- a/src/Makefile
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+++ b/src/Makefile
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@@ -1,54 +1,51 @@
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-CC = gcc $(CFLAGS)
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-CPP = g++ $(CFLAGS)
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-CFLAGS = -O3 # -Wall -W
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TRGT_DIR = ..
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all: ../anchors ../chaos ../order ../mlagan ../prolagan ../utils/bin2mf ../utils/bin2bl ../utils/cextract ../utils/cstat ../utils/contigorder ../utils/getbounds ../utils/getlength ../utils/getoverlap ../utils/rc ../utils/seqmerge ../utils/scorealign ../utils/scorecontigs ../utils/getcontigpos ../utils/fa2xfa ../utils/Glue ../utils/dotplot ../utils/overlay
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- (cd glocal; $(MAKE))
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+ (cd glocal && $(MAKE))
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clean:
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rm -f *.o *~ utils/*~ mlagan.purify core
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- (cd glocal; $(MAKE) clean)
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+ (cd glocal && $(MAKE) clean)
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../anchors: anchors.c skiplist.c
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- $(CC) -o $(TRGT_DIR)/anchors anchors.c skiplist.c
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/anchors anchors.c skiplist.c
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../chaos: fchaos.c thrtrie.c skiplist.c global.c translate.c mempage.c filebuffer.c
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- $(CC) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
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../order: order.c diagmatrix.c filebuffer.c
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- $(CC) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c
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../mlagan: mlagan.c diagmatrix.c multial.c skiplist.c filebuffer.c
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- $(CC) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
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../prolagan: prolagan.c diagmatrix.c multial.c skiplist.c filebuffer.c
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- $(CC) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
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../utils/bin2mf: utils/bin2mf.c
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- $(CC) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c
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../utils/bin2bl: utils/bin2bl.c
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- $(CC) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c
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../utils/cextract: utils/cextract.c
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- $(CC) -o $(TRGT_DIR)/utils/cextract utils/cextract.c
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cextract utils/cextract.c
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../utils/cstat: utils/cstat.c
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- $(CC) -o $(TRGT_DIR)/utils/cstat utils/cstat.c
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cstat utils/cstat.c
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../utils/contigorder: utils/contigorder.c
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- $(CC) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c
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../utils/getbounds: utils/getbounds.c
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- $(CC) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c
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../utils/getcontigpos: utils/getcontigpos.c
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- $(CC) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c
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../utils/getlength: utils/getlength.c
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- $(CC) -o $(TRGT_DIR)/utils/getlength utils/getlength.c
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getlength utils/getlength.c
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../utils/getoverlap: utils/getoverlap.c
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- $(CC) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c
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../utils/rc: utils/rc.c
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- $(CC) -o $(TRGT_DIR)/utils/rc utils/rc.c
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/rc utils/rc.c
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../utils/seqmerge: utils/seqmerge.c
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- $(CC) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c
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../utils/scorealign: utils/scorealign.c
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- $(CC) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm
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../utils/scorecontigs: utils/scorecontigs.c
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- $(CC) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm
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../utils/fa2xfa: utils/fa2xfa.c
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- $(CC) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c
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../utils/overlay: utils/overlay.c
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- $(CC) -o $(TRGT_DIR)/utils/overlay utils/overlay.c
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/overlay utils/overlay.c
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../utils/Glue: utils/Glue.cpp
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- $(CPP) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp
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+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp
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../utils/dotplot: utils/dotplot.cpp
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- $(CPP) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp
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+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp
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