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Patch 1 #334

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Patch 1 #334

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3af9941
bam2wig cant make
atongsa Feb 21, 2022
de29bc2
copy binary bam2wig
atongsa Feb 21, 2022
3ac6fa9
add binary bam2wig
atongsa Feb 21, 2022
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2 changes: 1 addition & 1 deletion auxprogs/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ all:
cd homGeneMapping; make;
cd joingenes; make;
cd utrrnaseq; make;
cd bam2wig; make;
#cd bam2wig; make;

clean:
cd aln2wig; make clean;
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55 changes: 1 addition & 54 deletions auxprogs/bam2wig/Makefile
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Expand Up @@ -10,63 +10,10 @@

include ../../common.mk

CC ?= gcc
CFLAGS := -Wall -O2 $(CFLAGS)

HTSERRHINT=""
ifndef INCLUDE_PATH_HTSLIB
# set INCLUDE_PATH_HTSLIB and LIBRARY_PATH_HTSLIB
# or HTSLIB_INSTALL_DIR if neither of these is specified as environment variable
# and libhts-dev is not installed
# keep compatibility with old versions still using TOOLDIR
ifdef TOOLDIR
HTSLIB_INSTALL_DIR = $(TOOLDIR)/htslib
endif
HTSLIB_INSTALL_DIR ?= $(HOME)/tools/htslib
ifneq ($(wildcard ${HTSLIB_INSTALL_DIR}/include/htslib/.),) # if HTSLIB_INSTALL_DIR exists and contains include/htslib
INCLUDE_PATH_HTSLIB = -I$(HTSLIB_INSTALL_DIR)/include/htslib
LIBRARY_PATH_HTSLIB = -L$(HTSLIB_INSTALL_DIR)/lib -Wl,-rpath,$(HTSLIB_INSTALL_DIR)/lib
else
ifneq ($(wildcard ${HTSLIB_INSTALL_DIR}/htslib/.),) # if HTSLIB_INSTALL_DIR exists and contains htslib
INCLUDE_PATH_HTSLIB = -I$(HTSLIB_INSTALL_DIR)/htslib
LIBRARY_PATH_HTSLIB = -L$(HTSLIB_INSTALL_DIR) -Wl,-rpath,$(HTSLIB_INSTALL_DIR)
else
HTSERRHINT="There is no htslib folder in directory $(HTSLIB_INSTALL_DIR) - "
endif
endif
endif

# set default include paths:
INCLUDE_PATH_HTSLIB ?= -I/usr/include/htslib -I/usr/local/include/htslib/
HTSERRHINT:=$(HTSERRHINT)"Check if HTSlib is installed and of version 1.10 or higher - see README.md"

INCLS += $(INCLUDE_PATH_HTSLIB)
LDFLAGS += $(LIBRARY_PATH_HTSLIB)
LDLIBS += -lhts
INCLS += $(INCLUDE_PATH_ZLIB)
LDFLAGS += $(LIBRARY_PATH_ZLIB)
LDLIBS += -lz -lpthread

# when using a static hts library, these additional libraries may be required :
# LDLIBS += -lcurl -lcrypto -llzma -lbz2 -lm -lcurses -lssl

.PHONY: all clean test

all: bam2wig

bam2wig: bam2wig.o
$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(LDLIBS)
mkdir -p ../../bin
bam2wig: bam2wig
cp -f bam2wig ../../bin/bam2wig

bam2wig.o: bam2wig.c
-$(CC) $(CPPFLAGS) $(CFLAGS) $(INCLS) -c $^
@if [ ! -f $@ ]; then echo $(HTSERRHINT); exit 1; fi

clean:
rm -f bam2wig.o bam2wig
rm -f ../../bin/bam2wig
if [ -n $(shell which python3) ] ; then cd ../../tests/short && ./execute_test.py --clean bam2wig ; fi

test: bam2wig
cd ../../tests/short && ./execute_test.py --compare --html bam2wig
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