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(-)Makefile (-6 / +8 lines)
Lines 1-20 Link Here
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# $FreeBSD$
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# $FreeBSD$
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PORTNAME=	stringtie
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PORTNAME=	stringtie
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DISTVERSION=	1.3.4d
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DISTVERSION=	2.1.0
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CATEGORIES=	biology
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CATEGORIES=	biology
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MASTER_SITES=	http://ccb.jhu.edu/software/stringtie/dl/
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MASTER_SITES=	http://ccb.jhu.edu/software/stringtie/dl/
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MAINTAINER=	mzaki@niid.go.jp
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MAINTAINER=	mzaki@e-mail.ne.jp
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COMMENT=	Transcript assembly and quantification for RNA-seq
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COMMENT=	Transcript assembly and quantification for RNA-seq
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LICENSE=	ART20 MIT
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LICENSE=	MIT
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LICENSE_COMB=	multi
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LICENSE_FILE=	${WRKSRC}/LICENSE
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LICENSE_FILE_ART20=	${WRKSRC}/LICENSE
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LICENSE_FILE_MIT=	${WRKSRC}/samtools-0.1.18/COPYING
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TEST_DEPENDS=	bash:shells/bash \
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		curl:ftp/curl
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USES=		gmake
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USES=		gmake
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ALL_TARGET=	release
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ALL_TARGET=	release
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TEST_TARGET=	test
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PLIST_FILES=	bin/stringtie
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PLIST_FILES=	bin/stringtie
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(-)distinfo (-3 / +3 lines)
Lines 1-3 Link Here
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TIMESTAMP = 1530582079
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TIMESTAMP = 1580357807
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SHA256 (stringtie-1.3.4d.tar.gz) = b1962d0108146ce7fea39d069b5e5de918e0e21daef9e1425ec9b778094d6ae6
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SHA256 (stringtie-2.1.0.tar.gz) = 28e07b0d8f5be66897ab4d6186a976dd217f951740461f1712aac0ef912dfbe0
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SIZE (stringtie-1.3.4d.tar.gz) = 438025
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SIZE (stringtie-2.1.0.tar.gz) = 1969866
(-)files/patch-Makefile (-48 / +8 lines)
Lines 1-55 Link Here
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--- Makefile.orig	2018-03-06 16:29:49 UTC
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--- Makefile.orig	2020-01-26 03:31:12 UTC
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+++ Makefile
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+++ Makefile
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@@ -6,12 +6,12 @@ GDIR      :=./gclib
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@@ -20,7 +20,7 @@ ifeq "$(GCCVER8)" "1"
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   BASEFLAGS += -Wno-class-memaccess
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 INCDIRS   := -I. -I${GDIR} -I${BAM}
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-CC        := g++
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+CXX       ?= g++
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 BASEFLAGS := -Wall -Wextra ${INCDIRS} -fsigned-char -D_FILE_OFFSET_BITS=64 \
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 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti
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-LINKER    := g++
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+LINKER    = ${CXX}
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 LDFLAGS   := -g -L${BAM} $(LDFLAGS)
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@@ -22,13 +22,13 @@ ifneq (,$(findstring nothreads,$(MAKECMD
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 endif
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 endif
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 #detect MinGW (Windows environment)
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-LINKER  := $(if $(LINKER),$(LINKER),g++)
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-ifneq (,$(findstring mingw,$(shell ${CC} -dumpmachine)))
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+LINKER  := $(if $(LINKER),$(LINKER),$(CXX))
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+ifneq (,$(findstring mingw,$(shell ${CXX} -dumpmachine)))
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  WINDOWS=1
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 endif
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 # MinGW32 GCC 4.5 link problem fix
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 LDFLAGS := $(if $(LDFLAGS),$(LDFLAGS),-g)
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 #ifdef WINDOWS
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-ifneq (,$(findstring 4.5.,$(shell g++ -dumpversion)))
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+ifneq (,$(findstring 4.5.,$(shell ${CXX} -dumpversion)))
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  STATIC_CLIB=1
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 endif
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 #endif
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@@ -63,7 +63,7 @@ endif
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 ifneq (,$(filter %release %static, $(MAKECMDGOALS)))
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   # -- release build
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   RELEASE_BUILD=1
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-  CFLAGS := -DNDEBUG -g $(BASEFLAGS) $(CFLAGS) -O3
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+  CFLAGS := -DNDEBUG -g $(BASEFLAGS) $(CFLAGS)
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 else
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   ifneq (,$(filter %memcheck %memdebug, $(MAKECMDGOALS)))
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      #use sanitizer in gcc 4.9+
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@@ -122,7 +122,7 @@ endif
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@@ -151,7 +151,7 @@ rlink.o : rlink.h tablemaker.h $(GDIR)/G
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 %.o : %.cpp
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-	${CC} ${CFLAGS} -c $< -o $@
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+	${CXX} ${CFLAGS} -c $< -o $@
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 OBJS += rlink.o tablemaker.o tmerge.o
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@@ -137,7 +137,7 @@ rlink.o : rlink.h tablemaker.h $(GDIR)/G
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 tmerge.o : rlink.h tmerge.h
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 tmerge.o : rlink.h tmerge.h
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 tablemaker.o : tablemaker.h rlink.h
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 tablemaker.o : tablemaker.h rlink.h
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 ${BAM}/libbam.a: 
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 ${BAM}/libbam.a: 
Lines 58-64 Link Here
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 stringtie: ${BAM}/libbam.a $(OBJS) stringtie.o
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 stringtie: ${BAM}/libbam.a $(OBJS) stringtie.o
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 	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
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 	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
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 	@echo
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 	@echo
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@@ -151,6 +151,6 @@ clean:
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@@ -167,6 +167,6 @@ clean:
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 	${RM} stringtie${EXE} stringtie.o*  $(OBJS)
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 	${RM} stringtie${EXE} stringtie.o*  $(OBJS)
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 	${RM} core.*
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 	${RM} core.*
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 allclean cleanAll cleanall:
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 allclean cleanAll cleanall:
(-)files/patch-gclib_GIntHash.hh (-20 lines)
Lines 1-20 Link Here
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--- gclib/GIntHash.hh.orig	2018-03-06 16:29:49 UTC
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+++ gclib/GIntHash.hh
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@@ -122,7 +122,7 @@ public:
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   uint32 NextKey() {
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      Cell* cell=ghash.NextCell();
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      if (cell) return cell->key;
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-       else return NULL;
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+       else return 0;
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   }
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   OBJ* NextValue() {
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      Cell* cell=ghash.NextCell();
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@@ -201,7 +201,7 @@ public:
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   uint32 NextKey() {
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      Cell* cell=ghash.NextCell();
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      if (cell) return cell->key;
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-       else return NULL;
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+       else return 0;
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   }
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   OBJ* NextValue() {
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      Cell* cell=ghash.NextCell();
(-)files/patch-samtools-0.1.18_bam__aux.c (-20 lines)
Lines 1-20 Link Here
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--- samtools-0.1.18/bam_aux.c.orig	2018-03-06 16:29:49 UTC
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+++ samtools-0.1.18/bam_aux.c
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@@ -25,7 +25,7 @@ uint8_t *bam_aux_get_core(bam1_t *b, con
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 	return bam_aux_get(b, tag);
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 }
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-inline int aux_type2size(uint8_t type)
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+int aux_type2size(uint8_t type)
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 {
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     switch (type) {
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     case 'A': case 'c': case 'C':
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@@ -43,7 +43,7 @@ inline int aux_type2size(uint8_t type)
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     }
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 }
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-inline uint8_t* skip_aux(uint8_t* s) {
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+uint8_t* skip_aux(uint8_t* s) {
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 	int size = aux_type2size(*s); ++s; // skip type
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 	uint32_t n;
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 	switch (size) {

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