fastp: Update to 0.24.3

[Jason Bacon (via pkgsrc-wip) <commit-notify%pkgsrc.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Sat May 31 16:09:50 2025 -0500
Changeset:	0acba54a44dba85c4d2c697fe470a0432e3841a7

Modified Files:
	fastp/DESCR
	fastp/Makefile
	fastp/distinfo
	fastp/patches/patch-Makefile

Log Message:
fastp: Update to 0.24.3

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=0acba54a44dba85c4d2c697fe470a0432e3841a7

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 fastp/DESCR                  |  6 +++---
 fastp/Makefile               |  4 +---
 fastp/distinfo               |  8 ++++----
 fastp/patches/patch-Makefile | 41 ++++++++++-------------------------------
 4 files changed, 18 insertions(+), 41 deletions(-)

diffs:
diff --git a/fastp/DESCR b/fastp/DESCR
index e799d025d6..84dda18a0b 100644
--- a/fastp/DESCR
+++ b/fastp/DESCR
@@ -1,3 +1,3 @@
-fastp is a tool designed to provide fast all-in-one preprocessing for FastQ
-files. This tool is developed in C++ with multithreading supported to afford
-high performance.
+fastp is a tool designed to provide fast all-in-one preprocessing for
+FastQ files. This tool is developed in C++ with multithreading
+supported to afford high performance.
diff --git a/fastp/Makefile b/fastp/Makefile
index 879a437b48..1cef319af4 100644
--- a/fastp/Makefile
+++ b/fastp/Makefile
@@ -1,8 +1,6 @@
 # $NetBSD$
 
-# 0.22.0 is the last release that doesn't depend on the non-portable
-# Intel isa-l library
-DISTNAME=	fastp-0.22.0
+DISTNAME=	fastp-0.24.3
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=OpenGene/}
 GITHUB_TAG=	v${PKGVERSION_NOREV}
diff --git a/fastp/distinfo b/fastp/distinfo
index bf7e4881e2..1cca475914 100644
--- a/fastp/distinfo
+++ b/fastp/distinfo
@@ -1,7 +1,7 @@
 $NetBSD$
 
-BLAKE2s (fastp-0.22.0.tar.gz) = fbeed45925f33bde6020054e68affd30b076a81a43f383650cf5c8b6e0d09e7d
-SHA512 (fastp-0.22.0.tar.gz) = 661e61c78fd77347e23380bb0da79e4269ef0acf7350e2b95dd104b85083db55e12b52330bb8fbcaf25554f22d649315db05e083704b8bdabf1e5fb345e34c41
-Size (fastp-0.22.0.tar.gz) = 141257 bytes
-SHA1 (patch-Makefile) = d55955d62ede0e5fad1be39c937fedb7e79b746d
+BLAKE2s (fastp-0.24.3.tar.gz) = 3f25bb88acf3ee7f5ce76cf7d72c836ff0f0db20a6183a9c505b4f0dea764a21
+SHA512 (fastp-0.24.3.tar.gz) = d307001de201db026a04eaa875eabec00ce4b6841782ced4cf31f22e89cb5f30c6d109002c9ded3a959f1669208d6eeff402290305b6e9b8864fde853b61909f
+Size (fastp-0.24.3.tar.gz) = 164518 bytes
+SHA1 (patch-Makefile) = 14f5ada5cb7cadd8b6b70cad3c2657b7e8578648
 SHA1 (patch-src_main.cpp) = d28fb587c72b59f4c86bc51fd66874344a9dd43d
diff --git a/fastp/patches/patch-Makefile b/fastp/patches/patch-Makefile
index d7a68e4911..b81c2625ab 100644
--- a/fastp/patches/patch-Makefile
+++ b/fastp/patches/patch-Makefile
@@ -1,50 +1,29 @@
 $NetBSD$
 
-# Respect env
+# Respect build env
 
---- Makefile.orig	2021-08-24 14:00:31.000000000 +0000
+--- Makefile.orig	2025-05-31 20:40:16.035281359 +0000
 +++ Makefile
-@@ -7,6 +7,8 @@ BINDIR ?= $(PREFIX)/bin
- INCLUDE_DIRS ?=
- LIBRARY_DIRS ?=
- 
-+STRIP	?= strip
-+
- SRC := $(wildcard ${DIR_SRC}/*.cpp)
- OBJ := $(patsubst %.cpp,${DIR_OBJ}/%.o,$(notdir ${SRC}))
- 
-@@ -15,13 +17,17 @@ TARGET := fastp
+@@ -15,15 +15,18 @@ TARGET := fastp
  BIN_TARGET := ${TARGET}
  
  CXX ?= g++
--CXXFLAGS := -std=c++11 -g -O3 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) ${CXXFLAGS}
+-CXXFLAGS := -std=c++11 -pthread -g -O3 -MD -MP -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) ${CXXFLAGS}
 +# Optional flags that the user can override by setting CXXFLAGS in the
 +# env or make argument
 +CXXFLAGS ?= -g -O3
 +# Required flags
 +CXXFLAGS += -std=c++11 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir))
- LIBS := -lz -lpthread
+ LIBS := -lisal -ldeflate -lpthread
+ STATIC_FLAGS := -static -Wl,--no-as-needed -pthread
 -LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS) $(LD_FLAGS)
 +LDFLAGS += $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS)
+ STATIC_LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(STATIC_FLAGS) $(LIBS) $(STATIC_LD_FLAGS)
  
- 
+-
  ${BIN_TARGET}:${OBJ}
 -	$(CXX) $(OBJ) -o $@ $(LD_FLAGS)
 +	$(CXX) $(OBJ) -o $@ $(LDFLAGS)
  
- ${DIR_OBJ}/%.o:${DIR_SRC}/%.cpp make_obj_dir
- 	$(CXX) -c $< -o $@ $(CXXFLAGS)
-@@ -43,6 +49,12 @@ make_obj_dir:
- 		mkdir $(DIR_OBJ) ; \
- 	fi
- 
-+# Respect DESTDIR for staged installs (used by most package managers)
- install:
--	install $(TARGET) $(BINDIR)/$(TARGET)
-+	mkdir $(DESTDIR)$(BINDIR)
-+	install $(TARGET) $(DESTDIR)$(BINDIR)/$(TARGET)
- 	@echo "Installed."
-+
-+# Many package managers use install-strip target if debugging is not enabled
-+install-strip: install
-+	$(STRIP) $(DESTDIR)$(BINDIR)/$(TARGET)
+ static:${OBJ}
+ 	$(CXX) $(OBJ) -o ${BIN_TARGET} $(STATIC_LD_FLAGS)