build: auto-detect deps via pkg-config, unify static/dynamic linking

1. Add pkg-config auto-detection for libhwy, libisal, libdeflate.
   When installed via package managers (conda, brew, apt), their
   include/lib paths are automatically picked up without needing
   to pass INCLUDE_DIRS/LIBRARY_DIRS manually.

2. Unify linking: on Linux, keep -static when all .a archives exist
   (default). When some .a are missing (conda/apt shared-only),
   fallback to .a + -l dynamic. macOS unchanged.

With this change, bioconda build.sh can simply call:
  make CXX=$CXX -j$CPU_COUNT
  make install PREFIX=$PREFIX

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: KimYannn

Makefile

@@ -7,6 +7,15 @@ BINDIR ?= $(PREFIX)/bin
 INCLUDE_DIRS ?=
 LIBRARY_DIRS ?=
 
+# Auto-detect library paths via pkg-config (works with conda, brew, system packages)
+PKG_CONFIG ?= pkg-config
+HWY_CFLAGS := $(shell $(PKG_CONFIG) --cflags libhwy 2>/dev/null)
+HWY_LIBS := $(shell $(PKG_CONFIG) --libs-only-L libhwy 2>/dev/null)
+ISAL_CFLAGS := $(shell $(PKG_CONFIG) --cflags libisal 2>/dev/null)
+ISAL_LIBS := $(shell $(PKG_CONFIG) --libs-only-L libisal 2>/dev/null)
+DEFLATE_CFLAGS := $(shell $(PKG_CONFIG) --cflags libdeflate 2>/dev/null)
+DEFLATE_LIBS := $(shell $(PKG_CONFIG) --libs-only-L libdeflate 2>/dev/null)
+
 SRC := $(wildcard ${DIR_SRC}/*.cpp)
 OBJ := $(patsubst %.cpp,${DIR_OBJ}/%.o,$(notdir ${SRC}))
 
@@ -15,23 +24,31 @@ TARGET := fastp
 BIN_TARGET := ${TARGET}
 
 CXX ?= g++
-CXXFLAGS := -std=c++11 -pthread -g -O3 -MD -MP -I. -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) ${CXXFLAGS}
+CXXFLAGS := -std=c++11 -pthread -g -O3 -MD -MP -I. -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) $(HWY_CFLAGS) $(ISAL_CFLAGS) $(DEFLATE_CFLAGS) ${CXXFLAGS}
 LIBS := -lisal -ldeflate -lhwy -lpthread
 
+PKG_LDFLAGS := $(HWY_LIBS) $(ISAL_LIBS) $(DEFLATE_LIBS)
+
 UNAME_S := $(shell uname -s)
+FIND_STATIC = $(firstword $(foreach d,$(LIBRARY_DIRS),$(wildcard $(d)/lib$(1).a)) $(wildcard /usr/local/lib/lib$(1).a /opt/homebrew/lib/lib$(1).a))
+STATIC_LIBS :=
+DYNAMIC_LIBS :=
+$(foreach lib,isal deflate hwy,\
+  $(if $(call FIND_STATIC,$(lib)),\
+    $(eval STATIC_LIBS += $(call FIND_STATIC,$(lib))),\
+    $(eval DYNAMIC_LIBS += -l$(lib))))
+
 ifeq ($(UNAME_S),Linux)
-  # Linux: fully static binary
-  LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) -static -Wl,--no-as-needed -pthread $(LIBS) $(LD_FLAGS)
+  ifeq ($(DYNAMIC_LIBS),)
+    # All .a found: fully static binary (default for Linux)
+    LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(PKG_LDFLAGS) -static -Wl,--no-as-needed -pthread $(LIBS) $(LD_FLAGS)
+  else
+    # Some .a missing (e.g. conda): link .a directly + dynamic fallback
+    LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(PKG_LDFLAGS) $(STATIC_LIBS) $(DYNAMIC_LIBS) -lpthread $(LD_FLAGS)
+  endif
 else
-  # macOS: link 3rd-party libs statically via .a when available, fallback to dynamic
-  FIND_STATIC = $(firstword $(foreach d,$(LIBRARY_DIRS),$(wildcard $(d)/lib$(1).a)) $(wildcard /usr/local/lib/lib$(1).a /opt/homebrew/lib/lib$(1).a))
-  STATIC_LIBS :=
-  DYNAMIC_LIBS :=
-  $(foreach lib,isal deflate hwy,\
-    $(if $(call FIND_STATIC,$(lib)),\
-      $(eval STATIC_LIBS += $(call FIND_STATIC,$(lib))),\
-      $(eval DYNAMIC_LIBS += -l$(lib))))
-  LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(STATIC_LIBS) $(DYNAMIC_LIBS) -lpthread $(LD_FLAGS)
+  # macOS: .a preferred, fallback to dynamic
+  LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(PKG_LDFLAGS) $(STATIC_LIBS) $(DYNAMIC_LIBS) -lpthread $(LD_FLAGS)
 endif