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sci-biology/consed: treeclean 

Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
This commit is contained in:
Jakov Smolić 2023-01-27 12:03:02 +01:00
parent 52964cfbf1
commit 76b3d8cb77
No known key found for this signature in database
GPG Key ID: 82295E1EFAE3208F
8 changed files with 0 additions and 1694 deletions
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6
profiles/package.mask
View File

@ -703,12 +703,6 @@ app-eselect/eselect-sh
# https://github.com/kdave/btrfs-progs/issues/562
=sys-fs/btrfs-progs-6.1
# David Seifert <soap@gentoo.org> (2022-12-26)
# Lots of K&R C, hidden behind an annoying authwall, fails with modern
# GCC and Clang (-fcommon), license prohibits distributing, EAPI 6,
# last release 8 years ago. Removal on 2023-01-25.
sci-biology/consed
# Ionen Wolkens <ionen@gentoo.org> (2022-12-24)
# Upstream dropped wxGTK support in >=games-emulation/pcsx2-1.7.3773,
# and it now always requires Qt6. Masked given Qt6 is also masked in

2
sci-biology/consed/Manifest
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@ -1,2 +0,0 @@
DIST consed-29-linux.tar.gz 36172715 BLAKE2B 6706576b404c0bccb7ed28ab6fe2dec86fdac6f7651406d3f30e35caac3e49a66b4762edace2133d2dfb776bbeb730b74797c7323deb950f2648a46c4594fe98 SHA512 63a95d84cb58009045a9d898c8b1a94f98516bed9189f624a5930338cc8f51562504257f309d945fafcc07e0811ffeea122b640789f75fbd6c94535178dab4dd
DIST consed-29-sources.tar.gz 3258845 BLAKE2B 508763ff2a240047cff0a43ba4b9b9a7f9302c0a023478c6b08f86bb77fb2c12a62a9b16165fe6257fe6c86af853dabe279bd9e05632c3e112e3fb7fad2c6bd3 SHA512 fd711a65a02ef1238cca12b90fe7fa9b67da6c37d43cd105f38c7b6475fbc073c1f4d7f99703dec9d3a0a7a2a9317cb14999a114bb6f52589cb9b6e34700eb93

110
sci-biology/consed/consed-29.ebuild
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@ -1,110 +0,0 @@
# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
inherit flag-o-matic toolchain-funcs
DESCRIPTION="A genome sequence finishing program"
HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
SRC_URI="
${P}-sources.tar.gz
${P}-linux.tar.gz"
LICENSE="phrap"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="examples"
COMMON_DEPEND="
x11-libs/libX11
x11-libs/motif:0
sci-biology/samtools:0.1-legacy
"
DEPEND="
${COMMON_DEPEND}
virtual/pkgconfig
"
RDEPEND="
${COMMON_DEPEND}
dev-lang/perl
>=sci-biology/phred-071220-r1
>=sci-biology/phrap-1.080812-r2
"
S="${WORKDIR}"
RESTRICT="fetch"
PATCHES=(
"${FILESDIR}/${PN}-29-fix-build-system.patch"
"${FILESDIR}/${PN}-29-fix-c++14.patch"
"${FILESDIR}/${PN}-29-fix-qa.patch"
"${FILESDIR}/${PN}-29-fix-perl-shebang.patch"
)
pkg_nofetch() {
einfo "Please visit ${HOMEPAGE} and obtain the file"
einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\""
einfo "and place it into your DISTDIR directory,"
einfo "obtain the file"
einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\""
einfo "and place it into your DISTDIR directory."
}
src_prepare() {
default
sed \
-e "s!\$szPhredParameterFile = .*!\$szPhredParameterFile = \$ENV{'PHRED_PARAMETER_FILE'} || \'"${EPREFIX}"/usr/share/phred/phredpar.dat\';!" \
-e "s:/usr/local/genome:${EPREFIX}/usr:" \
-e "s:niceExe = \"/bin/nice\":niceExe = \"${EPREFIX}/usr/bin/nice\":" \
-e "s:/wt1/gordon/genome:${EPREFIX}/usr/bin:" \
-i scripts/* contributions/* || die
}
src_configure() {
append-cflags -std=gnu99
append-lfs-flags
}
src_compile() {
emake \
CC="$(tc-getCC)" \
CXX="$(tc-getCXX)" \
CFLAGS="${CFLAGS}" \
CXXFLAGS="${CXXFLAGS}" \
CPPFLAGS="${CPPFLAGS}" \
LDFLAGS="${LDFLAGS}" \
SAMTOOLS_CPPFLAGS="-I${EPREFIX}/usr/include/bam-0.1-legacy" \
LIBS="-L${EPREFIX}/usr/$(get_libdir)" \
X11_LIBS="$($(tc-getPKG_CONFIG) --libs x11)" \
SAMTOOLS_LIBS="-lbam-0.1-legacy"
}
src_install() {
dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} scripts/* contributions/*
insinto /usr/lib/screenLibs
doins misc/*.{fa*,seq}
if use examples; then
insinto /usr/share/${PN}/examples
doins -r \
standard polyphred autofinish assembly_view 454_newbler \
align454reads align454reads_answer solexa_example \
solexa_example_answer selectRegions selectRegionsAnswer
fi
cat > 99consed <<-_EOF_ || die
CONSED_HOME=${EPREFIX}/usr
CONSED_PARAMETERS=${EPREFIX}/etc/consedrc
_EOF_
doenvd 99consed
dodoc README.txt *_announcement.txt
}
pkg_postinst() {
einfo "Package documentation is available at"
einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
}

197
sci-biology/consed/files/consed-29-fix-build-system.patch
View File

@ -1,197 +0,0 @@
Make build system semi-sane:
* Respect CC, CXX, CFLAGS, CXXFLAGS, CPPFLAGS, LDFLAGS and LIBS
* Remove default optimisation flags
* Remove -fpermissive from DEFS (as source builds fine now)
* Add large file support (LFS) via CPPFLAGS and not in Makefile
--- a/makefile
+++ b/makefile
@@ -47,23 +47,20 @@
#
# compilation
#
-CXX= g++
-KRCC= gcc
-CC=gcc
+CXX ?= g++
+CC ?= gcc
#
#
-CFLGS= -w -DINLINE_RWTPTRORDEREDVECTOR -DINLINE_RWTVALORDEREDVECTOR -DINLINE_MBTVALVECTOR -DLINUX_COMPILE -DSOCKLEN_T_DEFINED -D__BOOL_DEFINED -DANSI_C -DOFSTREAM_OPEN_WITHOUT_PERMISSIONS -fpermissive -DNO_POUND_POUND_MACROS -DUSE_USING_IN_PUBLIC_TEMPLATE_CLASSES -DINT_CHAR_OPERATOR -D_FILE_OFFSET_BITS=64 -DSAMTOOLS_AVAILABLE
+DEFS = -DINLINE_RWTPTRORDEREDVECTOR -DINLINE_RWTVALORDEREDVECTOR -DINLINE_MBTVALVECTOR -DLINUX_COMPILE -DSOCKLEN_T_DEFINED -D__BOOL_DEFINED -DANSI_C -DOFSTREAM_OPEN_WITHOUT_PERMISSIONS -DNO_POUND_POUND_MACROS -DUSE_USING_IN_PUBLIC_TEMPLATE_CLASSES -DINT_CHAR_OPERATOR -DSAMTOOLS_AVAILABLE
-OPT= -O
#
# Include directory for template classes must be included
# in both compilation & link lines, even if .h file is
# found in default path. C front, gotta love it.
#
-INC= -I/usr/X11R6/include -I/me1/gordon/samtools/samtools-0.1.18
+INCLUDES = $(SAMTOOLS_CPPFLAGS)
-DEPENDENCIES=
#
#
# Linking
@@ -80,12 +77,9 @@
# /lib/ld-linux.so.2 (0x003ee000)
#
# To fix cut/paste bug, I've made X11 always dynamic.
-CLIBS= -lX11
-LPATH= -L/usr/X11R6/lib
-ARCHIVES= /usr/X11R6/lib/libXm.a \
-/usr/X11R6/lib/libXt.a /usr/X11R6/lib/libSM.a \
-/usr/X11R6/lib/libICE.a /usr/X11R6/lib/libXext.a /usr/X11R6/lib/libXmu.a \
-/usr/X11R6/lib/libXp.a /usr/lib/libm.a /me1/gordon/samtools/samtools-0.1.18/libbam.a /me1/gordon/samtools/samtools-0.1.18/bcftools/libbcf.a /me1/gordon/zlib/zlib-1.2.5/libz.a
+
+MOTIF_LIBS ?= -lXm -lXt
+ALL_LIBS = $(LIBS) $(MOTIF_LIBS) $(X11_LIBS) $(SAMTOOLS_LIBS)
@@ -94,7 +88,6 @@
#
#LDFLGS= -g
# static linking
-LDFLGS= -g -rdynamic
#
# the subdirectory used by cfront compilers gets cleaned
@@ -112,10 +105,10 @@
# general compilation rules for .cpp, .cxx, .c files
#
.cpp.o:
- $(CXX) $(CFLGS) $(OPT) $(INC) -c $<
+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c $<
.c.o:
- $(CXX) $(CFLGS) $(OPT) $(INC) -c $<
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c $<
#
# targets file included in generated makefile
@@ -593,17 +586,23 @@
writeToRewriteReferenceFile.o \
xsynchronize.o
+SUBDIRS := misc/454 misc/mktrace misc/phd2fasta
+
+all: consed $(SUBDIRS)
+
+$(SUBDIRS):
+ $(MAKE) -C $@
+
+.PHONY: all $(SUBDIRS)
+
consed: $(CONSED_OBJS) makefile checkLicenseKeyStub.o
- $(CXX) $(INC) $(LDFLGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o \
- $(ARCHIVES) $(LPATH) $(WARNINGS) $(CLIBS) $(XLIBS)
+ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o $(ALL_LIBS)
trial_consed: $(CONSED_OBJS) makefile checkLicenseKey.o
- $(CXX) $(INC) $(LDFLGS) -o trial_consed $(CONSED_OBJS) checkLicenseKey.o \
- $(ARCHIVES) $(LPATH) $(WARNINGS) $(CLIBS) $(XLIBS)
+ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o trial_consed $(CONSED_OBJS) checkLicenseKey.o $(ALL_LIBS)
pure: $(CONSED_OBJS) makefile checkLicenseKeyStub.o
- $(PURIFY) $(CXX) $(INC) $(LDFLGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o \
- $(ARCHIVES) $(LPATH) $(WARNINGS) $(CLIBS) $(XLIBS)
+ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o $(ALL_LIBS)
clean:
rm -rf *.o core $(TEMPLATE_DIR)
@@ -613,15 +612,15 @@
# the Solaris 5.x compiler cannot optimize the following
consedResources.o:
- $(CXX) $(WARNINGS) $(CFLGS) $(INC) $(DEPENDENCIES) -c consedResources.cpp
+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c consedResources.cpp
consedResources2.o:
- $(CXX) $(WARNINGS) $(CFLGS) $(INC) $(DEPENDENCIES) -c consedResources2.cpp
+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c consedResources2.cpp
# tlingit cannot optimize the following:
guiEditResources.o:
- $(CXX) $(WARNINGS) $(CFLGS) $(INC) $(DEPENDENCIES) -c guiEditResources.cpp
+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c guiEditResources.cpp
guiEditResources.o : \
assemblyViewTagTypeAndLine.h assert.h bIsNumericDouble.h \
--- a/misc/454/Makefile
+++ b/misc/454/Makefile
@@ -0,0 +1,16 @@
+CC ?= cc
+LIBM = -lm
+
+DEFS = -DANSI_C
+
+OBJS= sff2scf.c
+
+sff2scf: $(OBJS)
+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(LIBM)
+
+.c.o:
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) -c $<
+
+clean:
+ rm -f $(OBJS) sff2scf
+
--- a/misc/mktrace/Makefile
+++ b/misc/mktrace/Makefile
@@ -1,13 +1,17 @@
-CC= cc
-CFLAGS= -g
-CLIB= -lm
+CC ?= cc
+LIBM = -lm
+
+DEFS = -DANSI_C
OBJS= mktrace.o readFASTA.o writeSCF.o synTrace.o \
freeTrace.o rwUtil.o writePhd.o getTime.o \
readQUAL.o
mktrace: $(OBJS)
- $(CC) $(CFLAGS) -o mktrace $(OBJS) $(CLIB)
+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(LIBM)
+
+.c.o:
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) -c $<
clean:
rm -f $(OBJS) mktrace
--- a/misc/phd2fasta/Makefile
+++ b/misc/phd2fasta/Makefile
@@ -1,8 +1,9 @@
-CC=cc
-CFLAGS=-O -w
-CLIB=-lm
+CC ?= cc
+LIBM = -lm
-OBJ= phd2fasta.o \
+DEFS = -DANSI_C
+
+OBJS= phd2fasta.o \
readParam.o initParam.o checkParam.o \
freeParam.o helpParam.o \
readFOF.o readDIR.o readFOX.o \
@@ -15,10 +16,11 @@
INC= phd2fasta.h
-SRC = $(OBJ:.o=.c)
-
-phd2fasta: $(OBJ)
- $(CC) $(CFLAGS) -o phd2fasta $(OBJ) $(CLIB)
+phd2fasta: $(OBJS)
+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(LIBM)
+
+.c.o:
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) -c $<
clean:
rm -f $(OBJ) phd2fasta

376
sci-biology/consed/files/consed-29-fix-c++14.patch
View File

@ -1,376 +0,0 @@
Fix building with C++14:
* Add 'noexcept(false)' to throwing destructors in C++11 mode
* Properly guard C declarations with extern "C" scopes
* Avoid erroneous overloaded suffix operator errors, due to missing spaces
* Add explicit casts to avoid -Wnarrowing errors
* Add 'this->' for dependent identifiers in derived class templates,
previously required -fpermissive
--- a/bvAlignedReads.cpp
+++ b/bvAlignedReads.cpp
@@ -126,7 +126,11 @@
}
-bvAlignedReads :: ~bvAlignedReads() {
+bvAlignedReads :: ~bvAlignedReads()
+#if __cplusplus >= 201103L
+ noexcept(false)
+#endif
+{
assert( pBamView_->aBVAlignedReads_.remove( this ) );
--- a/bvAlignedReads.h
+++ b/bvAlignedReads.h
@@ -81,7 +81,11 @@
const FileName& filReferenceSequenceFile,
bamView* pBamView );
- ~bvAlignedReads();
+ ~bvAlignedReads()
+#if __cplusplus >= 201103L
+ noexcept(false)
+#endif
+ ;
bool operator==( const bvAlignedReads& myBVAlignedReads ) const {
return( this == &myBVAlignedReads );
--- a/chromatData.h
+++ b/chromatData.h
@@ -58,6 +58,9 @@
#ifndef CHROMATDATA_DEFINED
#define CHROMATDATA_DEFINED
+#ifdef __cplusplus
+extern "C" {
+#endif
#ifndef FLOAT
#define FLOAT double
@@ -131,4 +134,8 @@
int freeChromatData();
#endif
+#ifdef __cplusplus
+}
+#endif
+
#endif
--- a/compareContigs.cpp
+++ b/compareContigs.cpp
@@ -126,6 +126,9 @@
compareContigs :: ~compareContigs()
+#if __cplusplus >= 201103L
+ noexcept(false)
+#endif
{
if ( !bCalledFromMakeJoins_ ) {
--- a/compareContigs.h
+++ b/compareContigs.h
@@ -137,7 +137,11 @@
compareContigs( ContigWin* pContigWin, const int nConsPos1);
compareContigs(); // for assemblyView
- ~compareContigs();
+ ~compareContigs()
+#if __cplusplus >= 201103L
+ noexcept(false)
+#endif
+ ;
// this makes RWTPtrOrderedVector in ConsEd happy
bool operator==( const compareContigs& compC ) const {
--- a/filePopupAndGetAceFilename.cpp
+++ b/filePopupAndGetAceFilename.cpp
@@ -317,7 +317,7 @@
struct tm* pTM = localtime( &( pAceFile->stat_.st_mtime ) );
strftime( szDateTime, nDateTimeSize,
- quote(%H)":"quote(%M)":"quote(%S)" %e-%h-%Y",
+ quote(%H) ":" quote(%M) ":" quote(%S) " %e-%h-%Y",
pTM );
RWCString soDescription = RWCString( szDateTime ) + " " + (*pAceFile);
@@ -620,7 +620,7 @@
struct tm* pTM = localtime( &( pAceFile->stat_.st_mtime ) );
strftime( szDateTime, nDateTimeSize,
- quote(%H)":"quote(%M)":"quote(%S)" %e-%h-%Y",
+ quote(%H) ":" quote(%M) ":" quote(%S) " %e-%h-%Y",
pTM );
RWCString soDescription = RWCString( szDateTime ) + " " + (*pAceFile);
--- a/findTraceExtrema.h
+++ b/findTraceExtrema.h
@@ -44,8 +44,15 @@
#include "chromatData.h"
+#ifdef __cplusplus
+extern "C" {
+#endif
+
int findTraceExtrema( ChromatData *chromatData );
+#ifdef __cplusplus
+}
+#endif
#endif
--- a/makeUpper.h
+++ b/makeUpper.h
@@ -42,6 +42,14 @@
#ifndef MAKEUPPER_INCLUDED
#define MAKEUPPER_INCLUDED
+#ifdef __cplusplus
+extern "C" {
+#endif
+
void makeUpper( char* szStringOfMixedCase );
+#ifdef __cplusplus
+}
+#endif
+
#endif
--- a/nextPhredPipeline.cpp
+++ b/nextPhredPipeline.cpp
@@ -476,7 +476,7 @@
void nextPhredPipeline :: openAndLockControlFile() {
- nFDControlFile_ = open( filControlFile_.data(), O_CREAT |O_RDWR );
+ nFDControlFile_ = open( filControlFile_.data(), O_CREAT |O_RDWR, 0600);
if ( nFDControlFile_ == -1 ) {
THROW_FILE_ERROR( filControlFile_ );
}
--- a/readABI.h
+++ b/readABI.h
@@ -56,10 +56,18 @@
#include "chromatData.h"
+#ifdef __cplusplus
+extern "C" {
+#endif
+
#ifdef ANSI_C
ChromatData *readABI( char *fn, int *status );
#else
ChromatData *readABI();
#endif
+#ifdef __cplusplus
+}
+#endif
+
#endif
--- a/readData.h
+++ b/readData.h
@@ -44,6 +44,14 @@
#include "chromatData.h"
+#ifdef __cplusplus
+extern "C" {
+#endif
+
ChromatData *readData( char *filename, int* status );
+#ifdef __cplusplus
+}
+#endif
+
#endif
--- a/readESD.h
+++ b/readESD.h
@@ -53,6 +53,10 @@
#include "chromatData.h"
+#ifdef __cplusplus
+extern "C" {
+#endif
+
typedef unsigned int4 DWORD;
typedef unsigned char TCHAR;
typedef char BYTE;
@@ -187,5 +191,7 @@
ChromatData *readESD();
#endif
-
+#ifdef __cplusplus
+}
+#endif
--- a/readSCF.h
+++ b/readSCF.h
@@ -56,6 +56,10 @@
#include "chromatData.h"
+#ifdef __cplusplus
+extern "C" {
+#endif
+
/* ---- Constants ---- */
#define SCF_MAGIC (((((int4)'.'<<8)+(int4)'s'<<8)+(int4)'c'<<8)+(int4)'f')
#define scale(V,OLDMAX,NEWMAX) (int2)( (FLOAT) V * (FLOAT) NEWMAX / (FLOAT) OLDMAX )
@@ -144,4 +148,8 @@
int readSCF3();
#endif
+#ifdef __cplusplus
+}
+#endif
+
#endif
--- a/readsense_bitmaps.h
+++ b/readsense_bitmaps.h
@@ -56,10 +56,10 @@
static const int forward_bitmap_height = 19;
static char forward_bitmap_bits[] = {
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
- 0x00, 0x00, 0x00, 0x00, 0x38, 0x00, 0x00, 0x00, 0xf8, 0x07, 0x00, 0x00,
- 0xf8, 0xff, 0x00, 0x00, 0xf8, 0xff, 0x3f, 0x00, 0xf8, 0xff, 0xff, 0x07,
- 0xf8, 0xff, 0xff, 0x0f, 0xf8, 0xff, 0xff, 0x07, 0xf8, 0xff, 0x1f, 0x00,
- 0xf8, 0xff, 0x00, 0x00, 0xf8, 0x07, 0x00, 0x00, 0x38, 0x00, 0x00, 0x00,
+ 0x00, 0x00, 0x00, 0x00, 0x38, 0x00, 0x00, 0x00, (char)0xf8, 0x07, 0x00, 0x00,
+ (char)0xf8, (char)0xff, 0x00, 0x00, (char)0xf8, (char)0xff, 0x3f, 0x00, (char)0xf8, (char)0xff, (char)0xff, 0x07,
+ (char)0xf8, (char)0xff, (char)0xff, 0x0f, (char)0xf8, (char)0xff, (char)0xff, 0x07, (char)0xf8, (char)0xff, 0x1f, 0x00,
+ (char)0xf8, (char)0xff, 0x00, 0x00, (char)0xf8, 0x07, 0x00, 0x00, 0x38, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00};
@@ -67,10 +67,10 @@
static const int reverse_bitmap_height = 19;
static char reverse_bitmap_bits[] = {
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
- 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x07, 0x00, 0x00, 0xf8, 0x07,
- 0x00, 0xc0, 0xff, 0x07, 0x00, 0xff, 0xff, 0x07, 0xf8, 0xff, 0xff, 0x07,
- 0xfc, 0xff, 0xff, 0x07, 0xf8, 0xff, 0xff, 0x07, 0x00, 0xfe, 0xff, 0x07,
- 0x00, 0xc0, 0xff, 0x07, 0x00, 0x00, 0xf8, 0x07, 0x00, 0x00, 0x00, 0x07,
+ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x07, 0x00, 0x00, (char)0xf8, 0x07,
+ 0x00, (char)0xc0, (char)0xff, 0x07, 0x00, (char)0xff, (char)0xff, 0x07, (char)0xf8, (char)0xff, (char)0xff, 0x07,
+ (char)0xfc, (char)0xff, (char)0xff, 0x07, (char)0xf8, (char)0xff, (char)0xff, 0x07, 0x00, (char)0xfe, (char)0xff, 0x07,
+ 0x00, (char)0xc0, (char)0xff, 0x07, 0x00, 0x00, (char)0xf8, 0x07, 0x00, 0x00, 0x00, 0x07,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00};
--- a/readType.h
+++ b/readType.h
@@ -56,11 +56,19 @@
#include "chromatData.h"
+#ifdef __cplusplus
+extern "C" {
+#endif
+
#ifdef ANSI_C
int readType( char *filename );
#else
int readType();
#endif
+#ifdef __cplusplus
+}
+#endif
+
#endif
--- a/rwtptrsortedvector.h
+++ b/rwtptrsortedvector.h
@@ -57,7 +57,6 @@
#ifdef USE_USING_IN_PUBLIC_TEMPLATE_CLASSES
using RWTPtrOrderedVector<TP>::nCurrentLength_;
using RWTPtrOrderedVector<TP>::isEmpty;
- using RWTPtrOrderedVector<TP>::nCurrentLength_;
using RWTPtrOrderedVector<TP>::length;
using RWTPtrOrderedVector<TP>::ppArray_;
using RWTPtrOrderedVector<TP>::data;
@@ -84,7 +83,7 @@
if ( nInsertBeforeIndex == RW_NPOS )
nInsertBeforeIndex = nCurrentLength_;
- insertAt( nInsertBeforeIndex, pVal );
+ this->insertAt( nInsertBeforeIndex, pVal );
}
// don't copy this. copy mbtValOrderedVectorOfRWCString's method instead
--- a/rwtvalsortedvector.h
+++ b/rwtvalsortedvector.h
@@ -74,7 +74,7 @@
if ( nPos == RW_NPOS )
nPos = nCurrentLength_;
- insertAt( nPos, val );
+ this->insertAt( nPos, val );
}
--- a/rwUtil.h
+++ b/rwUtil.h
@@ -51,6 +51,10 @@
*|***************************************************************************|*
*/
+#ifdef __cplusplus
+extern "C" {
+#endif
+
#ifdef ANSI_C
int2 inSwpSint2( char *ptr );
int4 inSwpSint4( char *ptr );
@@ -97,3 +101,6 @@
int writeUint4();
#endif
+#ifdef __cplusplus
+}
+#endif
--- a/soGetDateTime.cpp
+++ b/soGetDateTime.cpp
@@ -62,13 +62,13 @@
else if ( nFormat == nDotInMiddle ) {
strftime( szDateTime,
nDateTimeSize,
- "%y%m%d."quote(%H)quote(%M)quote(%S),
+ "%y%m%d." quote(%H)quote(%M)quote(%S),
localtime( &timee ) );
}
else {
strftime( szDateTime,
nDateTimeSize,
- "%y%m%d:"quote(%H)quote(%M)quote(%S),
+ "%y%m%d:" quote(%H)quote(%M)quote(%S),
localtime( &timee ) );
}
--- a/szGetTime.h
+++ b/szGetTime.h
@@ -42,9 +42,15 @@
#ifndef szGetTime_included
#define szGetTime_included
-char *szGetTime();
+#ifdef __cplusplus
+extern "C" {
+#endif
+char *szGetTime();
+#ifdef __cplusplus
+}
+#endif
#endif

701
sci-biology/consed/files/consed-29-fix-perl-shebang.patch
View File

@ -1,701 +0,0 @@
Make perl shebangs portable, such that the scripts can also be used on Gentoo Prefix.
Rationale: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/
--- a/contributions/ace2fof
+++ b/contributions/ace2fof
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
# .-----------------------------------------------------------------------------------.
# | |
@@ -107,6 +107,7 @@
# | |
# `-----------------------------------------------------------------------------------'
#Fixed this file for taking Aracne's Ace file by syang 05152002
+use warnings;
use strict;
use POSIX qw(fmod);
--- a/contributions/ace2OligosWithComments.perl
+++ b/contributions/ace2OligosWithComments.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
#
# ace2Oligos.perl
#
@@ -18,6 +18,8 @@
# Rev: 020528 to print comments in oligo tags upon request (Peter Kos)
#
+use warnings;
+
$szUsage = "\nUsage: $0 (name of ace file) (name of oligo file) [Print|Comment|PrintComment]\n";
die "$szUsage" if (( $#ARGV != 1 ) && ( $#ARGV != 2 ));
--- a/contributions/aceContigs2Phds.perl
+++ b/contributions/aceContigs2Phds.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
#
# aceContigs2Phd.perl
#
@@ -13,6 +13,8 @@
# Acknowledgements: Borrowed as much as I could from determineReadTypes.Perl
# and fasta2Phd.perl
+use warnings;
+
$szUsage = "Usage: aceContigs2Phds.perl [-s minimum-contig-size] <name of ace file>";
$nContigLimit = 2000;
--- a/contributions/acestatus.pl
+++ b/contributions/acestatus.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
# acestatus.pl
# author: Cliff Wollam
@@ -14,6 +14,7 @@
# USAGE FROM THE COMMAND LINE:
# acestatus.pl ace_filename
+use warnings;
use strict;
if($#ARGV >= 0) {
--- a/contributions/cons.perl
+++ b/contributions/cons.perl
@@ -1,5 +1,6 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
+use warnings;
use strict;
use Cwd;
--- a/contributions/mergeAces.perl
+++ b/contributions/mergeAces.perl
@@ -1,4 +1,4 @@
-#! /usr/local/bin/perl -w
+#!/usr/bin/env perl
# Bugs and complaints to Bill Gilliland, billg@ucdavis.edu.
# mergeAces.perl v. 0.2 5/22/01
@@ -9,6 +9,7 @@
# project directory (if it doesn't already exist) with all the cgrams
# and phd files of the original projects.
+use warnings;
use Getopt::Long;
use File::Copy;
$pathRoot = $ENV{"PWD"};
--- a/contributions/phredPhrapWithPhdBalls
+++ b/contributions/phredPhrapWithPhdBalls
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
#
# phredPhrapWithPhdBalls
# modified from phredPhrap by Ben Allen at LANL
@@ -73,6 +73,7 @@
# Rev: 120312 to not duplicate consensus tags during miniassembly
# Rev: 120717 Ben Allen (LANL) to use reads from phdballs as well as phd_dir
+use warnings;
$szVersion = "120312";
--- a/contributions/recover_consensus_tags
+++ b/contributions/recover_consensus_tags
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
# Purpose: Transfers all consensus tags from a set of old assemblies to
# a new assembly.
@@ -14,6 +14,7 @@
# rct ace_filename <only ace file to be transfer (optional)>
# You must be in the edit_dir where the ace file is located
+use warnings;
use strict;
--- a/contributions/revert_fof
+++ b/contributions/revert_fof
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
# PURPOSE: If the user really screws up a read, to back out all changes.
# You must reassemble after using this.
@@ -19,6 +19,8 @@
# phd extensions.
# revert_fof use file of files to give reads to revert 3/14/01 SL
+use warnings;
+
$szUsage = "Enter a file of files name, please!";
die $szUsage if ( $#ARGV != 0 );
--- a/contributions/sff2phd.perl
+++ b/contributions/sff2phd.perl
@@ -1,4 +1,5 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
+use warnings;
use strict;
# SFF to PHD files converter, with 454 paired reads and MID support
# Version 0.15 - 111229
--- a/contributions/sff2phd_Samborskyy
+++ b/contributions/sff2phd_Samborskyy
@@ -1,4 +1,5 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
+use warnings;
use strict;
# SFF to PHD files converter, with 454 paired reads and MID support
# Version 0.10 - 101110
--- a/scripts/ace2Fasta.perl
+++ b/scripts/ace2Fasta.perl
@@ -1,7 +1,9 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
#
# Purpose: makes a contigs file out of an ace file
+use warnings;
+
$szUsage = "Usage: ace2Contigs.perl (ace file)";
--- a/scripts/ace2Oligos.perl
+++ b/scripts/ace2Oligos.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
#
# ace2Oligos.perl
#
@@ -16,6 +16,8 @@
# Rev: 000330 to handle comments in oligo tags
#
+use warnings;
+
$szUsage = "Usage: ace2Oligos.perl (name of ace file) (name of oligo file)";
if ( $ARGV[0] eq "-V" || $ARGV[0] eq "-v" ) {
--- a/scripts/add454Reads.perl
+++ b/scripts/add454Reads.perl
@@ -1,11 +1,11 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
# add454Reads.perl
# part of Consed package
#
# DG with help from Hao Wang to screen vector
-
+use warnings;
use File::Basename;
--- a/scripts/addReads2Consed.perl
+++ b/scripts/addReads2Consed.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
#
# Purpose: called by consed in order to add new reads to an
# existing assembly without reassemblying
@@ -29,6 +29,7 @@
# Rev: 080320 (David Gordon) to use discrep_lists instead of alignments
# Rev: 130828 (David Gordon) to handle slashes (/) in read names
+use warnings;
$szVersion = "130828";
if ( $#ARGV >= 0 ) {
--- a/scripts/addSangerReads.perl
+++ b/scripts/addSangerReads.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
# addSangerReads.perl
@@ -32,7 +32,7 @@
# added is printed in a report ending with ".log". The name of this
# file is listed in auto.fof
-
+use warnings;
$szVersion = "120717";
--- a/scripts/addSolexaReads.perl
+++ b/scripts/addSolexaReads.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
# addSolexaReads.perl
@@ -54,7 +54,7 @@
$szUsage = "addSolexaReads.perl -ace (ace file) -fastqfof (solexa files) -fasta (fasta file) -readsList (file of list of desired reads) where -readsList is optional";
-
+use warnings;
use Getopt::Long;
GetOptions( "ace=s" => \$szAceFile,
--- a/scripts/alignRNA2Genomic.perl
+++ b/scripts/alignRNA2Genomic.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
# alignRNA2Genomic.perl
@@ -6,6 +6,8 @@
# consed-ready ace and phd ball with the RNA aligned against the
# genomic with introns being represented by large gaps
+use warnings;
+
$szVersion = "120717";
if ( $#ARGV == 0 ) {
--- a/scripts/alignSolexaReads2Refs.perl
+++ b/scripts/alignSolexaReads2Refs.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
# Input: a file where each line looks like this:
# (solexa seq file) (read prefix)
@@ -10,6 +10,7 @@
# Output: a list of alignment files
+use warnings;
defined( $szConsedHome = $ENV{'CONSED_HOME'} ) ||
( $szConsedHome = "/usr/local/genome" );
--- a/scripts/amplifyTranscripts.perl
+++ b/scripts/amplifyTranscripts.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
# PURPOSE: runs consed -autoPCRAmplify in order to pick pcr primers
# for a large group of regions
@@ -40,7 +40,7 @@
# That is, the left primers are given in top strand orientation, and
# the right primers are given in bottom strand orientation.
-
+use warnings;
defined( $szConsedHome = $ENV{'CONSED_HOME'} ) ||
( $szConsedHome = "/usr/local/genome" );
--- a/scripts/autoPrimers.perl
+++ b/scripts/autoPrimers.perl
@@ -1,5 +1,6 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
+use warnings;
$szUsage = "autoPrimers.perl (fasta file of targets)";
$szVersion = "141226";
--- a/scripts/bam2Ace.perl
+++ b/scripts/bam2Ace.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
# Purpose: runs:
@@ -6,6 +6,7 @@
# 2) consed -renameDuplicates
# 3) consed -removeColumnsOfPads
+use warnings;
$szUsage = "usage: bam2Ace.perl -bamFile (bam file) -regionsFile (regions file) (see README.txt for format of the regions file) -exec (consed executable name) -newAceFile (new ace file name) where the -exec (exec) is optional";
--- a/scripts/convertBedToBamScape.perl
+++ b/scripts/convertBedToBamScape.perl
@@ -1,4 +1,6 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
+
+use warnings;
$szUsage = "usage: convertBedToBamScape.perl (Bed file) (BamScape file) (fasta file of all sequences) (conversion of reference names--optional)";
--- a/scripts/countEditedBases.perl
+++ b/scripts/countEditedBases.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
#
# countEditedBases.perl
#
@@ -11,6 +11,8 @@
#
#
+use warnings;
+
while(<>) {
if ( /^CO / ) {
@aWords = split;
--- a/scripts/determineReadTypes.perl
+++ b/scripts/determineReadTypes.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
# determineReadTypes.perl
#
# Purpose: to write into the phd file information about the template
@@ -173,6 +173,7 @@
#
###############################################################
+use warnings;
# you can remove or comment out this line when you are satisfied with
# your customized version of this file.
--- a/scripts/fasta2Ace.perl
+++ b/scripts/fasta2Ace.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
#
# manyFasta2Ace.perl
#
@@ -13,6 +13,7 @@
#
# NOTE: you must run this in edit_dir
+use warnings;
use Getopt::Long;
$szRevision = "141212";
--- a/scripts/fasta2PhdBall.perl
+++ b/scripts/fasta2PhdBall.perl
@@ -1,4 +1,6 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
+
+use warnings;
$nQuality = 20;
--- a/scripts/fasta2Phd.perl
+++ b/scripts/fasta2Phd.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
#
# fasta2Phd.perl
#
@@ -20,6 +20,7 @@
# June 2002, Bill Gilliland to allow the user to specify
# the quality value
+use warnings;
use Getopt::Long;
GetOptions( "quality=i" => \$qualityValue);
--- a/scripts/fastq2Phrap.perl
+++ b/scripts/fastq2Phrap.perl
@@ -1,4 +1,6 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
+
+use warnings;
$szUsage = "fastq2Phrap.perl (fastq) or for paired reads fastq2Phrap.perl (fastq1) (fastq2) where fastq1 and fastq2 have corresponding mate pairs--e.g., the 5th read in fastq1 is the mate of the 5th read in fastq2--these fastq files are assumed to be in ../solexa_dir--not the current directory\n";
--- a/scripts/filter454Reads.perl
+++ b/scripts/filter454Reads.perl
@@ -1,6 +1,6 @@
-#!/usr/bin/perl -w
-
+#!/usr/bin/env perl
+use warnings;
use File::Basename;
--- a/scripts/findSequenceMatchesForConsed.perl
+++ b/scripts/findSequenceMatchesForConsed.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
# findSequenceMatchesForConsed.perl
@@ -16,6 +16,8 @@
# REVISIONS: 021127 (DG) to write (project).(date).(time).fasta instead of
# (project).fasta.screen.ace.1.(date).(time).fasta
+use warnings;
+
$szVersion = "021127";
$szUsage = "Usage: findSequenceMatchesForConsed.perl (ace file) (crossmatch parameters, if any)";
--- a/scripts/fixContigEnd.perl
+++ b/scripts/fixContigEnd.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
# fixContigEnd.perl
@@ -7,6 +7,7 @@
# consed -ace (acefile) -fixContigEnds
#
+use warnings;
$szUsage = "fixContigEnd.perl (fasta file of reads for input) (fof for ace file, output)";
--- a/scripts/lib2Phd.perl
+++ b/scripts/lib2Phd.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
#
# lib2Phd.perl
#
@@ -23,6 +23,8 @@
# accept fasta library files as input. The output file is named
# according to the first, non-space block of text on each fasta defline.
+use warnings;
+
$nQuality = 20;
$szUsage = "Usage: lib2Phd.perl <name of file with fasta library>";
--- a/scripts/makePhdBall.perl
+++ b/scripts/makePhdBall.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
# PURPOSE: concatenate all phd file into a single phd.ball
# for the purpose of fast startup of consed
@@ -9,6 +9,7 @@
#
# February 2008, David Gordon
+use warnings;
if ( $#ARGV >= 0 ) {
if ( $ARGV[0] eq "-v" || $ARGV[0] eq "-V" ) {
--- a/scripts/makeRegionsFile.perl
+++ b/scripts/makeRegionsFile.perl
@@ -1,10 +1,12 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
# makeRegionsFile.perl
# To be used with consed -bam2Ace
# Takes a fasta file of sequences and makes a regions file that
# specifies the entire length of each sequence.
+use warnings;
+
$szUsage = "makeRegionsFile.perl (name of fasta file)";
$szVersion = "110914";
--- a/scripts/orderPrimerPairs.perl
+++ b/scripts/orderPrimerPairs.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
# PURPOSE: puts the primers in 96 well format for ordering.
# creates a file that can be emailed to
@@ -13,6 +13,8 @@
# 2) a file of primer pairs, sorted by product size
# 3) a fasta file of the primers, for your convenience for analysis
+use warnings;
+
$| = 1;
$szUsage = "orderPrimerPairs.perl";
--- a/scripts/phd2Ace.perl
+++ b/scripts/phd2Ace.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
#
# phd2Ace.perl
#
@@ -13,6 +13,8 @@
# REV: 981002 (David Gordon) for new ace format
# 981210 (DG) to eliminate warning message
+use warnings;
+
$szPhdDirPath = "../phd_dir";
$szUsage = "Usage: phd2Ace.perl <filename (without directory) of phd file>\nThe phd file is assumed to reside in $szPhdDirPath";
--- a/scripts/phredPhrap
+++ b/scripts/phredPhrap
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
#
# phredPhrap
#
@@ -70,6 +70,8 @@
# Rev: 110609 to allow masking of vector sequence when doing miniassemblies
# Rev: 120312 to not duplicate consensus tags during miniassembly
+use warnings;
+
$szVersion = "120312";
--- a/scripts/picard2Regions.perl
+++ b/scripts/picard2Regions.perl
@@ -1,10 +1,12 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
# PURPOSE: takes a file of locations in the format for bamScape custom
# navigation (Picard IntervalList format), adds 2000 bases of context
# to each side of each location, and prints a region file in format to
# be used by bam2Ace
+use warnings;
+
$szRevision = "140903"; # David Gordon
if ( defined( $ARGV[0] ) &&
--- a/scripts/removeReads
+++ b/scripts/removeReads
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
#
# PURPOSE: removes a list of chromats from an assembly. After running this,
# you must reassemble to create an ace file without the given phd files.
@@ -16,6 +16,8 @@
# removeReads (name of fof's)
#
+use warnings;
+
$szUsage = "Usage: removeReads listOfReads.fof";
die "$szUsage" if ( $#ARGV != 0 );
--- a/scripts/revertToUneditedRead
+++ b/scripts/revertToUneditedRead
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
#
# PURPOSE: If the user really screws up a read, to back out all changes.
# You must reassemble after using this.
@@ -16,6 +16,7 @@
# REV: 7/24/98 (DG)
# REV: 8/28/2013 (DG) to handle readnames with slashes (/)
+use warnings;
$szUsage = "Usage: revertToUneditedRead (read name without any .phd.# extension)";
--- a/scripts/selectOneRegion.perl
+++ b/scripts/selectOneRegion.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
# selectOneRegion.perl
#
@@ -11,6 +11,7 @@
# and you will create an ace file chr15_51000000.ace or chr15_51000000.ace.1
# (or higher extension)
+use warnings;
use Getopt::Long;
--- a/scripts/selectRegions.perl
+++ b/scripts/selectRegions.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
# selectRegions.perl
#
@@ -43,7 +43,7 @@
# my_new_ace.ace says what the ace file should be called (the
# extension may not start at 1 if there is already a .1
-
+use warnings;
$SIG{__WARN__} = dieWhenGetWarning;
sub dieWhenGetWarning {
--- a/scripts/tagRepeats.perl
+++ b/scripts/tagRepeats.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
#
# PROGRAM: tagRepeats.perl
# PURPOSE: to put consensus tags on any found ALU or any other
@@ -10,6 +10,7 @@
# INPUTS: The ace file. You must also provide a fasta file of the
# ALU or any other sequence you want to tag
+use warnings;
$szVersion = "090209";
if ( $#ARGV >= 0 ) {
--- a/scripts/testSocket.perl
+++ b/scripts/testSocket.perl
@@ -1,7 +1,8 @@
-#! /usr/local/bin/perl -w
+#!/usr/bin/env perl
# open a socket to consed
-
+
+use warnings;
use IO::Socket;
# Consed makes a file which has nothing but the port number.
--- a/scripts/transferConsensusTags.perl
+++ b/scripts/transferConsensusTags.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
#
# Purpose: Transfers consensus tags from an old assembly to
# a new assembly.
@@ -44,6 +44,8 @@
# Nov 2001, DG to handle cloneEnd tags which have orientation
# Mar 2012, DG to prevent duplicating tags after miniassembly
+use warnings;
+
$szUsage = "Usage: transferConsensusTags.perl (old ace file) (new ace file) (file of list of old contigs with consensus tags to be transferred)";
if ( $ARGV[0] eq "-V" || $ARGV[0] eq "-v" ) {

294
sci-biology/consed/files/consed-29-fix-qa.patch
View File

@ -1,294 +0,0 @@
Fix various QA violations, due to
* implicit declarations
* incorrect printf() format specifiers
* incorrect function prototypes
* remove unsafe gets() fucntion
--- a/misc/454/sff2scf.c
+++ b/misc/454/sff2scf.c
@@ -39,6 +39,7 @@
void writeScfFile(char *filearg, char *outfile);
void writeScfCommand(char *filearg, char *outfile);
+int sffinfo(int argc, char *argv[], FILE* pTempFile );
int main(int argc, char *argv[])
{
--- a/misc/mktrace/mktrace.c
+++ b/misc/mktrace/mktrace.c
@@ -70,9 +70,9 @@
else
{
printf( "enter FASTA filename: " );
- gets( ifnm );
+ fgets( ifnm, sizeof(ifnm), stdin );
printf( "enter output filename: " );
- gets( ofnm );
+ fgets( ofnm, sizeof(ofnm), stdin );
}
/*
@@ -192,7 +192,7 @@
/*
** Write phd file.
*/
- if( writePhd( ofnm, numBase, seq, qual, pos, numPoint, trace ) == ERROR )
+ if( writePhd( ofnm, numBase, seq, qual, pos, numPoint ) == ERROR )
{
fprintf( stderr, "mktrace: error: bad status: writePhd\n" );
free( seq );
--- a/misc/mktrace/mktrace.h
+++ b/misc/mktrace/mktrace.h
@@ -37,8 +37,8 @@
int writeSCF( char *filename, int numBase, char *seq, int numPoint, float **trace );
int freeTrace( float **trace );
char *readFASTA( char *filename, char *entryName, char *comments, int *len );
-int writePhd( char *ofnm, int numBase, char *seq, int *pos, int numPoint );
int *readQUAL( char *filename, char *entryName, char *comments, int *len );
+char *getTime( void );
#else
int writePhd();
float **synTrace();
--- a/misc/phd2fasta/phd2fasta.h
+++ b/misc/phd2fasta/phd2fasta.h
@@ -276,6 +276,10 @@
Comments *comments, Seq *seq, TagList *tagList, char *emsg );
int checkIntString( char *string );
int delimiterTest( char *string, unsigned int mask );
+int checkParam( Option *option );
+char* getVersion( void );
+int showDoc( void );
+char* getTime( void );
#else
Option *getOption();
struct Tag *allocTag();
--- a/misc/phd2fasta/readStdTag.c
+++ b/misc/phd2fasta/readStdTag.c
@@ -699,11 +699,11 @@
if( fstat )
{
fprintf( stderr,
- "readStdTag: %s: line: %d: unexpected delimiter %s\n",
+ "readStdTag: %s: line: %p: unexpected delimiter %s\n",
filename,
nline,
line );
- sprintf( emsg, "%s: line: %d: unexpected delimiter %s\n",
+ sprintf( emsg, "%s: line: %p: unexpected delimiter %s\n",
filename,
nline,
line );
--- a/misc/phd2fasta/readWholeReadTag.c
+++ b/misc/phd2fasta/readWholeReadTag.c
@@ -393,11 +393,11 @@
if( fstat )
{
fprintf( stderr,
- "readWholeReadTag: %s: line: %d: unexpected delimiter %s\n",
+ "readWholeReadTag: %s: line: %p: unexpected delimiter %s\n",
filename,
nline,
line );
- sprintf( emsg, "%s: line: %d: unexpected delimiter %s\n",
+ sprintf( emsg, "%s: line: %p: unexpected delimiter %s\n",
filename,
nline,
line );
--- a/misc/phd2fasta/writeFasta.c
+++ b/misc/phd2fasta/writeFasta.c
@@ -39,7 +39,7 @@
#include "phd2fasta.h"
#ifdef ANSI_C
-writeFasta( FILE *sfp, FILE *qfp, FILE *bfp,
+int writeFasta( FILE *sfp, FILE *qfp, FILE *bfp,
int outBasePosOption,
Comments *comments, Seq *seq, TagList *tagList, char *emsg )
#else
--- a/motifutils.cpp
+++ b/motifutils.cpp
@@ -202,13 +202,13 @@
void printButtonEvent( XButtonEvent* pEvent ) {
printf( "type = %d\n", pEvent->type );
- printf( "serial = %d\n", pEvent->serial );
+ printf( "serial = %lu\n", pEvent->serial );
printf( "send_event = %s\n", szPrintBool( pEvent->send_event ) );
- printf( "*display = %x\n", pEvent->display );
- printf( "window = %x\n", pEvent->window );
- printf( "root = %x\n", pEvent->root );
- printf( "subwindow = %x\n", pEvent->subwindow );
- printf( "time = %d\n", pEvent->time );
+ printf( "*display = %p\n", pEvent->display );
+ printf( "window = %lu\n", pEvent->window );
+ printf( "root = %lu\n", pEvent->root );
+ printf( "subwindow = %lu\n", pEvent->subwindow );
+ printf( "time = %lu\n", pEvent->time );
printf( "x = %d\n", pEvent->x );
printf( "y = %d\n", pEvent->y );
printf( "x_root = %d\n", pEvent->x_root );
--- a/parseAceFile.cpp
+++ b/parseAceFile.cpp
@@ -45,6 +45,7 @@
using namespace std;
#include "basesegment.h"
#include <stdio.h>
+#include <stddef.h>
#include <string.h>
#include <sstream>
#include "mbt_errors.h"
@@ -292,7 +293,7 @@
char* szPossibleComp = szReadName + nLength - nCOMP;
if (memcmp( szPossibleComp, szCOMP, nCOMP ) == 0 ) {
- szPossibleComp = '\0';
+ szPossibleComp = NULL;
return( true );
}
else
--- a/phaster2PhdBall.cpp
+++ b/phaster2PhdBall.cpp
@@ -547,7 +547,7 @@
int nTokens =
sscanf( soLine_.data(),
- "%s %*s %d %d %lld %s %s %*s %d %d %lld %s %s\n",
+ "%s %*s %d %d %ld %s %s %*s %d %d %ld %s %s\n",
soReadName_.data(),
&nRead1Left_,
&nRead1Right_,
--- a/printAutoFinishMiscInfo.cpp
+++ b/printAutoFinishMiscInfo.cpp
@@ -80,7 +80,7 @@
int nError = stat( (char*) soAceFileFullPathname.data(), &statBuffer );
if (nError == 0 ) {
- fprintf( pAO,"size: %d date: %s\n",
+ fprintf( pAO,"size: %ld date: %s\n",
(long) statBuffer.st_size,
ctime( &( statBuffer.st_mtime )) );
--- a/printAutoFinishParameters.cpp
+++ b/printAutoFinishParameters.cpp
@@ -206,7 +206,7 @@
pCP->nInexactSearchForStringMaxPerCentMismatch_ );
fprintf( pAO, "! when using the inexact search for string, allow up to this\n");
- fprintf( pAO, "! % mismatch: the sum of the insertion, deletion, and substitution\n");
+ fprintf( pAO, "! %% mismatch: the sum of the insertion, deletion, and substitution\n");
fprintf( pAO, "! differences divided by the length of the query string\n");
fprintf( pAO, "! (YES)\n");
fprintf( pAO, "consed.onlyAllowOneReadWriteConsedAtATime: %s\n",
@@ -825,7 +825,7 @@
fprintf( pAO, "! template will be 1500 bases from the forward read. But if this template\n");
fprintf( pAO, "! has an insert that is shorter than average, the walk may walk into vector.\n");
fprintf( pAO, "! To be conservative, we may want to assume that the insert is somewhat \n");
- fprintf( pAO, "! shorter than average. By default, we assume that it is 90% as large as \n");
+ fprintf( pAO, "! shorter than average. By default, we assume that it is 90%% as large as \n");
fprintf( pAO, "! the average. This parameter gives that percentage. This parameter\n");
fprintf( pAO, "! is used both by Consed and Autofinish.\n");
fprintf( pAO, "! (OK)\n");
@@ -1249,9 +1249,9 @@
pCP->nAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_ );
fprintf( pAO, "! Autofinish computes the per cent of existing reads are aligned at\n");
- fprintf( pAO, "! each base position. Typically, this number starts at around 0% at\n");
- fprintf( pAO, "! base position 1, rises to close to 100% at around base position 300,\n");
- fprintf( pAO, "! and then drops again to 0% at base position 800 or so. This number\n");
+ fprintf( pAO, "! each base position. Typically, this number starts at around 0%% at\n");
+ fprintf( pAO, "! base position 1, rises to close to 100%% at around base position 300,\n");
+ fprintf( pAO, "! and then drops again to 0%% at base position 800 or so. This number\n");
fprintf( pAO, "! specifies how high the number must be for Autofinish to consider an\n");
fprintf( pAO, "! Autofinish read to cover a single subclone region.\n");
fprintf( pAO, "! (OK)\n");
@@ -1295,7 +1295,7 @@
( ( pCP->bCheckIfTooManyWalks_ ) ? "true" : "false" ) );
fprintf( pAO, "! this just checks if the number of walks, pcr ends, and unknown reads\n");
- fprintf( pAO, "! exceeds 20% of the total number of reads. If this is exceeded, then \n");
+ fprintf( pAO, "! exceeds 20%% of the total number of reads. If this is exceeded, then \n");
fprintf( pAO, "! a warning message is given. Typically, such a warning indicates\n");
fprintf( pAO, "! that you have incorrectly customized determineReadTypes.perl\n");
fprintf( pAO, "! (OK)\n");
@@ -1446,7 +1446,7 @@
( ( pCP->bProcessMatePairsAtStartup_ ) ? "true" : "false" ) );
fprintf( pAO, "! This is necessary to show the mate pair flags, but it does add\n");
- fprintf( pAO, "! around 15% to startup time.\n");
+ fprintf( pAO, "! around 15%% to startup time.\n");
fprintf( pAO, "! (OK)\n");
fprintf( pAO, "consed.maximumNumberOfTracesShown: %d\n",
pCP->nMaximumNumberOfTracesShown_ );
@@ -1796,7 +1796,7 @@
(char*)pCP->soStoreTracePeakPositions_.data() );
fprintf( pAO, "! never, always or whenChromatAvailable\n");
- fprintf( pAO, "! changing this to \"always\" increases memory usage by close to 100%,\n");
+ fprintf( pAO, "! changing this to \"always\" increases memory usage by close to 100%%,\n");
fprintf( pAO, "! especially if the assembler is Newbler. always means it will store\n");
fprintf( pAO, "! the positions if they are present in the phd file/ball.\n");
fprintf( pAO, "! \"whenChromatAvailable\" means it will store trace peak positions for\n");
--- a/readPrimerScreenSequences.cpp
+++ b/readPrimerScreenSequences.cpp
@@ -167,7 +167,7 @@
++nSequenceNumber ) {
if ( pnLengthOfSequence[ nSequenceNumber ] !=
strlen( pszSequence[ nSequenceNumber ] ) ) {
- sprintf( szErrorMessage, "inconsistency between pnLengthOfSequence %d and pszSequence %d for sequence number %d",
+ sprintf( szErrorMessage, "inconsistency between pnLengthOfSequence %d and pszSequence %zu for sequence number %d",
pnLengthOfSequence[ nSequenceNumber ],
strlen( pszSequence[ nSequenceNumber ] ),
nSequenceNumber );
--- a/rwcstring.cpp
+++ b/rwcstring.cpp
@@ -235,7 +235,7 @@
nMaxLength_ = nDefaultLengthForConversions;
- nCurrentLength_ = sprintf( sz_, "%d", lNumberToConvert );
+ nCurrentLength_ = sprintf( sz_, "%ld", lNumberToConvert );
if ( nCurrentLength_ > nMaxLength_ ) {
// big trouble--might not even make it here--might segmentation fault
--- a/someOtherProgramSentACommandToConsed.cpp
+++ b/someOtherProgramSentACommandToConsed.cpp
@@ -89,7 +89,7 @@
char szLine2[ nMaxLine ];
- sprintf( szLine2, "# of chars = %d %s", strlen( szLine ), szLine );
+ sprintf( szLine2, "# of chars = %zu %s", strlen( szLine ), szLine );
cout << szLine2 << endl;
--- a/tag.cpp
+++ b/tag.cpp
@@ -466,7 +466,7 @@
fprintf( pPhdFile, "DATE: %s\n", soDate_.data() );
if ( lID_ != nUndefinedTagID ) {
- fprintf( pPhdFile, "ID: %d\n", lID_ );
+ fprintf( pPhdFile, "ID: %ld\n", lID_ );
}
--- a/userDefinedTagField.cpp
+++ b/userDefinedTagField.cpp
@@ -64,7 +64,7 @@
void userDefinedIntegerTagField :: writeThyselfToAceFileOrPhdBall( FILE* pFile ) {
- fprintf( pFile, "%s %d\n",
+ fprintf( pFile, "%s %ld\n",
pUserDefinedTagFieldType_->soFieldName_.data(),
l_ );
}
@@ -119,7 +119,7 @@
void userDefinedPointerTagField :: writeThyselfToAceFileOrPhdBall( FILE* pFile ) {
- fprintf( pFile, "%s %d\n",
+ fprintf( pFile, "%s %ld\n",
pUserDefinedTagFieldType_->soFieldName_.data(),
lID_ );

8
sci-biology/consed/metadata.xml
View File

@ -1,8 +0,0 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
</pkgmetadata>