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biology/stringtie: Update 1.3.4d -> 2.1.1
PR: 243718 Submitted by: Motomichi Matsuzaki <mzaki@e-mail.ne.jp> (maintainer)
This commit is contained in:
Yuri Victorovich
parent
13f745c5b9
commit
0d3f38dc37
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=526322
@ -1,20 +1,22 @@
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# $FreeBSD$
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PORTNAME= stringtie
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DISTVERSION= 1.3.4d
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DISTVERSION= 2.1.1
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CATEGORIES= biology
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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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LICENSE= ART20 MIT
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LICENSE_COMB= multi
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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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LICENSE= MIT
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LICENSE_FILE= ${WRKSRC}/LICENSE
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TEST_DEPENDS= bash:shells/bash \
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curl:ftp/curl
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USES= gmake
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ALL_TARGET= release
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TEST_TARGET= test
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PLIST_FILES= bin/stringtie
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@ -1,3 +1,3 @@
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TIMESTAMP = 1530582079
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SHA256 (stringtie-1.3.4d.tar.gz) = b1962d0108146ce7fea39d069b5e5de918e0e21daef9e1425ec9b778094d6ae6
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SIZE (stringtie-1.3.4d.tar.gz) = 438025
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TIMESTAMP = 1580533096
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SHA256 (stringtie-2.1.1.tar.gz) = 7ea152b791856b1bd5dd2d475b06fae05398ee7e03f2f9844418010376edcca2
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SIZE (stringtie-2.1.1.tar.gz) = 1969917
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@ -1,55 +1,15 @@
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--- Makefile.orig 2018-03-06 16:29:49 UTC
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--- Makefile.orig 2020-01-26 03:31:12 UTC
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+++ Makefile
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@@ -6,12 +6,12 @@ GDIR :=./gclib
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INCDIRS := -I. -I${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,$(MAKECMD
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@@ -20,7 +20,7 @@ ifeq "$(GCCVER8)" "1"
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BASEFLAGS += -Wno-class-memaccess
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endif
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#detect MinGW (Windows environment)
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-ifneq (,$(findstring mingw,$(shell ${CC} -dumpmachine)))
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+ifneq (,$(findstring mingw,$(shell ${CXX} -dumpmachine)))
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WINDOWS=1
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endif
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-LINKER := $(if $(LINKER),$(LINKER),g++)
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+LINKER := $(if $(LINKER),$(LINKER),$(CXX))
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# MinGW32 GCC 4.5 link problem fix
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#ifdef WINDOWS
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-ifneq (,$(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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LDFLAGS := $(if $(LDFLAGS),$(LDFLAGS),-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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@@ -151,7 +151,7 @@ rlink.o : rlink.h tablemaker.h $(GDIR)/G
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tmerge.o : rlink.h tmerge.h
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tablemaker.o : tablemaker.h rlink.h
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${BAM}/libbam.a:
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@ -58,7 +18,7 @@
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stringtie: ${BAM}/libbam.a $(OBJS) stringtie.o
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${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
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@echo
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@@ -151,6 +151,6 @@ clean:
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@@ -167,6 +167,6 @@ clean:
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${RM} stringtie${EXE} stringtie.o* $(OBJS)
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${RM} core.*
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allclean cleanAll cleanall:
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@ -1,20 +0,0 @@
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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();
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@ -1,20 +0,0 @@
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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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