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Merge pull request #89 from HKU-BAL/r11
update version to v0.1-r11
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,59 @@ | ||
| OS := $(shell uname) | ||
| ARCH := $(shell arch) | ||
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| PYTHON ?= python3 | ||
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| all : libhts.a longphase libclair3.so | ||
| clean : clean_htslib clean_longphase clean_libclair3 | ||
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| SAMVER = 1.10 | ||
| LPVER = 1.0 | ||
| GCC ?= gcc | ||
| GXX ?= g++ | ||
| PREFIX ?= ${CONDA_PREFIX} | ||
| LDFLAGS = -L ${PREFIX}/lib | ||
| CFLAGS = -fpic -std=c99 -O3 -I ${PREFIX}/include -L ${PREFIX}/lib | ||
| CPPFLAGS = -std=c++11 -Wall -O3 -I ${PREFIX}/include -L ${PREFIX}/lib -Wl,-rpath=${PREFIX}/lib | ||
| LP_CPPFLAGS = -std=c++11 -Wall -g -O3 -I ${PREFIX}/include -L ${PREFIX}/lib -Wl,-rpath=${PREFIX}/lib | ||
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| samtools-$(SAMVER)/Makefile: | ||
| curl -L -o samtools-${SAMVER}.tar.bz2 https://github.com/samtools/samtools/releases/download/${SAMVER}/samtools-${SAMVER}.tar.bz2; \ | ||
| tar -xjf samtools-${SAMVER}.tar.bz2; \ | ||
| rm samtools-${SAMVER}.tar.bz2 | ||
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| libhts.a: samtools-$(SAMVER)/Makefile | ||
| # this is required only to add in -fpic so we can build python module | ||
| @echo "\x1b[1;33mMaking $(@F)\x1b[0m" | ||
| cd samtools-${SAMVER}/htslib-${SAMVER}; CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" ./configure; make CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" | ||
| cp samtools-${SAMVER}/htslib-${SAMVER}/$@ $@ | ||
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| longphase-$(LPVER)/Makefile: | ||
| curl -L -o longphase-${LPVER}.tar.gz https://github.com/twolinin/longphase/archive/refs/tags/v${LPVER}.tar.gz; \ | ||
| tar -zxvf longphase-${LPVER}.tar.gz; \ | ||
| rm longphase-${LPVER}.tar.gz | ||
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| longphase: longphase-$(LPVER)/Makefile | ||
| @echo "\x1b[1;33mMaking $(@F)\x1b[0m" | ||
| cd longphase-${LPVER}; autoreconf -i; CPPFLAGS="${CPPFLAGS}" ./configure; make CC=${GCC} CXX=${GXX} CPPFLAGS="${CPPFLAGS}" | ||
| cp longphase-${LPVER}/$@ $@ | ||
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| libclair3.so: samtools-${SAMVER}/htslib-${SAMVER} | ||
| ${PYTHON} build.py | ||
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| .PHONY: clean_htslib | ||
| clean_htslib: | ||
| cd samtools-${SAMVER} && make clean || exit 0 | ||
| cd samtools-${SAMVER}/htslib-${SAMVER} && make clean || exit 0 | ||
| rm libhts.a | ||
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| .PHONY: clean_longphase | ||
| clean_longphase: | ||
| cd longphase-${LPVER} && make clean || exit 0 | ||
| rm longphase | ||
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| .PHONY: clean_libclair3 | ||
| clean_libclair3: | ||
| rm libclair3.* |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,76 @@ | ||
| import itertools | ||
| import os | ||
| import platform | ||
| from subprocess import run | ||
| from cffi import FFI | ||
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| samver = "1.10" | ||
| file_directory = os.path.dirname(os.path.realpath(__file__)) | ||
| htslib_dir = os.path.join(file_directory, 'samtools-{}'.format(samver), 'htslib-{}'.format(samver)) | ||
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| libraries = ['m', 'z', 'lzma', 'bz2', 'pthread', 'curl', 'crypto'] | ||
| extra_link_args = [] | ||
| library_dirs = [htslib_dir] | ||
| src_dir = os.path.join(file_directory, 'src') | ||
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| extra_compile_args = ['-std=c99', '-O3'] | ||
| if platform.machine() in {"aarch64", "arm64"}: | ||
| if platform.system() == "Darwin": | ||
| pass | ||
| else: | ||
| extra_compile_args.append("-march=armv8-a+simd") | ||
| else: | ||
| extra_compile_args.append("-mtune=haswell") | ||
| libraries.append('deflate') | ||
| try: | ||
| conda_path = os.environ['CONDA_PREFIX'] | ||
| extra_link_args = ['-Wl,-rpath={}/lib'.format(conda_path)] | ||
| except: | ||
| print("[WARNING] Conda prefix not found, please activate clair3 conda environment first!") | ||
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| ffibuilder = FFI() | ||
| ffibuilder.set_source("libclair3", | ||
| r""" | ||
| #include "kvec.h" | ||
| #include "khash.h" | ||
| #include "levenshtein.h" | ||
| #include "medaka_bamiter.h" | ||
| #include "medaka_common.h" | ||
| #include "medaka_khcounter.h" | ||
| #include "clair3_pileup.h" | ||
| #include "clair3_full_alignment.h" | ||
| """, | ||
| libraries=libraries, | ||
| library_dirs=library_dirs, | ||
| include_dirs=[src_dir, htslib_dir], | ||
| sources=[ | ||
| os.path.join(src_dir, x) for x in ( | ||
| 'levenshtein.c', | ||
| 'medaka_bamiter.c', | ||
| 'medaka_common.c', | ||
| 'medaka_khcounter.c', | ||
| 'clair3_pileup.c', | ||
| 'clair3_full_alignment.c')], | ||
| extra_compile_args=extra_compile_args, | ||
| extra_link_args=extra_link_args, | ||
| extra_objects=['libhts.a'] | ||
| ) | ||
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| cdef = [ | ||
| "typedef struct { ...; } bam_fset;" | ||
| "bam_fset* create_bam_fset(char* fname);" | ||
| "void destroy_bam_fset(bam_fset* fset);" | ||
| ] | ||
| for header in ('clair3_pileup.h', 'clair3_full_alignment.h'): | ||
| with open(os.path.join(src_dir, header), 'r') as fh: | ||
| # remove directives | ||
| lines = ''.join(x for x in fh.readlines() if not x.startswith('#')) | ||
| cdef.append(lines) | ||
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| ffibuilder.cdef('\n\n'.join(cdef)) | ||
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| if __name__ == "__main__": | ||
| ffibuilder.compile(verbose=True) | ||
| run("cp {}/libclair3*.so {}/libclair3.so".format(file_directory, file_directory), shell=True) | ||
|
|
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