/
Makefile
191 lines (159 loc) · 7.28 KB
/
Makefile
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OS := $(shell uname)
ifeq ($(OS), Darwin)
# mainly for dev builds using homebrew things
EXTRA_LDFLAGS ?= -L$(shell brew --prefix openssl@1.1)/lib
ARGP ?= $(shell brew --prefix argp-standalone)/lib/libargp.a
ARGP_INC ?= -I$(shell brew --prefix argp-standalone)/include
CFLAGS ?= -fpic -O3 ${ARGP_INC}
ZCAT = "gzcat"
else
ARGP ?=
ARGP_INC ?=
CFLAGS ?= -fpic -msse3 -O3 ${ARGP_INC}
ZCAT = "zcat"
endif
VALGRIND ?= valgrind
CC ?= gcc
STATIC_HTSLIB ?= htslib/libhts.a
EXTRA_CFLAGS ?=
EXTRA_LDFLAGS ?=
EXTRA_LIBS ?=
EXTRA_LIBS ?=
HTS_CONF_ARGS ?=
NOTHREADS ?=
ifeq ($(NOTHREADS), 1)
CFLAGS += -DNOTHREADS
endif
# we can't do pedantic because min/max macros lead to:
# "ISO C forbids braced-groups within expressions [-Werror=pedantic]"
ifeq ($(shell $(CC) --version | grep clang | wc -l), 0)
WARNINGS = -Werror -Wall -Wextra -Wno-incompatible-pointer-types
else
WARNINGS = -Werror -Wall -Wextra -Wpedantic -Wno-language-extension-token -Wno-gnu-statement-expression -Wno-incompatible-function-pointer-types
endif
.PHONY: default
default: fastcat bamstats bamindex
htslib/libhts.a:
@echo Compiling $(@F)
cd htslib/ \
&& autoheader \
&& autoconf \
&& autoreconf --install \
&& CFLAGS="$(CFLAGS) $(EXTRA_CFLAGS)" ./configure $(HTS_CONF_ARGS) \
&& make -j 4
zlib-ng/libz.a:
@echo Compiling $(@F)
cd zlib-ng/ \
&& CFLAGS="$(CFLAGS) $(EXTRA_CFLAGS)" ./configure --zlib-compat \
&& make -j 4 libz.a
src/%.o: src/%.c
$(CC) -Isrc -Ihtslib -c -pthread $(WARNINGS) -fstack-protector-strong -D_FORTIFY_SOURCE=2 \
$(CFLAGS) $(EXTRA_CFLAGS) $^ -o $@
fastcat: src/fastcat/main.o src/fastcat/args.o src/fastcat/writer.o src/fastqcomments.o src/common.o src/stats.o src/kh_counter.o $(STATIC_HTSLIB) zlib-ng/libz.a
$(CC) -Isrc $(WARNINGS) -fstack-protector-strong -D_FORTIFY_SOURCE=2 \
$(CFLAGS) $(EXTRA_CFLAGS) $(EXTRA_LDFLAGS) \
$^ $(ARGP) \
-lm $(EXTRA_LIBS) \
-o $@
bamstats: src/bamstats/main.o src/bamstats/args.o src/bamstats/readstats.o src/bamstats/bamiter.o src/fastqcomments.o src/common.o src/stats.o src/kh_counter.o $(STATIC_HTSLIB)
$(CC) -Isrc -Ihtslib $(WARNINGS) -fstack-protector-strong -D_FORTIFY_SOURCE=2 \
$(CFLAGS) $(EXTRA_CFLAGS) $(EXTRA_LDFLAGS) \
$^ $(ARGP) \
-lm -lz -llzma -lbz2 -lpthread -lcurl -lcrypto $(EXTRA_LIBS) \
-o $@
bamindex: src/bamindex/main.o src/bamindex/build_main.o src/bamindex/fetch_main.o src/bamindex/dump_main.o src/bamindex/index.o $(STATIC_HTSLIB)
$(CC) -Isrc -Ihtslib $(WARNINGS) -fstack-protector-strong -D_FORTIFY_SOURCE=2 \
$(CFLAGS) $(EXTRA_CFLAGS) $(EXTRA_LDFLAGS) \
$^ $(ARGP) \
-lm -lz -llzma -lbz2 -lpthread -lcurl -lcrypto $(EXTRA_LIBS) \
-o $@
.PHONY: clean
clean:
rm -rf fastcat bamstats bamindex src/fastcat/*.o src/bamstats/*.o src/bamindex/*.o src/*.o
.PHONY: clean_htslib
clean_htslib:
cd htslib && make clean
.PHONY: mem_check_fastcat
mem_check_fastcat: fastcat
rm -rf fastcat-histograms
$(VALGRIND) --error-exitcode=1 --tool=memcheck --leak-check=full --show-leak-kinds=all -s \
./fastcat test/data/*.fastq.gz > /dev/null
.PHONY: mem_check_fastcat_demultiplex
mem_check_fastcat_demultiplex: fastcat
rm -rf demultiplex
$(VALGRIND) --error-exitcode=1 --tool=memcheck --leak-check=full --show-leak-kinds=all -s \
./fastcat test/data/*.fastq.gz --demultiplex demultiplex > /dev/null
.PHONY: mem_check_bamstats
mem_check_bamstats: bamstats
$(VALGRIND) --error-exitcode=1 --tool=memcheck --leak-check=full --show-leak-kinds=all -s \
./bamstats test/bamstats/400ecoli.bam
.PHONY: mem_check_bamstats_duplex
mem_check_bamstats_duplex: bamstats
[ -d bamstats-histograms ] && rm -rf bamstats-histograms
$(VALGRIND) --error-exitcode=1 --tool=memcheck --leak-check=full --show-leak-kinds=all -s \
./bamstats test/bamstats/310dx.bam
.PHONY: mem_check_bamindex-build
mem_check_bamindex-build: bamindex
$(VALGRIND) --error-exitcode=1 --tool=memcheck --leak-check=full --show-leak-kinds=all -s \
./bamindex build test/bamindex/400.bam
test/bamindex/400.bam.bci: bamindex
./bamindex dump test/bamindex/400.bam.bci
.PHONY: mem_check_bamindex-dump
mem_check_bamindex-dump: bamindex test/bamindex/400.bam.bci
$(VALGRIND) --error-exitcode=1 --tool=memcheck --leak-check=full --show-leak-kinds=all -s \
./bamindex dump test/bamindex/400.bam.bci
.PHONY: mem_check_bamindex-fetch
mem_check_bamindex-fetch: bamindex test/bamindex/400.bam.bci
$(VALGRIND) --error-exitcode=1 --tool=memcheck --leak-check=full --show-leak-kinds=all --track-origins=yes -s \
./bamindex fetch test/bamindex/400.bam --chunk 5 > /dev/null
.PHONY: mem_check_bamindex
mem_check_bamindex: mem_check_bamindex-build mem_check_bamindex-dump mem_check_bamindex-fetch
.PHONY: test_bamstats_NM
test_bamstats_NM: bamstats
if [ -d test/test-tmp ]; then rm -r test/test-tmp; fi
mkdir test/test-tmp && \
cd test/test-tmp && \
../../bamstats ../bamstats_badNM/test.sam 2> err || grep "appears to contain implausible alignment information" err && rm -rf bamstats-histograms && \
../../bamstats ../bamstats_zeroNM/test.sam
rm -r test/test-tmp
.PHONY: regression_test_fastcat
regression_test_fastcat: fastcat
if [ -d test/test-tmp ]; then rm -r test/test-tmp; fi
mkdir test/test-tmp && \
cd test/test-tmp && \
../../fastcat ../data -s sample --reheader -f per-file-stats.tsv -r per-read-stats.tsv \
> concat.sorted.fastq && \
bash -c 'diff <(sort per-file-stats.tsv) \
<(sort ../fastcat_expected_results/per-file-stats.tsv)' && \
bash -c 'diff <(sort per-read-stats.tsv) \
<(sort ../fastcat_expected_results/per-read-stats.tsv)' && \
bash -c "diff \
<(cat concat.sorted.fastq | paste -d '|' - - - - | sort | tr '|' '\n') \
<(${ZCAT} ../fastcat_expected_results/concat.reheader.sorted.fastq.gz | \
paste -d '|' - - - - | sort | tr '|' '\n')" && \
rm -rf fastcat-histograms/ && \
../../fastcat ../data -s sample -f per-file-stats.tsv -r per-read-stats.tsv \
> concat.sorted.fastq && \
bash -c "diff \
<(cat concat.sorted.fastq | paste -d '|' - - - - | sort | tr '|' '\n') \
<(${ZCAT} ../fastcat_expected_results/concat.sorted.fastq.gz | \
paste -d '|' - - - - | sort | tr '|' '\n')"
rm -r test/test-tmp
# samtools fastq -T'*' sam2fastq/wf_basecalling_demo.sam > sam2fastq/wf_basecalling_demo.fastq
.PHONY: regression_test_sam_to_fastcat
regression_test_sam_to_fastcat: fastcat
if [ -d test/test-tmp ]; then rm -r test/test-tmp; fi
mkdir test/test-tmp && \
cd test/test-tmp && \
../../fastcat ../sam2fastq/wf_basecalling_demo.fastq -s sample -H \
--histograms fastcat-histograms1 -r per-read-stats.fastcat_once.tsv -f per-file-stats.fastcat_once.tsv \
> wf_basecalling_demo.fastcat_once.fastq && \
../../fastcat wf_basecalling_demo.fastcat_once.fastq -s sample -H \
--histograms fastcat-histograms2 -r per-read-stats.fastcat_twice.tsv -f per-file-stats.fastcat_twice.tsv \
> wf_basecalling_demo.fastcat_twice.fastq && \
diff wf_basecalling_demo.fastcat_once.fastq wf_basecalling_demo.fastcat_twice.fastq && \
bash -c 'diff <(sort -d per-file-stats.fastcat_once.tsv | sed 's,../sam2fastq/wf_basecalling_demo.fastq,FILE,') \
<(sort -d per-file-stats.fastcat_twice.tsv | sed 's,wf_basecalling_demo.fastcat_once.fastq,FILE,')' && \
bash -c 'diff <(sort per-read-stats.fastcat_once.tsv | sed 's,../sam2fastq/wf_basecalling_demo.fastq,FILE,') \
<(sort per-read-stats.fastcat_twice.tsv | sed 's,wf_basecalling_demo.fastcat_once.fastq,FILE,')'
rm -r test/test-tmp