Remove expired ports:

2018-06-06 biology/ssaha: Broken for more than 6 months
2018-06-06 biology/crux: Broken for more than 6 months
2018-06-06 biology/ariadne: Broken for more than 6 months
2018-06-06 cad/sceptre: Broken for more than 6 months
2018-06-06 cad/cider: Broken for more than 6 months
2018-06-06 chinese/scim-array: Broken for more than 6 months
2018-06-06 chinese/xpdf: Broken for more than 6 months
2018-06-06 chinese/telnet: Broken for more than 6 months
2018-06-06 comms/java-commapi-freebsd: Depends on BROKEN and expiring comms/java-commapi
2018-06-06 comms/soundmodem: Broken for more than 6 months
2018-06-06 comms/jsdr: Broken for more than 6 months
2018-06-06 comms/java-commapi: Broken for more than 6 months
2018-06-06 converters/pdf2djvu: Broken for more than 6 months
2018-06-06 databases/rdb: Broken for more than 6 months
2018-06-06 databases/animenfo-client: Broken for more than 6 months
2018-06-06 databases/ruby-mysql: Broken for more than 6 months
2018-06-06 databases/riak: Broken for more than 6 months
2018-06-06 databases/animenfo-client-gtk: Broken for more than 6 months
2018-06-06 databases/rdfdb: Broken for more than 6 months
2018-06-06 databases/riak2: Broken for more than 6 months
2018-06-06 devel/subversion-static: Broken for more than 6 months
2018-06-06 japanese/xgate: Broken for more than 6 months
2018-06-06 textproc/opengrm-ngram: Broken for more than 6 months
2018-06-06 textproc/ocaml-tyxml: Depends on BROKEN and expiring www/ocaml-net
2018-06-06 www/ocaml-net: Broken for more than 6 months
2018-06-06 audio/linux-genpuid: Broken for more than 6 months
2018-06-06 x11/enventor: Broken for more than 6 months
2018-06-06 audio/xmms-timidity: Broken for more than 6 months
2018-06-06 audio/kaudiocreator: Broken for more than 6 months
2018-06-06 audio/jxm: Depends on BROKEN and expiring comms/java-commapi
2018-06-06 audio/deforaos-mixer: Broken for more than 6 months
2018-06-06 audio/gkrellmss2: Broken for more than 6 months
2018-06-06 audio/ogg2mp3: Broken for more than 6 months
2018-06-06 audio/abcmidi: Broken for more than 6 months
2018-06-06 benchmarks/netpipe: Broken for more than 6 months
2018-06-06 biology/plink: Broken for more than 6 months

51 files changed, 0 insertions, 1777 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 6484d87ac4c9..f1252060e8b9 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -3,7 +3,6 @@
 
     COMMENT = Biology
 
-    SUBDIR += ariadne
     SUBDIR += artemis
     SUBDIR += avida
     SUBDIR += babel
@@ -23,7 +22,6 @@
     SUBDIR += clustalw
     SUBDIR += clustalx
     SUBDIR += consed
-    SUBDIR += crux
     SUBDIR += ddocent
     SUBDIR += diamond
     SUBDIR += emboss
@@ -93,7 +91,6 @@
     SUBDIR += phred
     SUBDIR += phylip
     SUBDIR += phyml
-    SUBDIR += plink
     SUBDIR += plinkseq
     SUBDIR += primer3
     SUBDIR += protomol
@@ -122,7 +119,6 @@
     SUBDIR += sim4
     SUBDIR += slclust
     SUBDIR += smithwaterman
-    SUBDIR += ssaha
     SUBDIR += stacks
     SUBDIR += tRNAscan-SE
     SUBDIR += t_coffee
diff --git a/biology/ariadne/Makefile b/biology/ariadne/Makefile
deleted file mode 100644
index 3ce04c057ed9..000000000000
--- a/biology/ariadne/Makefile
+++ /dev/null
@@ -1,38 +0,0 @@
-# Created by: Fernan Aguero <fernan@iib.unsam.edu.ar>
-# $FreeBSD$
-
-PORTNAME=	ariadne
-PORTVERSION=	1.3
-CATEGORIES=	biology
-MASTER_SITES=	http://www.well.ox.ac.uk/ariadne/
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	Programs to compare protein sequences and profiles
-
-WRKSRC=		${WRKDIR}/SRC-${PORTVERSION}
-
-BROKEN=		No public distfiles
-DEPRECATED=	Broken for more than 6 months
-EXPIRATION_DATE=	2018-06-06
-
-PLIST_FILES+=	bin/ariadne bin/prospero
-USES=		gmake tar:Z
-PORTDOCS=	README
-MAKE_ARGS+=	CC="${CC}"
-
-OPTIONS_DEFINE=	DOCS
-
-MAKE_JOBS_UNSAFE=	yes
-
-post-patch:
-	@${REINPLACE_CMD} -e 's|CFLAGS =|CFLAGS +=| ; \
-		s|-c $$(OPTIMISE)|-c ${CFLAGS} ${OPTIMIZE}|g' \
-		${WRKSRC}/Makefile
-
-do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/${OPSYS}/ariadne ${STAGEDIR}${PREFIX}/bin
-	${INSTALL_PROGRAM} ${WRKSRC}/${OPSYS}/prospero ${STAGEDIR}${PREFIX}/bin
-	@${MKDIR} ${STAGEDIR}${DOCSDIR}
-	${INSTALL_DATA} ${WRKSRC}/README ${STAGEDIR}${DOCSDIR}
-
-.include <bsd.port.mk>
diff --git a/biology/ariadne/distinfo b/biology/ariadne/distinfo
deleted file mode 100644
index f68ade35372a..000000000000
--- a/biology/ariadne/distinfo
+++ /dev/null
@@ -1,2 +0,0 @@
-SHA256 (ariadne-1.3.tar.Z) = 8b6b0acb6e8d02b1303d94b20906bf2bf1dee3de4eceeb1b927cfba7a96fd00d
-SIZE (ariadne-1.3.tar.Z) = 69427
diff --git a/biology/ariadne/pkg-descr b/biology/ariadne/pkg-descr
deleted file mode 100644
index e7566af34e4d..000000000000
--- a/biology/ariadne/pkg-descr
+++ /dev/null
@@ -1,18 +0,0 @@
-ARIADNE is a package of two programs, ariadne and prospero, that compare
-protein sequences and profiles using the Smith-Waterman algorithm, and
-assesses statistical significance using a new accurate formula,
-described in Mott, 2000, "Accurate Formula for P-values of gapped local
-sequence and profile alignments" J. Mol Biol. 300:649-659.
-
-The sequence/profile comparison algorithms used in ARIADNE are standard,
-and are probably not the fastest implementations available. The novel
-part is the method for determining statistical significance, which will
-give thresholds of significance that are accurate to within 5% 95% of
-the time.
-
-The package is written in ANSI C. You are free to incorporate the method
-used for assessing statistical significance into third-party code,
-provided you cite the above reference. The routines for assessing
-significance are all in gaplib.c
-
-WWW: http://www.well.ox.ac.uk/ariadne/
diff --git a/biology/crux/Makefile b/biology/crux/Makefile
deleted file mode 100644
index 339ee827f79c..000000000000
--- a/biology/crux/Makefile
+++ /dev/null
@@ -1,56 +0,0 @@
-# Created by: Jason Evans <jasone@FreeBSD.org>
-# $FreeBSD$
-
-PORTNAME=	crux
-PORTVERSION=	1.2.0
-PORTREVISION=	9
-CATEGORIES=	biology python
-MASTER_SITES=	http://www.canonware.com/download/Crux/
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	Software toolkit for phylogenetic inference
-
-LICENSE=	BSD2CLAUSE BSD3CLAUSE
-LICENSE_COMB=	multi
-
-BROKEN=		No public distfiles
-DEPRECATED=	Broken for more than 6 months
-EXPIRATION_DATE=	2018-06-06
-BROKEN_aarch64=		Fails to link: ImportError: /lib/libgcc_s.so.1: version GCC_4.5.0 required by /usr/local/lib/gcc5/libgfortran.so.3 not found
-BROKEN_armv6=		Fails to link: ImportError: /usr/local/lib/gcc49/libgfortran.so.3: Undefined symbol "__aeabi_ldivmod"
-BROKEN_armv7=		Fails to link: ImportError: /usr/local/lib/gcc49/libgfortran.so.3: Undefined symbol "__aeabi_ldivmod"
-
-USES=		fortran gmake python tar:bzip2
-USE_CSTD=	gnu99
-GNU_CONFIGURE=	yes
-CONFIGURE_ARGS=	--datadir=${PREFIX}/lib \
-		--with-python=${PYTHON_CMD} \
-		--disable-mpi
-
-CPPFLAGS+=	-I${LOCALBASE}/include
-LDFLAGS+=	-L${LOCALBASE}/lib
-
-MAKE_JOBS_UNSAFE=	yes
-
-OPTIONS_DEFINE=		SYS_LINALG
-
-SYS_LINALG_DESC=	Enable system ATLAS/LAPACK
-SYS_LINALG_LIB_DEPENDS=	libatlas.so:math/atlas
-SYS_LINALG_CONFIGURE_ENABLE=	sys-linalg
-
-post-patch:
-	@${REINPLACE_CMD} -e '/altivec/s|-f|-m|' ${WRKSRC}/configure
-	@${REINPLACE_CMD} -e \
-		's|\([[:blank:]]\)\($$(BINDIR)\)|\1$$(DESTDIR)\2| ; \
-		 s|\([[:blank:]]\)\($$(DATADIR)\)|\1$$(DESTDIR)\2| ; \
-		 s|\(,\)\(@site_packages@\)|\1$$(DESTDIR)\2| ; \
-		 s|\([[:blank:]]\)\(@site_packages@\)|\1$$(DESTDIR)\2|' \
-		${WRKSRC}/Makefile.in
-
-post-install:
-	@(${FIND} ${STAGEDIR}${PREFIX}/lib/Crux/lib -maxdepth 1 -type f \
-		-name "*.so" | ${XARGS} ${STRIP_CMD})
-	@(${FIND} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} -maxdepth 3 -type f \
-		-name "*.so" | ${XARGS} ${STRIP_CMD})
-
-.include <bsd.port.mk>
diff --git a/biology/crux/distinfo b/biology/crux/distinfo
deleted file mode 100644
index 7a42e305350a..000000000000
--- a/biology/crux/distinfo
+++ /dev/null
@@ -1,2 +0,0 @@
-SHA256 (crux-1.2.0.tar.bz2) = 11f677e8bf62db69e75271670ea50fb5a23c8a2c526fa9d16ccf2e736e5212c5
-SIZE (crux-1.2.0.tar.bz2) = 1187274
diff --git a/biology/crux/files/patch-lib_Crux_CxPpc.c b/biology/crux/files/patch-lib_Crux_CxPpc.c
deleted file mode 100644
index ea100b5c9928..000000000000
--- a/biology/crux/files/patch-lib_Crux_CxPpc.c
+++ /dev/null
@@ -1,18 +0,0 @@
---- lib/Crux/CxPpc.c.orig	2009-09-19 04:31:04 UTC
-+++ lib/Crux/CxPpc.c
-@@ -8,14 +8,11 @@ bool CxgPpcUseAltivec;
- void
- CxPpcCpuInit(void)
- {
--    int mib[2];
-     int result, error;
-     size_t len;
- 
--    mib[0] = CTL_HW;
--    mib[1] = HW_VECTORUNIT;
-     len = sizeof(result);
--    error = sysctl(mib, 2, &result, &len, NULL, 0);
-+    error = sysctlbyname("hw.altivec", &result, &len, NULL, 0);
-     if (error != 0)
-     {
- 	CxgPpcUseAltivec = false;
diff --git a/biology/crux/files/pkg-install b/biology/crux/files/pkg-install
deleted file mode 100644
index c2e494752edd..000000000000
--- a/biology/crux/files/pkg-install
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/sh
-
-case $2 in
-POST-INSTALL)
-	${PKG_PREFIX}/bin/crux -b -q /dev/null
-	exit 0
-	;;
-esac
diff --git a/biology/crux/pkg-descr b/biology/crux/pkg-descr
deleted file mode 100644
index 5a27474d58b3..000000000000
--- a/biology/crux/pkg-descr
+++ /dev/null
@@ -1,19 +0,0 @@
-Crux is a software toolkit for molecular phylogenetic inference. It is
-structured as a set of Python modules, which makes it possible to quickly
-develop Python scripts that perform unique, non-canned analyses. Features
-include:
-* Tree log-likelihoods can be computed under a variety of models,
-  including all specializations of GTR+I+G and mixture models. Tree
-  likelihoods can be computed in parallel via pthreads.
-* Bayesian Markov chain Monte Carlo (MCMC) methods (with Metropolis
-  coupling) can sample among non-nested models using reversible model
-  jumps.
-* Crux is capable of simulating character data under any model its
-  likelihood engine is capable of.
-* The neighbor joining (NJ) and relaxed neighbor joining (RNJ)
-  implementations are among the fastest in existence.
-* Pairwise distances between sequences can be computed based on percent
-  identity, or using methods that correct for multiple hits
-  (Jukes-Cantor, Kimura, and logDet).
-
-WWW: http://www.canonware.com/Crux/
diff --git a/biology/crux/pkg-plist b/biology/crux/pkg-plist
deleted file mode 100644
index 643a68f48e4a..000000000000
--- a/biology/crux/pkg-plist
+++ /dev/null
@@ -1,56 +0,0 @@
-bin/crux
-bin/redpoint
-bin/MrRogers
-lib/Crux/lib/libCx.so
-lib/Crux/parsers/Fasta.log
-lib/Crux/parsers/Fasta.pickle
-%%PYTHON_SITELIBDIR%%/Crux/CTMatrix.so
-%%PYTHON_SITELIBDIR%%/Crux/Character.so
-%%PYTHON_SITELIBDIR%%/Crux/Config.py
-@rmtry %%PYTHON_SITELIBDIR%%/Crux/Config.pyo
-%%PYTHON_SITELIBDIR%%/Crux/Copying.py
-@rmtry %%PYTHON_SITELIBDIR%%/Crux/Copying.pyo
-%%PYTHON_SITELIBDIR%%/Crux/DistMatrix/Nj.so
-%%PYTHON_SITELIBDIR%%/Crux/DistMatrix/__init__.py
-%%PYTHON_SITELIBDIR%%/Crux/DistMatrix/__init__.so
-%%PYTHON_SITELIBDIR%%/Crux/Fasta.so
-%%PYTHON_SITELIBDIR%%/Crux/Mc3/Chain.so
-%%PYTHON_SITELIBDIR%%/Crux/Mc3/Post.so
-%%PYTHON_SITELIBDIR%%/Crux/Mc3/__init__.py
-%%PYTHON_SITELIBDIR%%/Crux/Mc3/__init__.so
-%%PYTHON_SITELIBDIR%%/Crux/Newick.so
-%%PYTHON_SITELIBDIR%%/Crux/Taxa.so
-%%PYTHON_SITELIBDIR%%/Crux/Tree/Bipart.so
-%%PYTHON_SITELIBDIR%%/Crux/Tree/Lik.so
-%%PYTHON_SITELIBDIR%%/Crux/Tree/Sumt.so
-%%PYTHON_SITELIBDIR%%/Crux/Tree/__init__.py
-%%PYTHON_SITELIBDIR%%/Crux/Tree/__init__.so
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/CTMatrix.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Character.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/CxMath.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/CxMat.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/CxNewickLexer.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/CxRi.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/Cx.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/DistMatrix/CxDistMatrixLexer.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/Tree/CxLik.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix/Nj.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix/__init__.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Fasta.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3/Chain.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3/Post.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3/__init__.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Newick.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/SFMT/SFMT.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Taxa.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/Bipart.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/Lik.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/Sumt.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/__init__.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/__init__.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/libc.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/libm.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Parsing.pxd
-%%PYTHON_SITELIBDIR%%/Crux/__init__.py
-%%PYTHON_SITELIBDIR%%/Crux/__init__.so
-%%PYTHON_SITELIBDIR%%/Parsing.so
diff --git a/biology/plink/Makefile b/biology/plink/Makefile
deleted file mode 100644
index b77e97515548..000000000000
--- a/biology/plink/Makefile
+++ /dev/null
@@ -1,30 +0,0 @@
-# $FreeBSD$
-
-PORTNAME=	plink
-PORTVERSION=	1.07
-PORTREVISION=	8
-CATEGORIES=	biology science
-MASTER_SITES=	http://pngu.mgh.harvard.edu/~purcell/plink/dist/
-DISTNAME=	${PORTNAME}-${PORTVERSION}-src
-
-MAINTAINER=	jwb@FreeBSD.org
-COMMENT=	Whole genome association analysis toolset
-
-BROKEN=		no public distfiles
-DEPRECATED=	Broken for more than 6 months
-EXPIRATION_DATE=	2018-06-06
-
-LICENSE=	GPLv2
-
-LIB_DEPENDS=	liblapack.so:math/lapack
-
-# We need Fortran LDFLAGS to link with Lapack.
-USES=		fortran gmake zip
-
-PLIST_FILES=	bin/plink
-
-do-install:
-	${MKDIR} ${STAGEDIR}${PREFIX}/bin
-	${INSTALL_PROGRAM} ${WRKSRC}/plink ${STAGEDIR}${PREFIX}/bin
-
-.include <bsd.port.mk>
diff --git a/biology/plink/distinfo b/biology/plink/distinfo
deleted file mode 100644
index 0e6de032e915..000000000000
--- a/biology/plink/distinfo
+++ /dev/null
@@ -1,2 +0,0 @@
-SHA256 (plink-1.07-src.zip) = 4af56348443d0c6a1db64950a071b1fcb49cc74154875a7b43cccb4b6a7f482b
-SIZE (plink-1.07-src.zip) = 2257297
diff --git a/biology/plink/files/patch-Makefile b/biology/plink/files/patch-Makefile
deleted file mode 100644
index e98b69aa6559..000000000000
--- a/biology/plink/files/patch-Makefile
+++ /dev/null
@@ -1,53 +0,0 @@
---- Makefile.orig	2009-10-10 11:00:20.000000000 -0500
-+++ Makefile	2012-09-07 08:24:26.000000000 -0500
-@@ -26,25 +26,25 @@
- WITH_WEBCHECK = 1
- FORCE_32BIT = 
- WITH_ZLIB = 1
--WITH_LAPACK = 
--FORCE_DYNAMIC = 
-+WITH_LAPACK = 1
-+FORCE_DYNAMIC = 1
- 
- # Put C++ compiler here; Windows has it's own specific version
- CXX_UNIX = g++
- CXX_WIN = c:\bin\mingw\bin\mingw32-g++.exe
- 
- # Any other compiler flags here ( -Wall, -g, etc)
--CXXFLAGS = 
-+# CXXFLAGS = 
- 
- # Misc
--LIB_LAPACK = /usr/lib/liblapack.so.3
-+LIB_LAPACK = ${LDFLAGS} -L${LOCALBASE}/lib -llapack -lblas
- 
- 
- # --------------------------------------------------------------------
- # Do not edit below this line
- # --------------------------------------------------------------------
- 
--CXXFLAGS += -O3 -I.
-+CXXFLAGS += -I.
- OUTPUT = plink
- 
- # Some system specific flags
-@@ -58,8 +58,8 @@
- endif
- 
- ifeq ($(SYS),UNIX)
-- CXXFLAGS += -DUNIX
-- CXX = $(CXX_UNIX)
-+ CXXFLAGS += -DUNIX -Dfopen64=fopen
-+ CXX ?= $(CXX_UNIX)
-  ifndef FORCE_DYNAMIC
-   CXXFLAGS += -static
-  endif
-@@ -128,7 +128,7 @@
- LIB += -ldl
- endif
- ifeq ($(SYS),UNIX)
--LIB += -ldl -lcrypt
-+LIB += -lcrypt
- endif
- endif
- 
diff --git a/biology/plink/files/patch-elf.cpp b/biology/plink/files/patch-elf.cpp
deleted file mode 100644
index 0cc22cb84e6a..000000000000
--- a/biology/plink/files/patch-elf.cpp
+++ /dev/null
@@ -1,25 +0,0 @@
---- elf.cpp.orig	2013-11-16 17:09:56.000000000 +0100
-+++ elf.cpp	2013-11-16 17:10:24.000000000 +0100
-@@ -1175,10 +1175,10 @@
- 	  << setw(8) << gcnt << " "
- 	  << setw(8) << (double)cnt / (double)gcnt << "\n";
- 
--      map<int,int>::iterator i = chr_cnt.begin();
--      while ( i != chr_cnt.end() )
-+      map<int,int>::iterator ichr = chr_cnt.begin();
-+      while ( ichr != chr_cnt.end() )
- 	{
--	  int c = i->first;
-+	  int c = ichr->first;
- 	  int x = chr_cnt.find( c )->second;
- 	  int y = chr_gcnt.find( c )->second;
- 	  
-@@ -1189,7 +1189,7 @@
- 	      << setw(8) << y << " "
- 	      << setw(8) << (double)x / (double)y << "\n";
- 	  
--	  ++i;
-+	  ++ichr;
- 	}
-       
-     }
diff --git a/biology/plink/files/patch-idhelp.cpp b/biology/plink/files/patch-idhelp.cpp
deleted file mode 100644
index c0026984f854..000000000000
--- a/biology/plink/files/patch-idhelp.cpp
+++ /dev/null
@@ -1,19 +0,0 @@
---- idhelp.cpp.orig	2013-11-16 17:11:42.000000000 +0100
-+++ idhelp.cpp	2013-11-16 17:12:53.000000000 +0100
-@@ -772,12 +772,12 @@
-       for (int j = 0 ; j < jointField.size(); j++ )
- 	{
- 	  set<IDField*> & jf = jointField[j];
--	  set<IDField*>::iterator j = jf.begin();
-+	  set<IDField*>::iterator jfit = jf.begin();
- 	  PP->printLOG(" { ");
--	  while ( j != jf.end() )
-+	  while ( jfit != jf.end() )
- 	    {
--	      PP->printLOG( (*j)->name + " " );
--	      ++j;
-+	      PP->printLOG( (*jfit)->name + " " );
-+	      ++jfit;
- 	    }
- 	  PP->printLOG(" }");
- 	}
diff --git a/biology/plink/files/patch-sets.cpp b/biology/plink/files/patch-sets.cpp
deleted file mode 100644
index 4d773fb36db2..000000000000
--- a/biology/plink/files/patch-sets.cpp
+++ /dev/null
@@ -1,18 +0,0 @@
---- sets.cpp.orig	2013-11-16 17:06:29.000000000 +0100
-+++ sets.cpp	2013-11-16 17:07:12.000000000 +0100
-@@ -768,11 +768,11 @@
-       //////////////////////////////////////////////
-       // Reset original missing status
- 
--      vector<Individual*>::iterator i = PP->sample.begin();
--      while ( i != PP->sample.end() )
-+      vector<Individual*>::iterator ipp = PP->sample.begin();
-+      while ( ipp != PP->sample.end() )
- 	{
--	  (*i)->missing = (*i)->flag;
--	  ++i;
-+	  (*ipp)->missing = (*ipp)->flag;
-+	  ++ipp;
- 	}
- 
-       ////////////////////////////////////////////////
diff --git a/biology/plink/pkg-descr b/biology/plink/pkg-descr
deleted file mode 100644
index cc38aca9112e..000000000000
--- a/biology/plink/pkg-descr
+++ /dev/null
@@ -1,5 +0,0 @@
-PLINK is a free, open-source whole genome association analysis toolset,
-designed to perform a range of basic, large-scale analyses in a
-computationally efficient manner.
-
-WWW: http://pngu.mgh.harvard.edu/~purcell/plink/
diff --git a/biology/ssaha/Makefile b/biology/ssaha/Makefile
deleted file mode 100644
index a80bfbee2f64..000000000000
--- a/biology/ssaha/Makefile
+++ /dev/null
@@ -1,44 +0,0 @@
-# Created by: Fernan Aguero <fernan@iib.unsam.edu.ar>
-# $FreeBSD$
-
-PORTNAME=	ssaha
-PORTVERSION=	3.1c
-PORTREVISION=	6
-CATEGORIES=	biology
-MASTER_SITES=	ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha/
-DISTNAME=	${PORTNAME}_v${PORTVERSION:S/.//}
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	Very fast matching and alignment of DNA sequences
-
-BROKEN=		No public distfiles
-DEPRECATED=	Broken for more than 6 months
-EXPIRATION_DATE=	2018-06-06
-
-NO_WRKSUBDIR=	yes
-BUILD_WRKSRC=		${WRKSRC}/Binary
-
-USES=		gmake
-USE_GCC=	any
-MAKE_ENV=	CCC="${CXX}" OPTIM="${CXXFLAGS}" THREAD_LIB="-pthread"
-MAKEFILE=	makefile
-ALL_TARGET=	ssaha
-
-PLIST_FILES=	bin/ssaha %%DATADIR%%/testSSAHA.csh \
-		${DATA_FILES:S,^,%%DATADIR%%/,}
-
-DATA_FILES=	test.fasta test_extract.fasta test_filter.fail \
-		test_filter.fastq test_protein.fasta README
-
-do-install:
-	(cd ${BUILD_WRKSRC} && ${INSTALL_PROGRAM} ssaha \
-		${STAGEDIR}${PREFIX}/bin)
-	@${MKDIR} ${STAGEDIR}${DATADIR}
-	(cd ${BUILD_WRKSRC} && ${INSTALL_SCRIPT} testSSAHA.csh \
-		${STAGEDIR}${DATADIR})
-.for i in ${DATA_FILES}
-	(cd ${BUILD_WRKSRC} && ${INSTALL_DATA} ${i} \
-		${STAGEDIR}${DATADIR})
-.endfor
-
-.include <bsd.port.mk>
diff --git a/biology/ssaha/distinfo b/biology/ssaha/distinfo
deleted file mode 100644
index f2cb833259a0..000000000000
--- a/biology/ssaha/distinfo
+++ /dev/null
@@ -1,2 +0,0 @@
-SHA256 (ssaha_v31c.tar.gz) = 63fa38ccd2725db6ba10881f8cc94d899afd2eba9c2f6436223d9284c5abfced
-SIZE (ssaha_v31c.tar.gz) = 251510
diff --git a/biology/ssaha/files/patch-GlobalDefinitions.cpp b/biology/ssaha/files/patch-GlobalDefinitions.cpp
deleted file mode 100644
index dbf6ed8a038f..000000000000
--- a/biology/ssaha/files/patch-GlobalDefinitions.cpp
+++ /dev/null
@@ -1,11 +0,0 @@
---- ./Global/GlobalDefinitions.cpp.orig	2004-03-01 13:51:28.000000000 -0300
-+++ ./Global/GlobalDefinitions.cpp	2008-06-12 15:39:31.000000000 -0300
-@@ -119,7 +119,7 @@
- MakeIntoWord::MakeIntoWord( int bitsPerSymbol, const char* tt ):
- bitsPerSymbol_( bitsPerSymbol ), tt_( tt ) 
- {
--  for ( unsigned int i(0) ; i < (1<<bitsPerSymbol_) ; ++i )
-+  for ( unsigned int i(0) ; i < ( unsigned int )(1<<bitsPerSymbol_) ; ++i )
-   {
-     map_.insert( make_pair( (static_cast<char>(tolower(tt[i]))),i ) );
-     map_.insert( make_pair( (static_cast<char>(toupper(tt[i]))),i ) );
diff --git a/biology/ssaha/files/patch-GlobalDefinitions.h b/biology/ssaha/files/patch-GlobalDefinitions.h
deleted file mode 100644
index 49d686d331b5..000000000000
--- a/biology/ssaha/files/patch-GlobalDefinitions.h
+++ /dev/null
@@ -1,92 +0,0 @@
---- ./Global/GlobalDefinitions.h.orig	2004-03-01 13:51:28.000000000 -0300
-+++ ./Global/GlobalDefinitions.h	2008-06-12 15:39:31.000000000 -0300
-@@ -79,7 +79,8 @@
- #include <map>
- #include <utility>
- #include <sys/types.h>
--#include <stdio.h>
-+#include <cstdio>
-+#include <cstring>
- #include <sys/file.h>
- #include <sys/mman.h>
- #include <sys/stat.h>
-@@ -726,8 +727,6 @@
- template <typename T> class Allocator
- {
- public:
--  typedef T MyType;
--
-   Allocator( T** ptr, const string& name, ostream& monStream=cerr ) : 
-     ptr_(ptr), name_(name), size_(0), isAllocated_(false), 
-     monStream_( monStream )
-@@ -788,32 +787,34 @@
-  
-   virtual void allocate( unsigned long size )
-   {
--    size_=size;
--    (*ptr_)=new T[size_];
--    isAllocated_=true;
-+    Allocator<T>::size_=size;
-+    (*Allocator<T>::ptr_)=new T[Allocator<T>::size_];
-+    Allocator<T>::isAllocated_=true;
-   }
- 
-   virtual void allocateAndZero( unsigned long size ) 
-   {
-     const unsigned char zero(0);
-     allocate(size);
--    memset( (void*)(*ptr_), zero, size_*sizeof(MyType) );
-+    memset( (void*)(*Allocator<T>::ptr_), zero, Allocator<T>::size_*sizeof(T) );
-   }
-   virtual void load( unsigned long size )
-   {
-     allocate(size);
--    loadFromFile( name_, (char*)(*ptr_), size_*sizeof(MyType), monStream_ );
-+    loadFromFile( Allocator<T>::name_, (char*)(*Allocator<T>::ptr_),
-+        Allocator<T>::size_*sizeof(T), Allocator<T>::monStream_ );
-   }
-   virtual void save()
-   {
--    saveToFile( name_, (char*)(*ptr_), size_*sizeof(MyType), monStream_ );
-+    saveToFile( Allocator<T>::name_, (char*)(*Allocator<T>::ptr_),
-+        Allocator<T>::size_*sizeof(T), Allocator<T>::monStream_ );
-   }
- 
-   virtual void deallocate()
-   {
--    if (!isAllocated_) return;
--    delete [] (*ptr_);
--    isAllocated_=false;
-+    if (!Allocator<T>::isAllocated_) return;
-+    delete [] (*Allocator<T>::ptr_);
-+    Allocator<T>::isAllocated_=false;
-   }
- protected:
- };
-@@ -892,7 +893,7 @@
-     if (isAllocated_) return;
-     mode_ = MemoryMapper::createMap;
-     size_ = size;
--    (*ptr_) = (T*) linkToMap(mode_,name_,size_*sizeof(MyType));
-+    (*ptr_) = (T*) linkToMap(mode_,name_,size_*sizeof(T));
-     isAllocated_ = true;
-   }
- 
-@@ -908,7 +909,7 @@
-     if (isAllocated_) return;
-     mode_ = MemoryMapper::readMap;
-     size_ = size;
--    (*ptr_) = (T*) linkToMap(mode_,name_,size_*sizeof(MyType));
-+    (*ptr_) = (T*) linkToMap(mode_,name_,size_*sizeof(T));
-     isAllocated_ = true;
-   }
- 
-@@ -921,7 +922,7 @@
-   virtual void deallocate()
-   {
-     if (!isAllocated_) return;
--    if(munmap((caddr_t)(*ptr_), size_*sizeof(MyType)) < 0)
-+    if(munmap((caddr_t)(*ptr_), size_*sizeof(T)) < 0)
-       perror("unmap error"); // don't throw - called from destructor!
-     close(fileDesc_);
-     if (mode_.deleteFileOnExit) shm_unlink(name_.c_str());
diff --git a/biology/ssaha/files/patch-HashTable.cpp b/biology/ssaha/files/patch-HashTable.cpp
deleted file mode 100644
index c57e3745c639..000000000000
--- a/biology/ssaha/files/patch-HashTable.cpp
+++ /dev/null
@@ -1,20 +0,0 @@
---- ./HashTable/HashTable.cpp.orig	2004-03-01 13:51:28.000000000 -0300
-+++ ./HashTable/HashTable.cpp	2008-06-12 15:39:31.000000000 -0300
-@@ -265,7 +265,7 @@
- void HashTable::countWords( SequenceAdapter& thisSeq )
- {
- 
--   for ( int j(0) ; j < thisSeq.size() ; ++ j )
-+   for ( WordSequence::size_type j(0) ; j < thisSeq.size() ; ++ j )
-    {
-      // only count words that have not been flagged
-      pWordPositionInHitList_[(thisSeq[j]&(~gCursedWord))]
-@@ -284,7 +284,7 @@
-       // NB We stop at the last but one element of the 
-       // sequence (as the last isn't a full word)
- 
--   for ( int j(0) ; j < thisSeq.size() ; ++ j )
-+   for ( WordSequence::size_type j(0) ; j < thisSeq.size() ; ++ j )
-       {
- 	thisWord = thisSeq[j];
- 	// only hash words that have not been flagged
diff --git a/biology/ssaha/files/patch-HashTableGeneric.cpp b/biology/ssaha/files/patch-HashTableGeneric.cpp
deleted file mode 100644
index 0d1ffb441303..000000000000
--- a/biology/ssaha/files/patch-HashTableGeneric.cpp
+++ /dev/null
@@ -1,48 +0,0 @@
---- ./HashTable/HashTableGeneric.cpp.orig	2005-06-21 05:48:27.000000000 -0300
-+++ ./HashTable/HashTableGeneric.cpp	2008-06-12 15:39:31.000000000 -0300
-@@ -63,18 +63,18 @@
- ( ostream& monitoringStream,
-   const string& name,
-   Allocator<PositionInHitList>& arrayAllocator ) : 
--  isInitialized_( false ), 
--  monitoringStream_( monitoringStream ),
-   name_( name ),
--  bitsPerSymbol_( gBaseBits ), // default: may be overwritten in subclass ctor
-+  isInitialized_( false ), 
-   maxNumHits_( defaultMaxNumHits ),
-+  bitsPerSymbol_( gBaseBits ), // default: may be overwritten in subclass ctor
-   hitListFormat_( gNotSpecified ),
-+  monitoringStream_( monitoringStream ),
-   pArrayAllocator_
-   ( arrayAllocator.clone(&pWordPositionInHitList_,
- 			 name+(string)".head",
- 			 monitoringStream_) ),
--  pSequenceSizes_(NULL),
--  pNameReader_(NULL)
-+  pNameReader_(NULL),
-+  pSequenceSizes_(NULL)
-   {
-     monitoringStream_ << "constructing HashTableGeneric\n";
-     if (name_=="")
-@@ -290,7 +290,7 @@
-   WordSequence thisSeq;
-     
-   // NB sequences are numbered 1...n not 0...n-1
--  for ( unsigned int i(1); i <= numSeqs ; i++ )
-+  for ( int i(1); i <= numSeqs ; i++ )
-   {
-     if( sequenceReader.getNextSequence( thisSeq, wordLength_) == -1 ) 
-     {
-@@ -973,10 +973,10 @@
- 
- SequenceAdapterWithOverlap::SequenceAdapterWithOverlap
- ( int bitsPerSymbol, int wordLength, int stepLength ) :
-+SequenceAdapter(),
- bitsPerSymbol_( bitsPerSymbol ), 
- wordLength_( wordLength ), 
--stepLength_( stepLength ),
--SequenceAdapter() 
-+stepLength_( stepLength )
- {
- 
-   maskLeft_  = new Word[ wordLength_ ];
diff --git a/biology/ssaha/files/patch-HashTablePacked.cpp b/biology/ssaha/files/patch-HashTablePacked.cpp
deleted file mode 100644
index 6efc6d24bd77..000000000000
--- a/biology/ssaha/files/patch-HashTablePacked.cpp
+++ /dev/null
@@ -1,29 +0,0 @@
---- ./HashTable/HashTablePacked.cpp.orig	2004-03-01 13:51:29.000000000 -0300
-+++ ./HashTable/HashTablePacked.cpp	2008-06-12 15:39:31.000000000 -0300
-@@ -132,7 +132,7 @@
- void HashTablePacked::countWords( SequenceAdapter& thisSeq )
- {
- 
--   for ( int j(0) ; j < thisSeq.size() ; ++ j )
-+   for ( WordSequence::size_type j(0) ; j < thisSeq.size() ; ++ j )
-    {
-      // only count words that have not been flagged
-      pWordPositionInHitList_[(thisSeq[j]&(~gCursedWord))]
-@@ -151,7 +151,7 @@
-   // NB We stop at the last but one element of the 
-   // sequence (as the last isn't a full word)
- 
--   for ( int j(0) ; j < thisSeq.size() ; ++ j )
-+   for ( WordSequence::size_type j(0) ; j < thisSeq.size() ; ++ j )
-       {
- 	thisWord = thisSeq[j];
- 
-@@ -200,7 +200,7 @@
-       for ( WordSequence::const_iterator thisWord(seq.begin());
-             thisWord != last ; ++thisWord )
-       {
--	int oldSize(packedHits.size()); // %%%%%%
-+//	int oldSize(packedHits.size()); // %%%%%%
- 	matchWordDeluxe( *thisWord, packedHits, baseOffset );
- 	//	cout << printResidue(*thisWord, wordLength_) << " "
- 	//  << packedHits.size()-oldSize;
diff --git a/biology/ssaha/files/patch-HashTablePacked.h b/biology/ssaha/files/patch-HashTablePacked.h
deleted file mode 100644
index c00860d1bbfd..000000000000
--- a/biology/ssaha/files/patch-HashTablePacked.h
+++ /dev/null
@@ -1,16 +0,0 @@
---- ./HashTable/HashTablePacked.h.orig	2004-03-01 13:51:29.000000000 -0300
-+++ ./HashTable/HashTablePacked.h	2008-06-12 15:39:31.000000000 -0300
-@@ -236,11 +236,11 @@
-     HashTableView<PositionPacked,HashTablePacked>
-     (monitoringStream, name, hitListAllocator, arrayAllocator),
-     wordNum_(0),
-+    numRepeats_(0),
-+    substituteThreshold_(0),
-     pMatchSequence_(&HashTablePacked::matchSequenceStandard),
-     pMatchWord_(&HashTablePacked::matchWordStandard),
-     pGenerateSubstitutes_(&generateSubstitutesDNA),
--    numRepeats_(0),
--    substituteThreshold_(0),
-     sorter_(4,(sizeof(PositionPacked)*8)/4)
-     {
-       hitListFormat_ = g32BitPacked;
diff --git a/biology/ssaha/files/patch-HashTableTranslated.cpp b/biology/ssaha/files/patch-HashTableTranslated.cpp
deleted file mode 100644
index e4ab9af82423..000000000000
--- a/biology/ssaha/files/patch-HashTableTranslated.cpp
+++ /dev/null
@@ -1,77 +0,0 @@
---- ./HashTable/HashTableTranslated.cpp.orig	2004-03-01 13:51:29.000000000 -0300
-+++ ./HashTable/HashTableTranslated.cpp	2008-06-12 15:39:31.000000000 -0300
-@@ -50,9 +50,9 @@
-  		   Allocator<PositionPacked>& hitListAllocator,
- 		   Allocator<PositionInHitList>& arrayAllocator 
- 		   ):
--  queryFrame_(0),
-   HashTablePacked( monitoringStream, name, 
--		   hitListAllocator, arrayAllocator  ) 
-+		   hitListAllocator, arrayAllocator  ), 
-+  queryFrame_(0)
- {
-   hitListFormat_ = g32BitPackedProtein;
-   bitsPerSymbol_ = gResidueBits;
-@@ -135,12 +135,12 @@
-   Allocator<PositionPacked>& hitListAllocator,
-   Allocator<PositionInHitList>& arrayAllocator 
-   ):
-+  HashTablePacked( monitoringStream, name, 
-+		     hitListAllocator, arrayAllocator  ),
-+  codonEncoder_(5),
-   queryFrame_(0),
-   queryMult_(1),
--  codonEncoder_(5),
--  pMatchSequence_( &HashTablePackedProtein::matchSequenceProtein ),
--  HashTablePacked( monitoringStream, name, 
--		     hitListAllocator, arrayAllocator  ) 
-+  pMatchSequence_( &HashTablePackedProtein::matchSequenceProtein )
- {
-     hitListFormat_ = g32BitPackedProtein;
-     bitsPerSymbol_ = gResidueBits;
-@@ -249,14 +249,14 @@
-   Allocator<PositionPacked>& hitListAllocator,
-   Allocator<PositionInHitList>& arrayAllocator
-   ) :
-+  HashTableGeneric( monitoringStream, name, arrayAllocator ),
-   hashFwd_( monitoringStream, name+(string)"_fwd", 
- 	    hitListAllocator, arrayAllocator ),
-   hashRev_( monitoringStream, name+(string)"_rev", 
- 	    hitListAllocator, arrayAllocator ),
-   pHash_(&hashFwd_),
-   codonEncoder_(5),
--  pMatchSequence_( &HashTableTranslated::matchSequenceProtein ),
--  HashTableGeneric( monitoringStream, name, arrayAllocator ) 
-+  pMatchSequence_( &HashTableTranslated::matchSequenceProtein )
- {
-   bitsPerSymbol_=gResidueBits;
-   hitListFormat_ = gTranslated;
-@@ -344,8 +344,8 @@
- 
-     // Change encoding mode
-     SequenceReaderModeFlagReplace mode('X');
--    assert(ttCodon['X']==ttProtein['X']);
--    assert(ttCodon['X']!=nv);
-+    assert(ttCodon[(int)'X']==ttProtein[(int)'X']);
-+    assert(ttCodon[(int)'X']!=nv);
-     codonEncoder_.changeMode( &mode );
- 
- 
-@@ -418,7 +418,7 @@
-   seq->link( translatedSeq );
- 
-   // NB sequences are numbered 1...n not 0...n-1
--  for ( unsigned int i(1); i <= numSeqs ; i++ )
-+  for ( int i(1); i <= numSeqs ; i++ )
-   {
-     //    cout << "hashing sequence " << i << endl;
-     if( sequenceReader.getNextSequence( thisSeq, eDNAWordSizeForHashing) == -1 ) 
-@@ -520,7 +520,7 @@
- int HashTableTranslated::getHitTypeSize( void ) const 
- {
-   assert(1==0);
--  return NULL;
-+  return 0;
- }
- void HashTableTranslated::allocateHitList( unsigned long size ) 
- {
diff --git a/biology/ssaha/files/patch-MatchAligner.cpp b/biology/ssaha/files/patch-MatchAligner.cpp
deleted file mode 100644
index e7420b1ddec4..000000000000
--- a/biology/ssaha/files/patch-MatchAligner.cpp
+++ /dev/null
@@ -1,94 +0,0 @@
---- ./QueryManager/MatchAligner.cpp.orig	2004-03-01 13:51:29.000000000 -0300
-+++ ./QueryManager/MatchAligner.cpp	2008-06-12 15:39:31.000000000 -0300
-@@ -53,13 +53,13 @@
-   bool reverseQueryCoords,
-   bool doAlignment,
-   ostream& outputStream ):
-+  pAlign_(pAlign),
-+  outputStream_(outputStream),
-   querySource_(querySource), 
-   subjectSource_(subjectSource),
--  pAlign_(pAlign),
-   //  numCols_(numCols),
-   reverseQueryCoords_(reverseQueryCoords),
--  doAlignment_(doAlignment),
--  outputStream_(outputStream)
-+  doAlignment_(doAlignment)
- {
- } // ~MatchTaskAlign::MatchTaskAlign
- 
-@@ -194,10 +194,10 @@
-   int bandExtension,
-   ScoreTable* pTable,
-   ostream& outputStream ) :
-+  outputStream_(outputStream),
-   numCols_(numCols),
-   bandExtension_(bandExtension),
--  pTable_(pTable),
--  outputStream_(outputStream)
-+  pTable_(pTable)
- {
-   pBufSeq1_= new char [numCols+1];
-   pBufSeq2_= new char [numCols+1];
-@@ -563,17 +563,17 @@
-       //  cout << int ( ttDNA[ *(pChar++ ] << 4
-       //     | (ttDNA[ *(pChar++) ] << 2)
-       //     | ttDNA[ *(pChar++) ] ) << endl; 
--      if (    (ttDNA[ *(pChar)   ]==nv)
--           || (ttDNA[ *(pChar+1) ]==nv)
--           || (ttDNA[ *(pChar+2) ]==nv) )
-+      if (    (ttDNA[ (int) *(pChar)   ]==nv)
-+           || (ttDNA[ (int) *(pChar+1) ]==nv)
-+           || (ttDNA[ (int) *(pChar+2) ]==nv) )
-       {	
- 	*i='X';
-       } // ~if   
-       else
-       {
--	*i= gResidueNames[ ttCodon[ ttDNA[ *(pChar) ] << 4
--				  | ttDNA[ *(pChar+1) ] << 2
--				  | ttDNA[ *(pChar+2) ] ] ];
-+	*i= gResidueNames[ ttCodon[ ttDNA[ (int) *(pChar) ] << 4
-+				  | ttDNA[ (int) *(pChar+1) ] << 2
-+				  | ttDNA[ (int) *(pChar+2) ] ] ];
-       } // ~else
- 
-     } // ~for i
-@@ -983,7 +983,7 @@
- 
- void print( PathMatrix<PathType>& p )
- {
--  for (int i(0); i< p.front().size(); i++)
-+  for (size_t i(0); i< p.front().size(); i++)
-   {
-     for (vector<vector<PathType> >::iterator j(p.begin());
- 	 j!=p.end();++j)
-@@ -1249,16 +1249,16 @@
-   bandWidth_(p2Size-p1Size+1),
-   bandLength_(p1Size+1),
-   colSize_(p2Size-p1Size+1+(2*bandExtension_)),
--  fillCell_(),
-   finalFrame1_(p1FinalFrame),
-   finalFrame2_(p2FinalFrame),
-   numFrames1_((p1Trans[1]==NULL)?1:gNumReadingFrames),
-   numFrames2_((p2Trans[1]==NULL)?1:gNumReadingFrames),
-+  fillCell_(),
-+  getScore_(scoreTable),
-   v1_(colSize_, veryBadScore3D ), 
-   v2_(colSize_, veryBadScore3D ),
-   pLast_(&v1_),
--  pCurrent_(&v2_),
--  getScore_(scoreTable)
-+  pCurrent_(&v2_)
- {
-   
-   p1_[0] = p1Trans[0];
-@@ -1287,7 +1287,7 @@
- {
- 
-   //  ScoreType lastScore, prevFrameScore1, prevFrameScore2;
--  int i,j,k,l;
-+  int i,j;
- 
-   matrix.resize(bandLength_, vector<PathType3D>(colSize_) );
- 
diff --git a/biology/ssaha/files/patch-MatchAligner.h b/biology/ssaha/files/patch-MatchAligner.h
deleted file mode 100644
index 1eafad595c91..000000000000
--- a/biology/ssaha/files/patch-MatchAligner.h
+++ /dev/null
@@ -1,33 +0,0 @@
---- ./QueryManager/MatchAligner.h.orig	2004-03-01 13:51:29.000000000 -0300
-+++ ./QueryManager/MatchAligner.h	2008-06-12 15:39:31.000000000 -0300
-@@ -315,13 +315,13 @@
- 
-   static char getCodon( const char* pChar )
-   {
--    return (  (    (ttDNA[ *pChar ] ==nv)
--		   || (ttDNA[ *(pChar+1) ] ==nv)
--		   || (ttDNA[ *(pChar+2) ] ==nv) )
-+    return (  (    (ttDNA[ (int) *pChar ] ==nv)
-+		   || (ttDNA[ (int) *(pChar+1) ] ==nv)
-+		   || (ttDNA[ (int) *(pChar+2) ] ==nv) )
- 	      ? 'X'
--	      : gResidueNames[ ttCodon[ ttDNA[ *(pChar) ] << 4
--				      | ttDNA[ *(pChar+1) ] << 2
--				      | ttDNA[ *(pChar+2) ] ] ] );
-+	      : gResidueNames[ ttCodon[ ttDNA[ (int) *(pChar) ] << 4
-+				      | ttDNA[ (int) *(pChar+1) ] << 2
-+				      | ttDNA[ (int) *(pChar+2) ] ] ] );
-   } // ~getCodon
- 
- 
-@@ -519,8 +519,8 @@
-   : public vector<vector<PATH_TYPE> >
- {
- public:
--  typedef pair<vector<vector<PATH_TYPE> >::iterator,
--    vector<PATH_TYPE>::iterator> CellIterator;
-+  typedef pair<typename vector<vector<PATH_TYPE> >::iterator,
-+    typename vector<PATH_TYPE>::iterator> CellIterator;
- 
-   template<class MATRIX_FILLER> ScoreType fillIn( MATRIX_FILLER& doMatrix )
-   {
diff --git a/biology/ssaha/files/patch-MatchStore.h b/biology/ssaha/files/patch-MatchStore.h
deleted file mode 100644
index 076639489869..000000000000
--- a/biology/ssaha/files/patch-MatchStore.h
+++ /dev/null
@@ -1,54 +0,0 @@
---- ./QueryManager/MatchStore.h.orig	2004-03-01 13:51:29.000000000 -0300
-+++ ./QueryManager/MatchStore.h	2008-06-12 15:39:31.000000000 -0300
-@@ -93,20 +93,20 @@
-   virtual SequenceNumber getSubjectNum( void ) const 
-     { return subjectNum_; }
-   //  virtual inline string  getSubjectName( void ) const;
--  virtual inline const char*  getSubjectName( void ) const;
-+  virtual const char*  getSubjectName( void ) const;
-   virtual SequenceOffset getSubjectStart( void ) const 
-     { return subjectStart_; }
-   virtual SequenceOffset getSubjectEnd( void ) const 
-     { return subjectEnd_; }
- 
--  virtual inline SequenceNumber getQueryNum( void ) const;
--  virtual inline string         getQueryName( void ) const;
-+  virtual SequenceNumber getQueryNum( void ) const;
-+  virtual string         getQueryName( void ) const;
-   virtual SequenceOffset getQueryStart( void ) const 
-     { return queryStart_; }
-   virtual SequenceOffset getQueryEnd( void ) const 
-     { return queryEnd_; }
-   
--  virtual inline int  getQuerySize( void ) const; 
-+  virtual int  getQuerySize( void ) const; 
-   virtual int  getNumBases(void ) const 
-     { return numBases_; }
-   virtual bool isQueryForward( void ) const 
-@@ -127,7 +127,6 @@
-              SequenceOffset subjectEnd,
-              bool isQueryForward,
-              bool isSubjectForward ):
--    myStore_( myStore ),
-     subjectNum_( subjectNum ),  
-     numBases_( numBases ),  
-     queryStart_( queryStart ),
-@@ -135,7 +134,8 @@
-     subjectStart_( subjectStart ),
-     subjectEnd_( subjectEnd ),
-     isQueryForward_( isQueryForward ),
--    isSubjectForward_( isSubjectForward ){}
-+    isSubjectForward_( isSubjectForward ),
-+    myStore_( myStore )   {}
- 
-   SequenceNumber subjectNum_;
-   SequenceOffset numBases_;
-@@ -444,7 +444,7 @@
-   ( 
-     unsigned int maxToSort = 1<<30,
-     double partialThreshold = 0.0
--  ) : sorter_(), maxToSort_(maxToSort), partialThreshold_(partialThreshold) {}
-+  ) : maxToSort_(maxToSort), partialThreshold_(partialThreshold), sorter_()  {}
-   // TBD should be virtual???
-   void operator()(MatchStore& store )
-   {
diff --git a/biology/ssaha/files/patch-MatchStoreGapped.h b/biology/ssaha/files/patch-MatchStoreGapped.h
deleted file mode 100644
index 7252f06a6ad8..000000000000
--- a/biology/ssaha/files/patch-MatchStoreGapped.h
+++ /dev/null
@@ -1,25 +0,0 @@
---- ./QueryManager/MatchStoreGapped.h.orig	2004-03-01 13:51:29.000000000 -0300
-+++ ./QueryManager/MatchStoreGapped.h	2008-06-12 15:39:31.000000000 -0300
-@@ -57,7 +57,8 @@
- {
-  public:
-   MatchAlgorithm( int numRepeats ) : 
--    numRepeats_( numRepeats ), sortNeeded_(true) {}
-+    sortNeeded_(true), numRepeats_( numRepeats )  {}
-+  virtual ~MatchAlgorithm() {};
-   void operator()  
-     ( WordSequence& querySeq, 
-       MatchAdder& addMatch, 
-@@ -82,10 +83,10 @@
-  public:
-   MatchAlgorithmGapped
-     ( int maxGap, int maxInsert, int minToProcess, int numRepeats ):
-+    MatchAlgorithm( numRepeats ),
-     maxGap_( maxGap ),
-     maxInsert_( maxInsert ), 
--    minToProcess_( minToProcess ),
--    MatchAlgorithm( numRepeats )
-+    minToProcess_( minToProcess )
-     {}
- 
-   virtual void generateMatches
diff --git a/biology/ssaha/files/patch-MatchStoreUngapped.h b/biology/ssaha/files/patch-MatchStoreUngapped.h
deleted file mode 100644
index f71815fa673c..000000000000
--- a/biology/ssaha/files/patch-MatchStoreUngapped.h
+++ /dev/null
@@ -1,13 +0,0 @@
---- ./QueryManager/MatchStoreUngapped.h.orig	2004-03-01 13:51:29.000000000 -0300
-+++ ./QueryManager/MatchStoreUngapped.h	2008-06-12 15:39:31.000000000 -0300
-@@ -60,8 +60,8 @@
-  public:
-   MatchAlgorithmUngapped
-     ( int minToProcess, int numRepeats ):
--    minToProcess_( minToProcess ),
--    MatchAlgorithm( numRepeats )
-+    MatchAlgorithm( numRepeats ),
-+    minToProcess_( minToProcess )
-     {}
- 
-   virtual void generateMatches
diff --git a/biology/ssaha/files/patch-QueryManager.cpp b/biology/ssaha/files/patch-QueryManager.cpp
deleted file mode 100644
index bb80ea676c1d..000000000000
--- a/biology/ssaha/files/patch-QueryManager.cpp
+++ /dev/null
@@ -1,54 +0,0 @@
---- ./QueryManager/QueryManager.cpp.orig	2004-03-01 13:51:29.000000000 -0300
-+++ ./QueryManager/QueryManager.cpp	2008-06-12 15:39:31.000000000 -0300
-@@ -164,8 +164,8 @@
- // MatchPolicy member function definitions
- 
- MatchPolicy::MatchPolicy( HashTableGeneric& subjectTable ) :
--  subjectTable_( subjectTable ), 
--  queryWordLength_( subjectTable.getWordLength() ) 
-+  queryWordLength_( subjectTable.getWordLength() ),
-+  subjectTable_( subjectTable )
- {}
- 
- 
-@@ -203,8 +203,8 @@
- 
- MatchPolicyProteinProtein::MatchPolicyProteinProtein
- ( HashTablePackedProtein& subjectTable ) :
--subjectTable_( subjectTable ),
--MatchPolicy( subjectTable )
-+MatchPolicy( subjectTable ),
-+subjectTable_( subjectTable )
- {
- 
-   subjectTable_.setQueryProtein();
-@@ -386,9 +386,9 @@
-   QueryManager::QueryManager
-   ( SequenceReader& querySeqs,  
-     HashTableGeneric& subjectSeqs, ostream& monitoringStream ) :
--   queryReader_( querySeqs ), 
-    subjectTable_(  subjectSeqs ), 
--   monitoringStream_( monitoringStream )
-+   monitoringStream_( monitoringStream ),
-+   queryReader_( querySeqs ) 
-    {
-      monitoringStream_ << "constructing QueryManager\n";
- 
-@@ -518,7 +518,7 @@
- 
-       task( store );
- 
--      if ( queryReader_.getLastSequenceNumber() == queryEnd ) break;
-+      if ( (int)queryReader_.getLastSequenceNumber() == queryEnd ) break;
- 
-       // clear the query sequence ready to read in next query
-       querySeqFwd.clear();
-@@ -530,7 +530,7 @@
-     } // ~while
-     while ( numBasesInLast != -1 );
- 
--    if (    ( queryReader_.getLastSequenceNumber() < queryEnd  )
-+    if (    ( (int)queryReader_.getLastSequenceNumber() < queryEnd  )
-          && ( queryEnd != - 1 ) )
-     {
-       monitoringStream_ << "Info: requested final sequence (" << queryEnd
diff --git a/biology/ssaha/files/patch-QueryManager.h b/biology/ssaha/files/patch-QueryManager.h
deleted file mode 100644
index fef80e7b3865..000000000000
--- a/biology/ssaha/files/patch-QueryManager.h
+++ /dev/null
@@ -1,19 +0,0 @@
---- ./QueryManager/QueryManager.h.orig	2004-03-01 13:51:29.000000000 -0300
-+++ ./QueryManager/QueryManager.h	2008-06-12 15:39:31.000000000 -0300
-@@ -145,6 +145,7 @@
-     //    readFrame_(0), 
-     pStore_(NULL), 
-     subjectTable_( subjectTable ) {}
-+  virtual ~MatchAdder() {};
-   virtual void operator()(  SequenceNumber subjectNum,
- 			    SequenceOffset numBases,
- 			    SequenceOffset queryStart,
-@@ -172,7 +173,7 @@
- {
- public:
-   MatchAdderImp( HashTableGeneric& subjectTable ) : 
--    lastSubjectNum_(0), name_(), MatchAdder( subjectTable ) {}
-+    MatchAdder( subjectTable ), name_(), lastSubjectNum_(0)  {}
-     virtual void operator()(  SequenceNumber subjectNum,
- 				     SequenceOffset numBases,
- 				     SequenceOffset queryStart,
diff --git a/biology/ssaha/files/patch-README b/biology/ssaha/files/patch-README
deleted file mode 100644
index e1a8461090b7..000000000000
--- a/biology/ssaha/files/patch-README
+++ /dev/null
@@ -1,13 +0,0 @@
---- ./Binary/README.orig	2004-08-25 11:35:58.000000000 -0300
-+++ ./Binary/README	2008-06-12 15:39:31.000000000 -0300
-@@ -34,6 +34,10 @@
- 
- Patched for linux/g++3.2.2 25/8/4 AWS.
- 
-+This version was patched for Linux/GCC 4.0.2 and Mac OS X/GCC 4.0.1 by
-+Conrad Halling on 26 January 2006. See http://www.bifx.org/SSAHA/index.html
-+for more information.
-+
- 1. To compile the main ssaha executable
- 
- make ssaha
diff --git a/biology/ssaha/files/patch-SSAHAMain.cpp b/biology/ssaha/files/patch-SSAHAMain.cpp
deleted file mode 100644
index e0e078386263..000000000000
--- a/biology/ssaha/files/patch-SSAHAMain.cpp
+++ /dev/null
@@ -1,57 +0,0 @@
---- ./Global/SSAHAMain.cpp.orig	2004-03-01 14:12:38.000000000 -0300
-+++ ./Global/SSAHAMain.cpp	2008-06-12 15:39:31.000000000 -0300
-@@ -86,7 +86,8 @@
- Copyright (C) 2004 by Genome Research Limited\n\
- This software is released under the terms of version 2 of the GNU General\n\
- Public Licence, as published by the Free Software Foundation.\n\
--This is SSAHA Version 3.2, released 1st March 2004.\n\n";
-+This is SSAHA Version 3.2, released 1st March 2004,\n\
-+patched 26 January 2006.\n\n";
- 
-   Timer timeStamp;
- 
-@@ -623,7 +624,7 @@
-     {
-       pHashTable = new HashTablePacked( cerr, queryParams.saveName );
-       if (    ( queryParams.wordLength <= 0 )
--	      || ( queryParams.wordLength*gBaseBits > ( 8*sizeof(Word)) -1 ) )
-+	      || ( (size_t) queryParams.wordLength*gBaseBits > ( 8*sizeof(Word)) -1 ) )
-       {
- 	cerr << "Warning: word length (" << queryParams.wordLength 
- 	     << ") outside valid range (0 to " 
-@@ -656,7 +657,7 @@
-       } // ~if
- 
-       if (    ( queryParams.wordLength <= 0 )
--	      || ( queryParams.wordLength*gResidueBits > ( 8*sizeof(Word)) -1 ) )
-+	      || ( (size_t) queryParams.wordLength*gResidueBits > ( 8*sizeof(Word)) -1 ) )
-       {
- 	cerr << "Warning: word length (" << queryParams.wordLength 
- 	     << ") outside valid range (0 to " 
-@@ -782,7 +783,7 @@
-   cerr << "Info: would expect " << expectedNumHits 
-          << " hits per word for a random database of this size." << endl;
- 
--  queryParams.maxStore=1+(int)(expectedNumHits*queryParams.maxStore);
-+  queryParams.maxStore=(int)(expectedNumHits*queryParams.maxStore);
- 
-   cerr << "Info: will ignore hits on words that occur more than " 
-        << queryParams.maxStore << " times in the database." << endl;
-@@ -964,7 +965,7 @@ delete pQueryMode;
- 
-     } // ~else
- 
--    assert( pAligner!=false);
-+    assert(pAligner!=NULL);
- 
-     // ownership of *pAligner passes to *pPrintTask
-     pPrintTask = new MatchTaskAlign( *pQuery, *pSubjectSource, pAligner,
-@@ -1151,7 +1152,7 @@
-     } // ~if
-     dirent* dirEntry;
-     string entryName;
--    while( dirEntry = readdir(pDir) )
-+    while( 0 != ( dirEntry = readdir(pDir) ) )
-     {
-       entryName = (string) dirEntry->d_name;
-       if ((entryName == ".")||(entryName=="..")) continue;
diff --git a/biology/ssaha/files/patch-SSAHAMain.h b/biology/ssaha/files/patch-SSAHAMain.h
deleted file mode 100644
index 5cb9234f7c0f..000000000000
--- a/biology/ssaha/files/patch-SSAHAMain.h
+++ /dev/null
@@ -1,27 +0,0 @@
---- ./Global/SSAHAMain.h.orig	2004-03-01 13:51:28.000000000 -0300
-+++ ./Global/SSAHAMain.h	2008-06-12 15:39:31.000000000 -0300
-@@ -41,6 +41,7 @@
- #include <string>
- #include <iostream>
- #include <memory>
-+#include <cstdlib>
- class SequenceReaderMulti;
- class SequenceReader;
- class HashTable;
-@@ -131,7 +132,7 @@
-   -1,        // int    queryEnd; 
-   -1,        // int    wordLength;
-   -1,        // int    stepLength;
--  100000,    // int    maxToStore; 
-+  10000,     // int    maxToStore; 
-   1,         // int    minToPrint;
-   -1,        // int    maxGap;
-   0,         // int    maxInsert;
-@@ -174,6 +175,7 @@
- 
-   CommandLineArg( const string& nameLong, const string& nameShort ) :
-     nameLong_( nameLong ), nameShort_( nameShort ) {}
-+  virtual ~CommandLineArg() {};  // base class with virtual functions requires virtual constructor
-   // Is the current argument equal to 'my' argument name?
-   virtual bool isThisMe( const string& argName )
-   { 
diff --git a/biology/ssaha/files/patch-SequenceEncoder.cpp b/biology/ssaha/files/patch-SequenceEncoder.cpp
deleted file mode 100644
index 5832a96a40bb..000000000000
--- a/biology/ssaha/files/patch-SequenceEncoder.cpp
+++ /dev/null
@@ -1,75 +0,0 @@
---- ./SequenceReader/SequenceEncoder.cpp.orig	2004-03-01 13:51:29.000000000 -0300
-+++ ./SequenceReader/SequenceEncoder.cpp	2008-06-12 15:39:31.000000000 -0300
-@@ -54,10 +54,10 @@
-     ostream& monitoringStream):
-     monitoringStream_( monitoringStream ),
-     tt_(tt), sourceData_( sourceData ), bitsPerSymbol_(bitsPerSymbol),
-+    symbolMask_((1<<bitsPerSymbol)-1),
-     pState_( new SequenceReaderModeIgnore( monitoringStream ) ),
-     wordFlag_(0),
--    doubleBitShift_(bitsPerSymbol<<1),
--    symbolMask_((1<<bitsPerSymbol)-1)
-+    doubleBitShift_(bitsPerSymbol<<1)
-   //    numSymbolPairs_(wordLength>>1),
-   //   oddNumSymbols_(wordLength%1==1),
-   { 
-@@ -71,13 +71,13 @@
-   ett_( rhs.ett_ ),
-   sourceData_( rhs.sourceData_ ),
-   bitsPerSymbol_( rhs.bitsPerSymbol_ ),
-+  symbolMask_(rhs.symbolMask_),
-   wordLength_( rhs.wordLength_ ),
-     //  pSeq_( rhs.pSeq_ ),// don't want 2 encoders linking to same seq
-   pState_( rhs.pState_->clone() ),
-   wordFlag_(0),
-   //  numSymbolPairs_(rhs.numSymbolPairs_),
-   //  oddNumSymbols_(rhs.oddNumSymbols_),
--  symbolMask_(rhs.symbolMask_),
-   doubleBitShift_(rhs.doubleBitShift_)
-   {
-     monitoringStream_ << "copy constructing SequenceEncoder" << endl;
-@@ -218,7 +218,7 @@
-   {
-     pTemp = (uchar*)p;
-     //    cout << basesInLast << " doing odd char at end " << *pTemp << endl;
--    encodeChar( *p, thisWord, wordFlag_, basesInLast );
-+    encodeChar( *pTemp, thisWord, wordFlag_, basesInLast );
-   }
- 
-   pSeq_->setNumBasesInLast(basesInLast);
-@@ -453,7 +453,7 @@
- 
-     for( ; i!=lastWord ; ++i )
-     {
--      if (toCarry!=~0)
-+      if (toCarry!=(Word)~0)
-       (*pCodon++) = ( ((*i)&gCursedWord)|lastWordFlag )
- 	? flaggedChar
- 	: ( toCarry | (((*i) >> (4*gCodonBits + 2*gBaseBits))&maskBase ));
-@@ -488,7 +488,7 @@
- 
-     for( ; i!=lastWord ; ++i )
-     {
--      if (toCarry!=~0)
-+      if (toCarry!=(Word)~0)
-       (*pCodon++) = ( ((*i)&gCursedWord)|lastWordFlag )
- 	? flaggedChar
- 	: ( toCarry | (((*i) >> (4*gCodonBits + gBaseBits))&mask2Bases ));
-@@ -610,7 +610,7 @@
-     do
-     {
-       i--;
--      if (toCarry!=~0)
-+      if (toCarry!=(Word)~0)
-       (*pCodon++) = ( ((*i)&gCursedWord)|lastWordFlag )
- 	? flaggedChar
- 	: ( toCarry | ( ((*i) & mask2Bases ) << gBaseBits ) );
-@@ -650,7 +650,7 @@
-     do
-     {
-       i--;
--      if (toCarry!=~0)
-+      if (toCarry!=(Word)~0)
-       (*pCodon++) = ( ((*i)&gCursedWord)|lastWordFlag )
- 	? flaggedChar
- 	: ( toCarry | ( ((*i) & maskBase ) << (2*gBaseBits) ) );
diff --git a/biology/ssaha/files/patch-SequenceReader.cpp b/biology/ssaha/files/patch-SequenceReader.cpp
deleted file mode 100644
index 356c6e8363d9..000000000000
--- a/biology/ssaha/files/patch-SequenceReader.cpp
+++ /dev/null
@@ -1,20 +0,0 @@
---- ./SequenceReader/SequenceReader.cpp.orig	2004-03-01 13:51:29.000000000 -0300
-+++ ./SequenceReader/SequenceReader.cpp	2008-06-12 15:39:31.000000000 -0300
-@@ -179,7 +179,7 @@
- 
-   for ( ; i != reverseBuffer_.end() ; i++, j-- )
-   {
--    *i= reverseChar[ *j ];
-+    *i= reverseChar[ (int) *j ];
-     //    cout << "char: " << (int)*j << *j << " - " << (int)*i << *i << endl;
-   }
- 
-@@ -356,7 +356,7 @@
-       throw SSAHAException
- 	("Requested seq start exceeds requested seq end in SourceReaderIndex::extractSource");
-   } // ~if
--  else if (seqEnd>lastSourceSeq_.size() )
-+  else if (seqEnd>(int)lastSourceSeq_.size() )
-   {
-     cout << seqEnd << " " << lastSourceSeq_.size() << endl;
-       throw SSAHAException
diff --git a/biology/ssaha/files/patch-SequenceReader.h b/biology/ssaha/files/patch-SequenceReader.h
deleted file mode 100644
index c230fa08cbd8..000000000000
--- a/biology/ssaha/files/patch-SequenceReader.h
+++ /dev/null
@@ -1,11 +0,0 @@
---- ./SequenceReader/SequenceReader.h.orig	2004-03-01 13:51:29.000000000 -0300
-+++ ./SequenceReader/SequenceReader.h	2008-06-12 15:39:31.000000000 -0300
-@@ -264,6 +264,8 @@
-     pReader_( rhs.pReader_ ),
-     seqNum_( rhs.seqNum_ ) {}
- 
-+    // A virtual destructor is required because this is a base class.
-+    virtual ~SequenceReaderPrinter() {};
- 
-     SequenceReaderPrinter& operator()( SequenceNumber inSeqNum )
-     { 
diff --git a/biology/ssaha/files/patch-SequenceReaderFasta.cpp b/biology/ssaha/files/patch-SequenceReaderFasta.cpp
deleted file mode 100644
index eaf3a2a5477f..000000000000
--- a/biology/ssaha/files/patch-SequenceReaderFasta.cpp
+++ /dev/null
@@ -1,32 +0,0 @@
---- ./SequenceReader/SequenceReaderFasta.cpp.orig	2004-03-01 13:51:29.000000000 -0300
-+++ ./SequenceReader/SequenceReaderFasta.cpp	2008-06-12 15:39:31.000000000 -0300
-@@ -135,9 +135,9 @@
-     seqStopChar_( rhs.seqStopChar_ ),
-     pInputFileStream_( new ifstream( rhs.fileName_.c_str() ) ),
-     fileName_( rhs.fileName_.c_str() ),
--    seqPositions_( rhs.seqPositions_ ),
-     //   lastSourceSeqNum_(0),
--    pEncoder_( rhs.pEncoder_->clone() )
-+    pEncoder_( rhs.pEncoder_->clone() ),
-+    seqPositions_( rhs.seqPositions_ )
-   {
-     monitoringStream_ << "copy constructing SequenceReaderFile" << this 
- 		      << endl;
-@@ -603,7 +603,7 @@
-       throw SSAHAException
- 	("Requested seq start exceeds requested seq end in SequenceReaderFile::extractSource");
-   } // ~if
--  else if (seqEnd>lastSourceSeq_.size() )
-+  else if (seqEnd>(SequenceOffset)lastSourceSeq_.size() )
-   {
-       throw SSAHAException
- 	("Requested last byte exceeds end of seq in SequenceReaderFile::extractSource");
-@@ -628,7 +628,7 @@
-   computeNumSequencesInFile(); // ensure have scanned to end of file
-   fileFile << fileName_ << endl;
-   SeqIndexInfo* pIndex = new SeqIndexInfo[seqPositions_.size()];
--  for (int i(0) ; i < seqPositions_.size() ; i++)
-+  for (unsigned int i(0) ; i < seqPositions_.size() ; i++)
-   {
-     pIndex[i].fileNum=fileNumber;
-     pIndex[i].seqPos=seqPositions_[i];
diff --git a/biology/ssaha/files/patch-SequenceReaderFasta.h b/biology/ssaha/files/patch-SequenceReaderFasta.h
deleted file mode 100644
index a2988fbb91d8..000000000000
--- a/biology/ssaha/files/patch-SequenceReaderFasta.h
+++ /dev/null
@@ -1,11 +0,0 @@
---- ./SequenceReader/SequenceReaderFasta.h.orig	2004-03-01 13:51:29.000000000 -0300
-+++ ./SequenceReader/SequenceReaderFasta.h	2008-06-12 15:39:31.000000000 -0300
-@@ -55,7 +55,7 @@
- {
-  public:
-   SequenceReaderFileState( SequenceNumber lsn, std::streampos fp ) :
--  filePos_(fp),  SequenceReaderState(lsn) {}
-+  SequenceReaderState(lsn), filePos_(fp)  {}
-   // no point in making this private as it's const
-   const std::streampos filePos_;
- };
diff --git a/biology/ssaha/files/patch-SequenceReaderFilter.h b/biology/ssaha/files/patch-SequenceReaderFilter.h
deleted file mode 100644
index 38c65183fb7a..000000000000
--- a/biology/ssaha/files/patch-SequenceReaderFilter.h
+++ /dev/null
@@ -1,20 +0,0 @@
---- ./SequenceReader/SequenceReaderFilter.h.orig	2004-03-01 13:51:30.000000000 -0300
-+++ ./SequenceReader/SequenceReaderFilter.h	2008-06-12 15:39:31.000000000 -0300
-@@ -80,7 +80,7 @@
- 
-   size_t max( void ) const 
-   { 
--    int max(0);
-+    size_t max(0);
-     for (vector<vector<string*> >::const_iterator i(bins_.begin()); i!= bins_.end(); i++ )
-       if (i->size()>max) max=i->size();
-     return max;
-@@ -109,7 +109,7 @@
-  public:
-   SequenceReaderFilterState
-     ( SequenceNumber lsn, SequenceReader* ps ) :
--    pState_(ps->saveState()), SequenceReaderState(lsn) {}
-+    SequenceReaderState(lsn), pState_(ps->saveState())  {}
-   virtual ~SequenceReaderFilterState() {} //delete pState_;
-   // no point in making this private as it's const
-   // this is state info for *ps, whatever it is
diff --git a/biology/ssaha/files/patch-SequenceReaderLocal.cpp b/biology/ssaha/files/patch-SequenceReaderLocal.cpp
deleted file mode 100644
index f8629b6ffafe..000000000000
--- a/biology/ssaha/files/patch-SequenceReaderLocal.cpp
+++ /dev/null
@@ -1,28 +0,0 @@
---- ./SequenceReader/SequenceReaderLocal.cpp.orig	2004-03-01 13:51:30.000000000 -0300
-+++ ./SequenceReader/SequenceReaderLocal.cpp	2008-06-12 15:39:31.000000000 -0300
-@@ -46,10 +46,10 @@
-   // and seqNames_
- SequenceReaderLocal::SequenceReaderLocal
- ( SequenceReader& seqFile, int wordLength, ostream& monitoringStream ) :
--sourceData_( seqFile.getSourceDataType() ),
-+SequenceReader( monitoringStream ),
- wordLength_( wordLength ),
- bitsPerSymbol_( seqFile.getBitsPerSymbol() ),
--SequenceReader( monitoringStream )
-+sourceData_( seqFile.getSourceDataType() )
- {
-   monitoringStream_ 
-     << "constructing SequenceReaderLocal from SequenceReader" << endl;
-@@ -72,10 +72,10 @@
- 
- SequenceReaderLocal::SequenceReaderLocal
- ( int wordLength, int bitsPerSymbol, ostream& monitoringStream ) :
--sourceData_( gUnknownData ),
-+SequenceReader( monitoringStream ),
- wordLength_( wordLength ),
- bitsPerSymbol_( bitsPerSymbol ),
--SequenceReader( monitoringStream )
-+sourceData_( gUnknownData )
- {
-   monitoringStream_ 
-     << "constructing empty SequenceReaderLocal" << endl;
diff --git a/biology/ssaha/files/patch-SequenceReaderMulti.cpp b/biology/ssaha/files/patch-SequenceReaderMulti.cpp
deleted file mode 100644
index 1e160249d180..000000000000
--- a/biology/ssaha/files/patch-SequenceReaderMulti.cpp
+++ /dev/null
@@ -1,30 +0,0 @@
---- ./SequenceReader/SequenceReaderMulti.cpp.orig	2004-03-01 13:51:30.000000000 -0300
-+++ ./SequenceReader/SequenceReaderMulti.cpp	2008-06-12 15:39:31.000000000 -0300
-@@ -166,7 +166,7 @@
-   {
-     if (thisReader_->allSeqsRead_)
-     {
--      if ( currentSeqNum_ <= thisReader_->size_ )
-+      if ( currentSeqNum_ <= (SequenceNumber)thisReader_->size_ )
-       {
- 	//	assert( thisReader_->ptr_->findSequence( currentSeqNum_ ) == true );
- 	lastSequenceNumber_ = --seqNum; // last read = 1 behind current
-@@ -240,7 +240,7 @@
-     for ( vector<SeqReaderInfo>::iterator i = allReaders_.begin(); 
-           i != allReaders_.end(); i++ )
-     {
--      if ( seqNum <= i->size_ ) { thisReader_ = i; break; } // %%%%%
-+      if ( seqNum <= (SequenceNumber)i->size_ ) { thisReader_ = i; break; } // %%%%%
-       seqNum -= i->size_;
-     } // ~for i
- 
-@@ -276,7 +276,8 @@
-   {
-     DEBUG_L2( "SequenceReaderMulti::getNextSequence" );
- 
--    int numInLast;
-+    int numInLast = -1;  // Initialized to avoid -Wall possibly used before initialized warning.
-+                         // The algorithm should be checked carefully.
- 
-     while 
-       (    ( thisReader_ 
diff --git a/biology/ssaha/files/patch-SequenceReaderMulti.h b/biology/ssaha/files/patch-SequenceReaderMulti.h
deleted file mode 100644
index 72f079f97add..000000000000
--- a/biology/ssaha/files/patch-SequenceReaderMulti.h
+++ /dev/null
@@ -1,13 +0,0 @@
---- ./SequenceReader/SequenceReaderMulti.h.orig	2004-03-01 13:51:30.000000000 -0300
-+++ ./SequenceReader/SequenceReaderMulti.h	2008-06-12 15:39:31.000000000 -0300
-@@ -81,8 +81,9 @@
-     ( SequenceNumber lsn, 
-       vector<SeqReaderInfo>::iterator tr,
-       SequenceReaderState* ps ) :
-+  SequenceReaderState(lsn),
-   thisReader_(tr),  
--    pState_(ps), SequenceReaderState(lsn) {}
-+  pState_(ps)  {}
-   virtual ~SequenceReaderMultiState() {} //delete pState_;
-   // no point in making this private as it's const
-   const vector<SeqReaderInfo>::iterator thisReader_;
diff --git a/biology/ssaha/files/patch-SequenceReaderString.h b/biology/ssaha/files/patch-SequenceReaderString.h
deleted file mode 100644
index a35c0b7cfc01..000000000000
--- a/biology/ssaha/files/patch-SequenceReaderString.h
+++ /dev/null
@@ -1,26 +0,0 @@
---- ./SequenceReader/SequenceReaderString.h.orig	2004-03-01 13:51:30.000000000 -0300
-+++ ./SequenceReader/SequenceReaderString.h	2008-06-12 15:39:31.000000000 -0300
-@@ -65,9 +65,9 @@
-   // NB SequenceReaderStringBase takes ownership of *pEncoder
-   SequenceEncoder* pEncoder,
-   ostream& monitoringStream = cerr ) :
-+  SequenceReader( monitoringStream ),
-   sequenceString_( sequenceString ), 
--  pEncoder_( pEncoder ),
--  SequenceReader( monitoringStream )
-+  pEncoder_( pEncoder )
- {
-   monitoringStream_ << "constructing SequenceReaderStringBase" << endl;
- } // constructor
-@@ -78,9 +78,9 @@
-   // TYPE  NAME  IN/OUT COMMENT
-   // Returns: TYPE COMMENT
- SequenceReaderStringBase( const SequenceReaderStringBase& rhs ) :
-+SequenceReader( rhs.monitoringStream_ ),
- sequenceString_( rhs.sequenceString_ ), 
--pEncoder_( rhs.pEncoder_->clone() ),
--SequenceReader( rhs.monitoringStream_ )
-+pEncoder_( rhs.pEncoder_->clone() )
- {
-   monitoringStream_ << "copy constructing SequenceReaderStringBase" << endl;
- } // copy constructor
diff --git a/biology/ssaha/files/patch-makefile b/biology/ssaha/files/patch-makefile
deleted file mode 100644
index cc9cf1a7d330..000000000000
--- a/biology/ssaha/files/patch-makefile
+++ /dev/null
@@ -1,30 +0,0 @@
---- ./Binary/makefile.orig	2008-06-12 16:00:19.000000000 -0300
-+++ ./Binary/makefile	2008-06-12 16:00:43.000000000 -0300
-@@ -11,10 +11,10 @@
- # copy of the SSAHA directory structure you should be able to make files
- # straight away.
- # 
--# SSAHA_TOP_DIR=$(SSAHA_DIR?$(SSAHA_DIR):$(PWD)/../)
-+SSAHA_TOP_DIR=$(PWD)/../
- # Above is a nice idea, but syntax doesn't work for all versions of make
- # so must define CURRENT_SSAHA_VERSION, eg in your .cshrc file - TC 14.3.01
--SSAHA_TOP_DIR=$(CURRENT_SSAHA_VERSION)
-+# SSAHA_TOP_DIR=$(CURRENT_SSAHA_VERSION)
- 
- GLOBAL_DIR=${SSAHA_TOP_DIR}/Global
- SEQ_DIR=${SSAHA_TOP_DIR}/SequenceReader
-@@ -22,12 +22,12 @@
- QUERY_DIR=${SSAHA_TOP_DIR}/QueryManager
- EXEC_DIR=${SSAHA_TOP_DIR}/Executables
- 
--CCC = g++
-+CCC ?= g++
- # !!!! change -g to -O3 before making deliverable %%%%
- # NB use -ggdb to get gdb to work
- INCLUDE_PATHS = -I${SSAHA_TOP_DIR} \
- 	-I${GLOBAL_DIR} -I${SEQ_DIR} -I${HASH_DIR} -I${QUERY_DIR}
--OPTIM = -O3
-+OPTIM ?= -O3
- DEBUG_LEVEL = 
- # DEBUG_LEVEL = -DEBUG_LEVEL1
- # -D_REENTRANT necessary for thread safety - see pthread man page - TC 24.9.1
diff --git a/biology/ssaha/files/patch-testHashTableNoOverlap.cpp b/biology/ssaha/files/patch-testHashTableNoOverlap.cpp
deleted file mode 100644
index 721e03ae9134..000000000000
--- a/biology/ssaha/files/patch-testHashTableNoOverlap.cpp
+++ /dev/null
@@ -1,178 +0,0 @@
---- ./HashTable/testHashTableNoOverlap.cpp.orig	2004-03-01 13:51:29.000000000 -0300
-+++ ./HashTable/testHashTableNoOverlap.cpp	2008-06-12 15:39:31.000000000 -0300
-@@ -70,10 +70,10 @@
-   cout << "     Test of class HashTable" << endl << endl;
-   cout << "*******************************************" << endl << endl;
- 
--  int numSeqs = 10;
--  int seqSize = 100;
--  int wordLength = 10;
--  int maxHits = 50;
-+  unsigned int numSeqs = 10;
-+  unsigned int seqSize = 100;
-+  unsigned int wordLength = 10;
-+  unsigned int maxHits = 50;
- 
-   // Generate a random sequence of (numSeqs*seqSize) base pairs ...
-   // 1128 is the seed value for the random number generator
-@@ -116,7 +116,7 @@
-   // so we are checking that all sequence data 'finds itself' in the hash
-   // table in the correct position
- 
--  for ( int i(1) ; i <= numSeqs ; i++ )
-+  for ( unsigned int i(1) ; i <= numSeqs ; i++ )
-   { // for each sequence in testReader ...
-     testReader.getNextSequence(seq,wordLength);
- 
-@@ -131,7 +131,7 @@
-     cout << seq.getNumBasesInLast() << "!!\n";
-     // ... go through the Words in the sequence one by one and look
-     //    for matches in the hash table
--    for ( int j(0) ; j < (seqSize/wordLength) ; j++ )
-+    for ( unsigned int j(0) ; j < (seqSize/wordLength) ; j++ )
-     {
-        cout << j << " " << printBase(seq[j],wordLength) << endl; 
-       
-@@ -146,7 +146,7 @@
-        // ... and that the sequence number and offset for the hit are OK
- 
-        assert(hits[0].subjectNum == i );
--       assert(hits[0].diff == j*wordLength );
-+       assert((unsigned int)hits[0].diff == j*wordLength );
-        assert(hits[0].queryPos == 1);
-  
-        hits.clear();
-@@ -157,12 +157,12 @@
-     testHash.matchWord(seq,hits); 
-     cout << hits.size() << "!!!!!\n";
-     assert( hits.size() == (seqSize/wordLength) );
--    for ( int j(0) ; j < hits.size() ; j ++ )
-+    for ( unsigned int j(0) ; j < hits.size() ; j ++ )
-     {
- 
-       assert(hits[j].subjectNum == i);
-       assert(hits[j].diff   == 0);
--      assert(hits[j].queryPos == 1 + ( j * wordLength ) );
-+      assert((unsigned int)hits[j].queryPos == 1 + ( j * wordLength ) );
-      
-     } // ~for j
- 
-@@ -194,7 +194,7 @@
-   assert( testLoad.isInitialized() == true );
-   
-   // and that word length matches original
--  assert( testLoad.getWordLength() == wordLength );
-+  assert( (unsigned int)testLoad.getWordLength() == wordLength );
- 
-   testLoad.setMaxNumHits( testHash.getMaxNumHits() );
- 
-@@ -208,7 +208,7 @@
-   // and new hash tables, storing the resulting hits in hitsOrig and
-   // hitsCopy respectively.
- 
--  for ( int i(0) ; i < numSeqs ; i++ )
-+  for ( unsigned int i(0) ; i < numSeqs ; i++ )
-   {
- 
-     // ... check that the name strings match 
-@@ -258,7 +258,7 @@
-   HashTable   shiftHash(cout);
-   creator.createHashTable(shiftHash,shiftReader,wordLength,maxHits);
- 
--  for ( int i(0) ; i < wordLength ; i++ )
-+  for ( unsigned int i(0) ; i < wordLength ; i++ )
-   {
-     testSeq = testSeq.substr(1); // delete first character
-     { // braces ensure a new instance is created each time round loop
-@@ -460,7 +460,7 @@
-     SequenceEncoderCodon encoder;
-     encoder.setWordLength(wordLength);
- 
--    for ( int i(1) ; i < hashTrans.getNumSequences() ; i++ )
-+    for ( unsigned int i(1) ; i < hashTrans.getNumSequences() ; i++ )
-     {
- 
-       hashTrans.getSequenceName( s1, i );
-@@ -477,7 +477,7 @@
-       assert(hashTrans.getSequenceSize(i)==hashTrans2.getSequenceSize(i));
- 
-       assert( (((w1.size()-1) * gMaxBasesPerWord ) + w1.getNumBasesInLast())
--	      == hashTrans.getSequenceSize(i));
-+	      == (unsigned int)hashTrans.getSequenceSize(i));
- 
- 
-       // Sequence should produce same (nonzero) num hits in fwd direction
-@@ -573,19 +573,19 @@
-     string s, s1;
-     Word w;
-     vector<Word> subs;
--    int wl=15;
-+    unsigned int wl=15;
- 
-     // test substitution for DNA
-     // 
- 
--    for (int i(0); i<wl; i++) s+="A";
-+    for ( unsigned int i(0); i<wl; i++) s+="A";
- 
-     w = makeBase(s);
- 
-     generateSubstitutesDNA( w, subs, wl );
-     assert(subs.size()==wl);
-     
--    for (int i(0); i<wl ; i++)
-+    for (unsigned int i(0); i<wl ; i++)
-     {
-       cout << printWord(subs[i],wl) << endl;
-       s1=s;
-@@ -596,14 +596,14 @@
-     //
-     s=""; subs.clear();
- 
--    for (int i(0); i<wl; i++) s+="C";
-+    for (unsigned int i(0); i<wl; i++) s+="C";
- 
-     w = makeBase(s);
- 
-     generateSubstitutesDNA( w, subs, wl );
-     assert(subs.size()==wl);
-     
--    for (int i(0); i<wl ; i++)
-+    for (unsigned int i(0); i<wl ; i++)
-     {
-       cout << printWord(subs[i],wl) << endl;
-       s1=s;
-@@ -614,14 +614,14 @@
-     //
-     s=""; subs.clear();
- 
--    for (int i(0); i<wl; i++) s+="G";
-+    for (unsigned int i(0); i<wl; i++) s+="G";
- 
-     w = makeBase(s);
- 
-     generateSubstitutesDNA( w, subs, wl );
-     assert(subs.size()==wl);
-     
--    for (int i(0); i<wl ; i++)
-+    for (unsigned int i(0); i<wl ; i++)
-     {
-       cout << printWord(subs[i],wl) << endl;
-       s1=s;
-@@ -632,14 +632,14 @@
-     //
-     s=""; subs.clear();
- 
--    for (int i(0); i<wl; i++) s+="T";
-+    for (unsigned int i(0); i<wl; i++) s+="T";
- 
-     w = makeBase(s);
- 
-     generateSubstitutesDNA( w, subs, wl );
-     assert(subs.size()==wl);
-     
--    for (int i(0); i<wl ; i++)
-+    for (unsigned int i(0); i<wl ; i++)
-     {
-       cout << printWord(subs[i],wl) << endl;
-       s1=s;
diff --git a/biology/ssaha/files/patch-testQueryManager.cpp b/biology/ssaha/files/patch-testQueryManager.cpp
deleted file mode 100644
index 19f1ec879fd5..000000000000
--- a/biology/ssaha/files/patch-testQueryManager.cpp
+++ /dev/null
@@ -1,20 +0,0 @@
---- ./QueryManager/testQueryManager.cpp.orig	2004-03-01 13:51:29.000000000 -0300
-+++ ./QueryManager/testQueryManager.cpp	2008-06-12 15:39:31.000000000 -0300
-@@ -53,7 +53,7 @@
- void reverseString( string& seq )
- {
-   string rc;
--  for ( int i(0) ; i < seq.size() ; i++ )
-+  for ( unsigned int i(0) ; i < seq.size() ; i++ )
-   {
-     if  ( ( seq[i] == 'A' ) || (seq[i] == 'a') ) rc = 'T' + rc; 
-     else if ( ( seq[i] == 'T' ) || (seq[i] == 't') ) rc = 'A' + rc; 
-@@ -165,7 +165,7 @@
-   int numSeqs = 3;
-   int seqSize = 1000;
-   int wordLength = 7;
--  int maxHits = 50;
-+//  int maxHits = 50;
- 
-   // Generate a random sequence of (numSeqs*seqSize) base pairs ...
-   // 1128 is the seed value for the random number generator
diff --git a/biology/ssaha/files/patch-testSequenceReaderFasta.cpp b/biology/ssaha/files/patch-testSequenceReaderFasta.cpp
deleted file mode 100644
index 3bc005bff32b..000000000000
--- a/biology/ssaha/files/patch-testSequenceReaderFasta.cpp
+++ /dev/null
@@ -1,171 +0,0 @@
---- ./SequenceReader/testSequenceReaderFasta.cpp.orig	2004-08-25 11:31:17.000000000 -0300
-+++ ./SequenceReader/testSequenceReaderFasta.cpp	2008-06-12 15:39:31.000000000 -0300
-@@ -49,12 +49,12 @@
- // ### Function Definitions ###
- void capitalise( string& s )
- {
--  for ( int i(0) ; i < s.size() ; ++i ) s[i] = toupper(s[i]);
-+  for ( unsigned int i(0) ; i < s.size() ; ++i ) s[i] = toupper(s[i]);
- }
- void reverseString( string& seq )
- {
-   string rc;
--  for ( int i(0) ; i < seq.size() ; i++ )
-+  for ( unsigned int i(0) ; i < seq.size() ; i++ )
-   {
-     if  ( ( seq[i] == 'A' ) || (seq[i] == 'a') ) rc = 'T' + rc; 
-     else if ( ( seq[i] == 'T' ) || (seq[i] == 't') ) rc = 'A' + rc; 
-@@ -91,7 +91,7 @@
-   cout << "Test " << ++numTests <<": test of function getNextSequence" 
-        << endl << endl;
- 
--  int numSeqs = 10;
-+  unsigned int numSeqs = 10;
-   int seqSize = 57;
- 
-   // Generate a random sequence of (numSeqs*seqSize) base pairs ...
-@@ -118,7 +118,7 @@
- 
- 
- 
--  for ( int i(0) ; i < numSeqs ; i++ )
-+  for ( unsigned int i(0) ; i < numSeqs ; i++ )
-   {
-   
-     testReader.getNextSequence(w,wordLength);
-@@ -188,7 +188,7 @@
-   cout << "Test " << ++numTests <<": test of getSequence" 
-        << endl << endl;
- 
--    int toRead = 5;
-+    unsigned int toRead = 5;
- 
-     w.clear();
-     testReader.getSequence(w,toRead,wordLength);
-@@ -242,7 +242,7 @@
-     cout << "Test " << ++numTests <<": test of random access output functions" 
-        << endl << endl;
- 
--    for ( int i(1) ; i <= numSeqs; i++ )
-+    for ( unsigned int i(1) ; i <= numSeqs; i++ )
-     {
-       cout << testReader.getName(i) << endl;
-       cout << testReader.getSideInfo(i) << endl;
-@@ -275,7 +275,7 @@
-   // add on the end of the expected sequence string for it to match actual.
-   //  const string spareBases( wordLength - ( seqSize % wordLength ), 'A');
- 
--  for ( int i(0) ; i < numSeqs ; i++ )
-+  for ( unsigned int i(0) ; i < numSeqs ; i++ )
-   {
-   
-     testReaderFastq.getNextSequence(w,wordLength);
-@@ -403,7 +403,7 @@
-     cout << "Test " << ++numTests <<": test of random access output functions" 
-        << endl << endl;
- 
--    for ( int i(1) ; i <= numSeqs; i++ )
-+    for ( unsigned int i(1) ; i <= numSeqs; i++ )
-     {
-       cout << testReaderFastq.getName(i) << endl;
-       cout << testReaderFastq.getSideInfo(i) << endl;
-@@ -466,7 +466,7 @@
-     {
- 
-       testReader.rewind();
--      for ( int j(0) ; j < testReader.getNumSequencesInFile() ; j ++ ) 
-+      for ( unsigned int j(0) ; j < testReader.getNumSequencesInFile() ; j ++ ) 
-       {
- 		cout << i << " " << j << endl;
-         wSingle.clear(); wMulti.clear(); 
-@@ -772,7 +772,7 @@
-       
-       for (int wordLength(9); wordLength <= 12; wordLength++)
-       {
--	for (int i(0) ; i < fiftyAs.size(); i++)
-+	for (unsigned int i(0) ; i < fiftyAs.size(); i++)
- 	{
- 	  thisString=fiftyAs;
- 	  thisString[i]='X';
-@@ -793,7 +793,7 @@
- 	  stringReader.changeMode(&ignore);
- 	  w.clear();
- 	  numInLast = stringReader.getNextSequence(w,wordLength);
--	  assert(numInLast==(fiftyAs.size()-1)%wordLength);
-+	  assert(numInLast==(int)(fiftyAs.size()-1)%wordLength);
- 	  assert((w.size()-1)*wordLength+numInLast==fiftyAs.size()-1);
- 
- 	  for (WordSequence::iterator j(w.begin()); j!=w.end();j++)
-@@ -810,7 +810,7 @@
- 	  numInLast = stringReader.getNextSequence(w,wordLength);
- 	  cout << "blegh " << wordLength << " " << i  << " " << fiftyAs.size() << " " << numInLast << " " << w.size() << endl;
- 	  
--	  assert(numInLast==fiftyAs.size()%wordLength);
-+	  assert(numInLast==(int)fiftyAs.size()%wordLength);
- 	  assert((w.size()-1)*wordLength+numInLast==fiftyAs.size());
- 
- 	  for (WordSequence::iterator j(w.begin()); j!=w.end();j++)
-@@ -828,7 +828,7 @@
- 	  stringReader.changeMode(&tag);
- 	  w.clear();
- 	  numInLast = stringReader.getNextSequence(w,wordLength);
--	  assert(numInLast==fiftyAs.size()%wordLength);
-+	  assert(numInLast==(int)fiftyAs.size()%wordLength);
- 	  assert((w.size()-1)*wordLength+numInLast==fiftyAs.size());
- 
- 	  for (WordSequence::iterator j(w.begin()); j!=w.end();j++)
-@@ -915,7 +915,7 @@
-       cout << "actual:   " << printResidue(W,wordLength) << endl;
-       
- 
--      for ( int i(0),j(0);  i < protString.size() ; i+=wordLength,j++ )
-+      for ( unsigned int i(0),j(0);  i < protString.size() ; i+=wordLength,j++ )
- 	{
- 	  wordString = protString.substr(i, wordLength);
- 	  cout << wordString << " " << printResidue(W[j],wordLength) << endl;
-@@ -1163,7 +1163,7 @@
-           assert (    localReader.getNumSequencesInFile()
-                ==  testReader.getNumSequencesInFile() );
- 
--            for ( int j(0) ; j < testReader.getNumSequencesInFile() ; j ++ ) 
-+            for ( unsigned int j(0) ; j < testReader.getNumSequencesInFile() ; j ++ ) 
-         {
-           wSingle.clear(); wMulti.clear(); 
- 
-@@ -1244,7 +1244,7 @@
-      WordSequence seq;
-      string name;
- 
--     for ( int i(1) ; i <= filterer.getNumSequencesInFile() ; i++ )
-+     for ( unsigned int i(1) ; i <= filterer.getNumSequencesInFile() ; i++ )
-      {
-        filterer.getSequence(seq, i, 16);
-        filterer.getLastSequenceName(name);
-@@ -1330,12 +1330,12 @@
-        //       assert(v1==v1i);
-        //     assert(v2==v2i);
- 
--       for ( int (i(j)) ; i <=seqSize ; i++ ) assert(v1[i-j]==data[i-1]);
--       for ( int (i(j)) ; i <=seqSize ; i++ ) assert(v2[i-j]==data[i-1]);
--       for ( int (i(j)) ; i <=seqSize ; i++ ) assert(v1m[i-j]==data[i-1]);
--       for ( int (i(j)) ; i <=seqSize ; i++ ) assert(v2m[i-j]==data[i-1]);
--       for ( int (i(j)) ; i <=seqSize ; i++ ) assert(v1i[i-j]==data[i-1]);
--       for ( int (i(j)) ; i <=seqSize ; i++ ) assert(v2i[i-j]==data[i-1]);
-+       for ( int i(j) ; i <=seqSize ; i++ ) assert(v1[i-j]==data[i-1]);
-+       for ( int i(j) ; i <=seqSize ; i++ ) assert(v2[i-j]==data[i-1]);
-+       for ( int i(j) ; i <=seqSize ; i++ ) assert(v1m[i-j]==data[i-1]);
-+       for ( int i(j) ; i <=seqSize ; i++ ) assert(v2m[i-j]==data[i-1]);
-+       for ( int i(j) ; i <=seqSize ; i++ ) assert(v1i[i-j]==data[i-1]);
-+       for ( int i(j) ; i <=seqSize ; i++ ) assert(v2i[i-j]==data[i-1]);
- 
-      }
-      cout << "got through  first bit" << endl;
-@@ -1402,7 +1402,7 @@
- 
-      string n1,n2;
- 
--     for (int i(0);i<numSeqs; i++)
-+     for (unsigned int i(0);i<(unsigned int)numSeqs; i++)
-      {
-        cout << "i: " << i << endl;
-        w1.clear(); w2.clear();
diff --git a/biology/ssaha/pkg-descr b/biology/ssaha/pkg-descr
deleted file mode 100644
index 2a683e6cda7d..000000000000
--- a/biology/ssaha/pkg-descr
+++ /dev/null
@@ -1,11 +0,0 @@
-SSAHA is a software tool for very fast matching and alignment of DNA
-sequences. It stands for Sequence Search and Alignment by Hashing
-Algorithm. It achieves its fast search speed by converting sequence
-information into a `hash table' data structure, which can then be
-searched very rapidly for matches.
-
-SSAHA: a fast search method for large DNA databases (2001).
-Ning Z, Cox AJ, Mullikin JC. Genome Res. 11: 1725-9.
-PMID: 11591649
-
-WWW: http://www.sanger.ac.uk/resources/software/ssaha/