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Merge pull request #49 from ComparativeGenomicsToolkit/chop
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halUnclip
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glennhickey authored Sep 3, 2021
2 parents 47b86c8 + baa4dc1 commit 0834ba8
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Showing 3 changed files with 746 additions and 4 deletions.
18 changes: 14 additions & 4 deletions Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
rootPath = ./
include ./include.mk

all : hal2vg clip-vg halRemoveDupes halMergeChroms
all : hal2vg clip-vg halRemoveDupes halMergeChroms halUnclip

# Note: hdf5 from apt doesn't seem to work for static builds. It should be installed
# from source and configured with "--enable-static --disable-shared", then have its
Expand Down Expand Up @@ -33,13 +33,17 @@ ifeq ($(shell ldd halMergeChroms | grep "not a dynamic" | wc -l), $(shell ls hal
else
$(error ldd found dnymaic linked dependency in halMergeChroms)
endif

ifeq ($(shell ldd halUnclip | grep "not a dynamic" | wc -l), $(shell ls halUnclip | wc -l))
$(info ldd verified that halUnclip static)
else
$(error ldd found dnymaic linked dependency in halUnclip)
endif

cleanFast :
rm -f hal2vg hal2vg.o clip-vg clip-vg.o halRemoveDupes halRemoveDupes.o halMergeChroms halMergeChroms.o
rm -f hal2vg hal2vg.o clip-vg clip-vg.o halRemoveDupes halRemoveDupes.o halMergeChroms halMergeChroms.o halUnclip halUnclip.o

clean :
rm -f hal2vg hal2vg.o clip-vg clip-vg.o halRemoveDupes halRemoveDupes.o halMergeChroms halMergeChroms.o
rm -f hal2vg hal2vg.o clip-vg clip-vg.o halRemoveDupes halRemoveDupes.o halMergeChroms halMergeChroms.o halUnclip halUnclip.o
cd deps/sonLib && make clean
cd deps/pinchesAndCacti && make clean
cd deps/hal && make clean
Expand Down Expand Up @@ -81,6 +85,12 @@ halMergeChroms.o : halMergeChroms.cpp ${basicLibsDependencies}
halMergeChroms : halMergeChroms.o ${basicLibsDependencies}
${cpp} ${CXXFLAGS} -fopenmp -pthread halMergeChroms.o ${basicLibs} -o halMergeChroms

halUnclip.o : halUnclip.cpp subpaths.h ${basicLibsDependencies}
${cpp} ${CXXFLAGS} -I . halUnclip.cpp -c

halUnclip : halUnclip.o ${basicLibsDependencies}
${cpp} ${CXXFLAGS} -fopenmp -pthread halUnclip.o ${basicLibs} -o halUnclip

test :
make
cd tests && prove -v t
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