6863162eb9
Minor patches to utilize simde to emulate SSE (from Debian package) Add -fsigned-char since clang defaults to unsigned on aarch64 Remove -DPOPCNT_CAPABILITY (not truly safe even on amd64)
81 lines
2.1 KiB
Plaintext
81 lines
2.1 KiB
Plaintext
--- Makefile.orig 2020-07-24 20:07:54 UTC
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+++ Makefile
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@@ -23,9 +23,11 @@
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INC =
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GCC_PREFIX = $(shell dirname `which gcc`)
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GCC_SUFFIX =
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-CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
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-CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
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-CXX = $(CPP)
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+CC ?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
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+CPP ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX)
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+CXX ?= $(CPP)
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+INSTALL ?= install
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+
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HEADERS = $(wildcard *.h)
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BOWTIE_MM = 1
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BOWTIE_SHARED_MEM = 0
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@@ -55,7 +57,7 @@ ifneq (,$(findstring Darwin,$(shell uname)))
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MACOS = 1
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endif
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-EXTRA_FLAGS += -DPOPCNT_CAPABILITY -std=c++11
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+EXTRA_FLAGS += -std=c++11
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INC += -I. -I third_party
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MM_DEF =
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@@ -152,31 +154,9 @@ HISAT2_REPEAT_CPPS_MAIN = $(REPEAT_CPPS) $(BUILD_CPPS)
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SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
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VERSION = $(shell cat VERSION)
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-# Convert BITS=?? to a -m flag
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-BITS=32
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-ifeq (x86_64,$(shell uname -m))
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-BITS=64
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-endif
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-# msys will always be 32 bit so look at the cpu arch instead.
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-ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
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- ifeq (1,$(MINGW))
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- BITS=64
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- endif
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-endif
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-BITS_FLAG =
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-
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-ifeq (32,$(BITS))
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- BITS_FLAG = -m32
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-endif
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-
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-ifeq (64,$(BITS))
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- BITS_FLAG = -m64
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-endif
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-SSE_FLAG=-msse2
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-
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DEBUG_FLAGS = -O0 -g3 $(BITS_FLAG) $(SSE_FLAG)
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DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
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-RELEASE_FLAGS = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3
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+RELEASE_FLAGS = $(CXXFLAGS)
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RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
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NOASSERT_FLAGS = -DNDEBUG
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FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
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@@ -553,6 +533,20 @@ doc/manual.inc.html: MANUAL.markdown
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MANUAL: MANUAL.markdown
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perl doc/strip_markdown.pl < $^ > $@
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+
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+# Install per filesystem hierarchy standard:
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+# https://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard
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+
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+.PHONY: install
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+install:
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+ mkdir -p ${DESTDIR}${PREFIX}/bin
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+ ${INSTALL} -c -s ${HISAT2_BIN_LIST} ${DESTDIR}${PREFIX}/bin
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+ ${INSTALL} -c hisat2 hisat2-build hisat2-inspect \
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+ ${DESTDIR}${PREFIX}/bin
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+
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+ mkdir -p ${DESTDIR}${PREFIX}/libexec/hisat2
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+ ${INSTALL} -c scripts/*.sh scripts/*.pl scripts/*.py *.py \
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+ ${DESTDIR}${PREFIX}/libexec/hisat2
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.PHONY: clean
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clean:
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