gentoo auto-resync : 27:01:2023 - 13:58:28

17 files changed, 0 insertions, 2030 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 07cf870e4b14..c69bcbc42b0f 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/consed/Manifest b/sci-biology/consed/Manifest
deleted file mode 100644
index c13741cade0d..000000000000
--- a/sci-biology/consed/Manifest
+++ /dev/null
@@ -1,8 +0,0 @@
-AUX consed-29-fix-build-system.patch 5614 BLAKE2B 2ec980906ee2f9c7b0cede7b3eabad78cdc3e9c3d95c58275dc849ff36ee4ef9fa53dd3b321729ae60c9f2d2fc1ca4cd0ee2448175410acca7ffe6266d66ac44 SHA512 92df40d6465685aec77d73db1f0eb7a79d4c26fbbf7d9764c4e0a83208e4ef97b45db1a8175239bd174bd56aeed7a5aa0111c7b99764910f7d6c0ac63aba187d
-AUX consed-29-fix-c++14.patch 9261 BLAKE2B ff70814b39780dbbabc70eb7555359e8aee2ef72b40b7e149e2f63ccaeedfe7e0dc8822cb2b5c79d57c33e621a59e0e1cd273e49a0976daef0bdeb52f4f46569 SHA512 be5cd76d36cf437c1113d09e540d98d0eb92b7e2e732f4a5a308066b8046b5628048203e791a0fa316e44a4cc127d027418a7f038406df22c3f60552f5b87789
-AUX consed-29-fix-perl-shebang.patch 17375 BLAKE2B e34a358569d594f4ab60fc3745a6a84cab781cbad860421f5ac322154df9635e13b2e2349c92f4271b0ca161eda87285ba89bf0801992954fecaa11575c8baf9 SHA512 4caed1ab7229e2b3e367f03a8d650cafed2974232fcd6daa08e62c90512d49e09caceb34c5bb65c67a588bab314165d72d8c1687393549d4107425df78e3218d
-AUX consed-29-fix-qa.patch 11639 BLAKE2B 3b80fd91b60c09e69cb9fa9b8deb88393fd89f02a3a650076db275567725aeb4636bfe1fcc35f44c72be33ed9494796fa6dab1b4da8b4b9444ecc73ea9b141fb SHA512 083b23d03ef9a473b41fae21ce433cdd5cdd0948819fa9dcc6dbed3022e93674aaa8769894b9be69b5bccf47dd6e67435bdf0549a719ecc4c5517f89010c3988
-DIST consed-29-linux.tar.gz 36172715 BLAKE2B 6706576b404c0bccb7ed28ab6fe2dec86fdac6f7651406d3f30e35caac3e49a66b4762edace2133d2dfb776bbeb730b74797c7323deb950f2648a46c4594fe98 SHA512 63a95d84cb58009045a9d898c8b1a94f98516bed9189f624a5930338cc8f51562504257f309d945fafcc07e0811ffeea122b640789f75fbd6c94535178dab4dd
-DIST consed-29-sources.tar.gz 3258845 BLAKE2B 508763ff2a240047cff0a43ba4b9b9a7f9302c0a023478c6b08f86bb77fb2c12a62a9b16165fe6257fe6c86af853dabe279bd9e05632c3e112e3fb7fad2c6bd3 SHA512 fd711a65a02ef1238cca12b90fe7fa9b67da6c37d43cd105f38c7b6475fbc073c1f4d7f99703dec9d3a0a7a2a9317cb14999a114bb6f52589cb9b6e34700eb93
-EBUILD consed-29.ebuild 2727 BLAKE2B 09c3d1619c7c751c1b084bcf1bc25bd87cfa23f4d83b0b6432b9229f7ecbd05c4a424522f6cc4117d571fa2ce34dbde805b4d0224a95db5af0f200e21688b1f3 SHA512 86160fe6b03dcfddc756c3f6a5c15bcbfe6a94b3002fe4deb39157adfc445a52ee557fa7732f07711a6859357c475bc31cfa535563cb91efee4511281fdef854
-MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de
diff --git a/sci-biology/consed/consed-29.ebuild b/sci-biology/consed/consed-29.ebuild
deleted file mode 100644
index 32eba4cb16d0..000000000000
--- a/sci-biology/consed/consed-29.ebuild
+++ /dev/null
@@ -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"
-}
diff --git a/sci-biology/consed/files/consed-29-fix-build-system.patch b/sci-biology/consed/files/consed-29-fix-build-system.patch
deleted file mode 100644
index 30819f93ac80..000000000000
--- a/sci-biology/consed/files/consed-29-fix-build-system.patch
+++ /dev/null
@@ -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
diff --git a/sci-biology/consed/files/consed-29-fix-c++14.patch b/sci-biology/consed/files/consed-29-fix-c++14.patch
deleted file mode 100644
index 212b8d63d1e3..000000000000
--- a/sci-biology/consed/files/consed-29-fix-c++14.patch
+++ /dev/null
@@ -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
- 
diff --git a/sci-biology/consed/files/consed-29-fix-perl-shebang.patch b/sci-biology/consed/files/consed-29-fix-perl-shebang.patch
deleted file mode 100644
index a27a3537a8d1..000000000000
--- a/sci-biology/consed/files/consed-29-fix-perl-shebang.patch
+++ /dev/null
@@ -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" ) {
diff --git a/sci-biology/consed/files/consed-29-fix-qa.patch b/sci-biology/consed/files/consed-29-fix-qa.patch
deleted file mode 100644
index 90e180da0174..000000000000
--- a/sci-biology/consed/files/consed-29-fix-qa.patch
+++ /dev/null
@@ -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_ );
-    
diff --git a/sci-biology/consed/metadata.xml b/sci-biology/consed/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/consed/metadata.xml
+++ /dev/null
@@ -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>
diff --git a/sci-biology/phrap/Manifest b/sci-biology/phrap/Manifest
deleted file mode 100644
index 4fe85ddfb7b0..000000000000
--- a/sci-biology/phrap/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-AUX phrap-1.080812-fix-build-system.patch 3600 BLAKE2B 29a7846cd6394d17b35e525220b8ead461a22ab0f1301ae5668da36605649c07f23040c4c134424802d4da6e0c3b48fbbb05ec5708de50b33f024e4ba702ac49 SHA512 536ad862b9b8ce0fbc7ab67bc48db597e7d4b8c66018a5abefe5a59f4fbc30a4a76c94f4c13f5af7d42a422a22f5181d8f015b797d37f175238c3d4170adf21c
-DIST phrap-1.080812-distrib.tar.gz 317350 BLAKE2B 9cc53d05184b4a55a9a80e6112498f91a622b98a853b255daedd57c892b7c2bb8ef3091ed3d141e297864c158b7e03d02313a272448d2e0fb80e1c51a906e00a SHA512 6b125b9a99b6180eb5de16bccfe068abefdb59237fd3295924c418749f2f2d6e39cdbcecc6786e42738846975334c4d8a645eae8fd0fcbda6b0e99241deb15ca
-EBUILD phrap-1.080812-r2.ebuild 962 BLAKE2B 42c56565cc83f792878f8dac26badf57a7307d63dae27684a7799c6607521b5e564d0b21f49a7669ed291e0facd502b9745aec1a643226e9ac9ec8e0031d9d76 SHA512 abbc494349976d3a6371a424b4a6bce60e30f7963db4d05976a59c88cf0def994b690f8746d34db683629eb171322ebbcb2aa9325e746adeec9afd575468bc92
-MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de
diff --git a/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch b/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch
deleted file mode 100644
index 6d30c2ce326a..000000000000
--- a/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch
+++ /dev/null
@@ -1,100 +0,0 @@
-* Fix perl shebang to be portable
-* Make build system honour LDFLAGS
-
---- a/makefile
-+++ b/makefile
-@@ -25,9 +25,8 @@
- # Makefile for swat, phrap, cross_match, phrapview; also swprobs (currently inactivated)
- #CC= icc
- #CFLAGS= -O2 -wd266,880
--CC= cc
--CFLAGS= -O2
--LFLAGS= -lm
-+CC ?= cc
-+LIBS = -lm
- 
- SWATOBJS= swat.o weibull.o
- 
-@@ -96,46 +95,46 @@
- 	chmod a+x phrapview
- 
- swat: makefile $(SWATOBJS) $(SWOBJS)
--	$(CC) $(CFLAGS) -o $@ $(SWATOBJS) $(SWOBJS) $(LFLAGS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(SWATOBJS) $(SWOBJS) $(LIBS)
- 	chmod o-r swat
- 
- alpha_swat: makefile $(ALPHOBJS) $(SWOBJS) 
--	$(CC) $(CFLAGS) -o $@ $(ALPHOBJS) $(SWOBJS) $(LFLAGS) 
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(ALPHOBJS) $(SWOBJS) $(LIBS) 
- 	chmod o-r alpha_swat
- 
- swat_counts: makefile $(COUNOBJS) $(SWOBJS) 
--	$(CC) $(CFLAGS) -o $@ $(COUNOBJS) $(SWOBJS) $(LFLAGS) 
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(COUNOBJS) $(SWOBJS) $(LIBS) 
- 	chmod o-r swat_counts
- 
- swprobs: makefile $(PROBOBJS)
--	$(CC) $(CFLAGS) -o $@ $(PROBOBJS) $(LFLAGS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(PROBOBJS) $(LIBS)
- 
- phrap: makefile phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS)
--	$(CC) $(CFLAGS) -o $@ phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(LFLAGS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(LIBS)
- 	chmod o-r phrap
- 
- gcphrap: makefile gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS)
--	$(CC) $(CFLAGS) -o $@ gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LFLAGS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LIBS)
- 	chmod o-r gcphrap
- 
- cross_match: makefile cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS)
--	$(CC) $(CFLAGS) -o $@ cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(LFLAGS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(LIBS)
- 	chmod o-r cross_match
- 
- gccross_match: makefile gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS)
--	$(CC) $(CFLAGS) -o $@ gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LFLAGS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LIBS)
- 	chmod o-r gccross_match
- 
- cluster: makefile $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS)
--	$(CC) $(CFLAGS) -o $@ $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) $(LFLAGS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) $(LIBS)
- 	chmod o-r cluster
- 
- loco: makefile $(LOCOOBJS) $(SWOBJS)
--	$(CC) $(CFLAGS) -o $@ $(LOCOOBJS) $(SWOBJS) $(LFLAGS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(LOCOOBJS) $(SWOBJS) $(LIBS)
- 	chmod o-r loco
- 
- erf_test: $(ERFOBJS)
--	$(CC) $(CFLAGS) -o $@ $(ERFOBJS) $(LFLAGS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(ERFOBJS) $(LIBS)
- 
- loco.o: swat.h
- 
-@@ -228,7 +227,7 @@
- anomalies.o: swat.h 
- 
- fast_smith_wat.s: fast_smith_wat.c
--	cc -S -machine_code -source_listing -O3 fast_smith_wat.c
-+	$(CC) $(CFLAGS) -S -machine_code -source_listing fast_smith_wat.c
- #N.B. fast_smith_wat.s MUST BE EDITTED BEFORE USE!!!
- 
- tig_node.o: swat.h
---- a/phrapview
-+++ b/phrapview
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/env perl
- 
- 
- #/*****************************************************************************
-@@ -25,6 +25,7 @@
- #                                                                         
- #*****************************************************************************/
- 
-+use warnings;
- use strict;
- use Tk;
- #phrapview version 0.960731
diff --git a/sci-biology/phrap/metadata.xml b/sci-biology/phrap/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/phrap/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/phrap/phrap-1.080812-r2.ebuild b/sci-biology/phrap/phrap-1.080812-r2.ebuild
deleted file mode 100644
index 08ea5a1fb71f..000000000000
--- a/sci-biology/phrap/phrap-1.080812-r2.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs
-
-DESCRIPTION="Shotgun assembly and alignment utilities"
-HOMEPAGE="http://www.phrap.org/"
-SRC_URI="phrap-${PV}-distrib.tar.gz"
-
-LICENSE="phrap"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="
-	dev-lang/perl
-	dev-perl/Tk"
-
-S="${WORKDIR}"
-
-RESTRICT="fetch"
-PATCHES=( "${FILESDIR}/${PN}-1.080812-fix-build-system.patch" )
-
-pkg_nofetch() {
-	einfo "Please visit http://www.phrap.org/phredphrapconsed.html and obtain the file"
-	einfo "\"distrib.tar.gz\", then rename it to \"phrap-${PV}-distrib.tar.gz\""
-	einfo "and put it into your DISTDIR directory."
-}
-
-src_compile() {
-	emake CC="$(tc-getCC)" \
-		CFLAGS="${CFLAGS}" \
-		LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	dobin cross_match loco phrap phrapview swat
-	newbin cluster cluster_phrap
-
-	local i
-	for i in {general,phrap,swat}.doc; do
-		newdoc ${i} ${i}.txt
-	done
-}
diff --git a/sci-biology/phred/Manifest b/sci-biology/phred/Manifest
deleted file mode 100644
index 4807ae1d7349..000000000000
--- a/sci-biology/phred/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-AUX phred-071220-fix-build-system.patch 1981 BLAKE2B 0c9ae75ecf54eadd1d6cd3cfeed5d2f949f234b77d4f329133e2c176207410e93a35341c43636c5b2f742a2ee2d20825cf79bb65d5dac43ba28fc07f7c6bb69b SHA512 7647f6f6e9a1ae51cbf1aa3e39b337288e22fc26a95fdd88f92ce43fc6c0ef6ff59ec26919d14dfefff70be48e4a5604ddefef98bddf5d1d14d1e656665c878d
-AUX phred-071220-fix-qa.patch 787 BLAKE2B 79f687dc1e51dd51e9f97886e0ada9b515d7e4255dff0ec3e81dccb2103ba8b4bee691c8a5b9a321cbdde5576fe8d80dbadafdb740c2cdee81fe9748255084ab SHA512 27811a834358d0e1bf8281882e0420e0eb6bd9586871c8c72a4de79badc9539ea8e9258b9c3a3bf8ca1d3f6924d61abce2dcc0c0ed3b64e5fa53d4548109f5bc
-DIST phred-dist-071220.b-acd.tar.gz 357767 BLAKE2B ae1180f54eaa3631a4e32c2ffe388b35745302e3d014c8fa893119e7e488d4bb4316f7ee0588cd12db5cbbc23033f689f4a0a487cdc7fe42e8c7a67ceb3c43ae SHA512 0a6b0a733e6dcc0495eaab720b75f8e5815df494d0a773b8b8336d5208321c2ba475921084835a769367ec51aed156585ab97346a510100d4337e3215ec75276
-EBUILD phred-071220-r2.ebuild 941 BLAKE2B a2351e95dd63ab0655c6dc009dabffbc2bea88e2c4c45536094ca5b7e18c22e6040a44b2362b56a58cdb2ba002d2f5c3d9527b5775ba073c29ed70b6e0d25198 SHA512 5b0fc5afeb3847d9a8729b14addca1508add1a0cf6f857273c9a5671b65c82385b82c62e9545caa9b3a8f470b1852d9655ac8ca3ca33f745937a3101f7ebe084
-MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de
diff --git a/sci-biology/phred/files/phred-071220-fix-build-system.patch b/sci-biology/phred/files/phred-071220-fix-build-system.patch
deleted file mode 100644
index 997f39941a07..000000000000
--- a/sci-biology/phred/files/phred-071220-fix-build-system.patch
+++ /dev/null
@@ -1,82 +0,0 @@
-* Fix build system to honour CC, CFLAGS, CPPFLAGS and LDFLAGS
-* Specify a default target, in order to keep the ebuild slim
-
---- a/Makefile
-+++ b/Makefile
-@@ -12,9 +12,9 @@
- 
- # UNIX specific definitions (default)
- #
--CC= cc
--CFLAGS= -O -DANSI_C $(LXFLAGS)
--CLIB= -lm
-+CC ?= cc
-+CPPFLAGS += -DANSI_C $(LXFLAGS)
-+LIBS += -lm
- 
- # Windows 'nmake' specific definitions
- #
-@@ -133,9 +133,6 @@
-   $(objdir)writeSDF.o \
-   $(objdir)writeSeq.o
- 
--SRCS = $(OBJS:.o=.c)
--WOBJ = $(OBJS:.o=.obj)
--
- INCS = \
-   $(incdir)chromatData.h \
-   $(incdir)freeChromatData.h \
-@@ -179,48 +176,18 @@
- # UNIX make specific phred target
- # note: a horizontal tab character must precede `$(CC)'
- #
--phred: $(OBJS)
--	$(CC) $(CFLAGS) -o phred $(OBJS) $(CLIB)
- 
- 
--# Windows nmake specific phred target
--#
--forwindows: $(WOBJ)
--	$(CC) $(CFLAGS) /Fephred $(WOBJ)
--#	$(CC) $(CFLAGS) /Fedaev daev.c
-+.PHONY: all
-+all: phred daev
- 
- 
--# test CC: refuse to compile if
--#
--#   o  SunOS
--#
--#   AND
--#
--#   o  using /usr/ucb/cc compiler
--#
--#   NOTE: this compiler causes problems: see PHRED.DOC
--#
--test_cc:
--	@if [ `uname` = SunOS ] ; \
--        then \
--          if [ `which $(CC)` = "/usr/ucb/cc" ] ; \
--          then \
--            echo ""; \
-- echo "============================================================"; \
-- echo "|                                                          |"; \
-- echo "|   This SUN C compiler produces a bad phred executable.   |"; \
-- echo "|                                                          |"; \
-- echo "|   Please see the PHRED.DOC file for more information.    |"; \
-- echo "|                                                          |"; \
-- echo "============================================================"; \
--            echo ""; \
--             exit 1; \
--          fi \
--        fi
-+phred: $(OBJS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o phred $^ $(LIBS)
- 
- 
- daev: daev.o
--	$(CC) $(CFLAGS) -o daev daev.o -lm
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o daev $^ $(LIBS)
- 
- 
- clean:
diff --git a/sci-biology/phred/files/phred-071220-fix-qa.patch b/sci-biology/phred/files/phred-071220-fix-qa.patch
deleted file mode 100644
index ab4d2ea023f6..000000000000
--- a/sci-biology/phred/files/phred-071220-fix-qa.patch
+++ /dev/null
@@ -1,36 +0,0 @@
-Fix implicit declarations:
-* daev.c: In function ‘processParameters’:
-* daev.c:849:14: warning: implicit declaration of function ‘isdigit’ [-Wimplicit-function-declaration]
-*          if( !isdigit( argv[iarg][0] ) )
-
---- a/autoPhred.c
-+++ b/autoPhred.c
-@@ -57,6 +57,7 @@
- static int xstrcmp();
- #endif
- 
-+int freeMBRData( MBRData *mbrData );
- #ifdef ANSI_C
- int autoPhred( Option *option )
- #else
---- a/daev.c
-+++ b/daev.c
-@@ -58,6 +58,7 @@
- #include <sys/stat.h>
- #include <time.h>
- #include <math.h>
-+#include <ctype.h>
- 
- #ifndef _WIN32
- #include <dirent.h>
---- a/mergedBaseRead.c
-+++ b/mergedBaseRead.c
-@@ -63,7 +63,7 @@
-   Peak *peak;
-   Observed_peak *obs_peak;
- 
--  static initFlag = 0;
-+  static int initFlag = 0;
-   static char mchar[256][256];
- 
-   if( initFlag == 0 )
diff --git a/sci-biology/phred/metadata.xml b/sci-biology/phred/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/phred/metadata.xml
+++ /dev/null
@@ -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>
diff --git a/sci-biology/phred/phred-071220-r2.ebuild b/sci-biology/phred/phred-071220-r2.ebuild
deleted file mode 100644
index 2d33df654a1b..000000000000
--- a/sci-biology/phred/phred-071220-r2.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="A base caller for Sanger DNA sequencing"
-HOMEPAGE="http://phrap.org/phredphrapconsed.html"
-SRC_URI="${PN}-dist-${PV}.b-acd.tar.gz"
-S="${WORKDIR}"
-
-LICENSE="phrap"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-RESTRICT="fetch"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-071220-fix-build-system.patch
-	"${FILESDIR}"/${PN}-071220-fix-qa.patch
-)
-
-pkg_nofetch() {
-	einfo "Please visit ${HOMEPAGE} and obtain the file"
-	einfo "${SRC_URI}, then place it into your DISTDIR directory."
-}
-
-src_compile() {
-	emake CC="$(tc-getCC)" \
-		CFLAGS="${CFLAGS}" \
-		LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	dobin phred daev
-
-	insinto /usr/share/phred
-	doins phredpar.dat
-
-	newenvd - 99phred <<- EOF
-		PHRED_PARAMETER_FILE="${EPREFIX}/usr/share/phred/phredpar.dat"
-	EOF
-
-	newdoc DAEV.DOC DAEV.DOC.txt
-	newdoc PHRED.DOC PHRED.DOC.txt
-}