Attachment 194846 Details for Bug 229480 – svn diff

[patch] svn diff

stringtie-1.3.4d.diff (text/plain), 8.24 KB, created by Motomichi Matsuzaki on 2018-07-03 03:38:56 UTC

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Creator: Motomichi Matsuzaki

Created: 2018-07-03 03:38:56 UTC

Size: 8.24 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(nonexistent)
>+++ Makefile	(working copy)
>@@ -0,0 +1,25 @@
>+# $FreeBSD$
>+
>+PORTNAME=	stringtie
>+PORTVERSION=	1.3.4d
>+CATEGORIES=	biology
>+MASTER_SITES=	http://ccb.jhu.edu/software/stringtie/dl/
>+
>+MAINTAINER=	mzaki@niid.go.jp
>+COMMENT=	Transcript assembly and quantification for RNA-seq
>+
>+LICENSE=	ART20 MIT
>+LICENSE_COMB=	multi
>+LICENSE_FILE_ART20=	${WRKSRC}/LICENSE
>+LICENSE_FILE_MIT=	${WRKSRC}/samtools-0.1.18/COPYING
>+
>+USES=		gmake
>+
>+ALL_TARGET=	release
>+
>+PLIST_FILES=	bin/stringtie
>+
>+do-install:
>+	${INSTALL_PROGRAM} ${WRKSRC}/stringtie ${STAGEDIR}${PREFIX}/bin
>+
>+.include <bsd.port.mk>
>
>Property changes on: Makefile
>___________________________________________________________________
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:keywords
>## -0,0 +1 ##
>+FreeBSD=%H
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: distinfo
>===================================================================
>--- distinfo	(nonexistent)
>+++ distinfo	(working copy)
>@@ -0,0 +1,3 @@
>+TIMESTAMP = 1530582079
>+SHA256 (stringtie-1.3.4d.tar.gz) = b1962d0108146ce7fea39d069b5e5de918e0e21daef9e1425ec9b778094d6ae6
>+SIZE (stringtie-1.3.4d.tar.gz) = 438025
>
>Property changes on: distinfo
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
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>Index: files/patch-Makefile
>===================================================================
>--- files/patch-Makefile	(nonexistent)
>+++ files/patch-Makefile	(working copy)
>@@ -0,0 +1,68 @@
>+--- Makefile.orig	2018-03-06 16:29:49 UTC
>++++ Makefile
>+@@ -6,12 +6,12 @@ GDIR      :=./gclib
>+ 
>+ INCDIRS   := -I. -I${GDIR} -I${BAM}
>+ 
>+-CC        := g++
>++CXX       ?= g++
>+ 
>+ BASEFLAGS := -Wall -Wextra ${INCDIRS} -fsigned-char -D_FILE_OFFSET_BITS=64 \
>+ -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti
>+ 
>+-LINKER    := g++
>++LINKER    = ${CXX}
>+ 
>+ LDFLAGS   := -g -L${BAM} $(LDFLAGS)
>+ 
>+@@ -22,13 +22,13 @@ ifneq (,$(findstring nothreads,$(MAKECMD
>+ endif
>+ 
>+ #detect MinGW (Windows environment)
>+-ifneq (,$(findstring mingw,$(shell ${CC} -dumpmachine)))
>++ifneq (,$(findstring mingw,$(shell ${CXX} -dumpmachine)))
>+  WINDOWS=1
>+ endif
>+ 
>+ # MinGW32 GCC 4.5 link problem fix
>+ #ifdef WINDOWS
>+-ifneq (,$(findstring 4.5.,$(shell g++ -dumpversion)))
>++ifneq (,$(findstring 4.5.,$(shell ${CXX} -dumpversion)))
>+  STATIC_CLIB=1
>+ endif
>+ #endif
>+@@ -63,7 +63,7 @@ endif
>+ ifneq (,$(filter %release %static, $(MAKECMDGOALS)))
>+   # -- release build
>+   RELEASE_BUILD=1
>+-  CFLAGS := -DNDEBUG -g $(BASEFLAGS) $(CFLAGS) -O3
>++  CFLAGS := -DNDEBUG -g $(BASEFLAGS) $(CFLAGS)
>+ else
>+   ifneq (,$(filter %memcheck %memdebug, $(MAKECMDGOALS)))
>+      #use sanitizer in gcc 4.9+
>+@@ -122,7 +122,7 @@ endif
>+ 
>+ 
>+ %.o : %.cpp
>+-	${CC} ${CFLAGS} -c $< -o $@
>++	${CXX} ${CFLAGS} -c $< -o $@
>+ 
>+ OBJS += rlink.o tablemaker.o tmerge.o
>+ 
>+@@ -137,7 +137,7 @@ rlink.o : rlink.h tablemaker.h $(GDIR)/G
>+ tmerge.o : rlink.h tmerge.h
>+ tablemaker.o : tablemaker.h rlink.h
>+ ${BAM}/libbam.a: 
>+-	cd ${BAM} && make lib
>++	cd ${BAM} && ${MAKE} lib
>+ stringtie: ${BAM}/libbam.a $(OBJS) stringtie.o
>+ 	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
>+ 	@echo
>+@@ -151,6 +151,6 @@ clean:
>+ 	${RM} stringtie${EXE} stringtie.o*  $(OBJS)
>+ 	${RM} core.*
>+ allclean cleanAll cleanall:
>+-	cd ${BAM} && make clean
>++	cd ${BAM} && ${MAKE} clean
>+ 	${RM} stringtie${EXE} stringtie.o* $(OBJS)
>+ 	${RM} core.*
>
>Property changes on: files/patch-Makefile
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
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>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: files/patch-gclib_GIntHash.hh
>===================================================================
>--- files/patch-gclib_GIntHash.hh	(nonexistent)
>+++ files/patch-gclib_GIntHash.hh	(working copy)
>@@ -0,0 +1,20 @@
>+--- gclib/GIntHash.hh.orig	2018-03-06 16:29:49 UTC
>++++ gclib/GIntHash.hh
>+@@ -122,7 +122,7 @@ public:
>+   uint32 NextKey() {
>+      Cell* cell=ghash.NextCell();
>+      if (cell) return cell->key;
>+-       else return NULL;
>++       else return 0;
>+   }
>+   OBJ* NextValue() {
>+      Cell* cell=ghash.NextCell();
>+@@ -201,7 +201,7 @@ public:
>+   uint32 NextKey() {
>+      Cell* cell=ghash.NextCell();
>+      if (cell) return cell->key;
>+-       else return NULL;
>++       else return 0;
>+   }
>+   OBJ* NextValue() {
>+      Cell* cell=ghash.NextCell();
>
>Property changes on: files/patch-gclib_GIntHash.hh
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: files/patch-samtools-0.1.18_Makefile
>===================================================================
>--- files/patch-samtools-0.1.18_Makefile	(nonexistent)
>+++ files/patch-samtools-0.1.18_Makefile	(working copy)
>@@ -0,0 +1,10 @@
>+--- samtools-0.1.18/Makefile.orig	2018-03-06 16:29:49 UTC
>++++ samtools-0.1.18/Makefile
>+@@ -1,5 +1,5 @@
>+-CC=			gcc
>+-CFLAGS=		-g -Wall -fsigned-char -O2 #-m64 #-arch ppc
>++CC?=			gcc
>++CFLAGS?=		-g -Wall -fsigned-char -O2 #-m64 #-arch ppc
>+ DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 #-D_USE_KNETFILE 
>+ KNETFILE_O=	knetfile.o
>+ LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
>
>Property changes on: files/patch-samtools-0.1.18_Makefile
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: files/patch-samtools-0.1.18_bam__aux.c
>===================================================================
>--- files/patch-samtools-0.1.18_bam__aux.c	(nonexistent)
>+++ files/patch-samtools-0.1.18_bam__aux.c	(working copy)
>@@ -0,0 +1,20 @@
>+--- samtools-0.1.18/bam_aux.c.orig	2018-03-06 16:29:49 UTC
>++++ samtools-0.1.18/bam_aux.c
>+@@ -25,7 +25,7 @@ uint8_t *bam_aux_get_core(bam1_t *b, con
>+ 	return bam_aux_get(b, tag);
>+ }
>+ 
>+-inline int aux_type2size(uint8_t type)
>++int aux_type2size(uint8_t type)
>+ {
>+     switch (type) {
>+     case 'A': case 'c': case 'C':
>+@@ -43,7 +43,7 @@ inline int aux_type2size(uint8_t type)
>+     }
>+ }
>+ 
>+-inline uint8_t* skip_aux(uint8_t* s) {
>++uint8_t* skip_aux(uint8_t* s) {
>+ 	int size = aux_type2size(*s); ++s; // skip type
>+ 	uint32_t n;
>+ 	switch (size) {
>
>Property changes on: files/patch-samtools-0.1.18_bam__aux.c
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: pkg-descr
>===================================================================
>--- pkg-descr	(nonexistent)
>+++ pkg-descr	(working copy)
>@@ -0,0 +1,11 @@
>+StringTie is a fast and highly efficient assembler of RNA-seq alignments into
>+potential transcripts. The input can be the alignments of raw reads as usual;
>+it also accepts longer assembled sequences. The output can be processed by
>+downstream software including Ballgown, Cuffdiff, etc.
>+
>+Citation:
>+Pertea et al. (2015) StringTie enables improved reconstruction of a
>+transcriptome from RNA-seq reads.
>+Nature Biotechnology 33: 290-295 doi:10.1038/nbt.3122
>+
>+WWW: http://www.ccb.jhu.edu/software/stringtie/
>
>Property changes on: pkg-descr
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property

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Attachments on bug 229480: 194846