sci-biology/abyss: Remove old

Package-Manager: Portage-2.3.3, Repoman-2.3.1
Closes: https://github.com/gentoo/gentoo/pull/3183

7 files changed, 0 insertions, 158 deletions

diff --git a/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch
deleted file mode 100644
index 300868f52b76..000000000000
--- a/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch
+++ /dev/null
@@ -1,18 +0,0 @@
- configure.ac | 4 ++++
- 1 file changed, 4 insertions(+)
-
-diff --git a/configure.ac b/configure.ac
-index 5c6cb92..b99bedd 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -12,6 +12,10 @@ AC_PROG_CPP
- AC_PROG_CXX
- AC_PROG_INSTALL
- AC_PROG_RANLIB
-+AN_MAKEVAR([AR], [AC_PROG_AR])
-+AN_PROGRAM([ar], [AC_PROG_AR])
-+AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)])
-+AC_PROG_AR
- 
- # Checks for header files.
- AC_CHECK_HEADERS([dlfcn.h fcntl.h float.h limits.h \
diff --git a/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch
deleted file mode 100644
index 42066f7f2152..000000000000
--- a/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- ParseAligns/abyss-fixmate.cc |    1 +
- 1 files changed, 1 insertions(+), 0 deletions(-)
-
-diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc
-index 506ea0c..a0a403c 100644
---- a/ParseAligns/abyss-fixmate.cc
-+++ b/ParseAligns/abyss-fixmate.cc
-@@ -15,6 +15,7 @@
- #include <iterator>
- #include <sstream>
- #include <string>
-+#include <unistd.h>
- 
- using namespace std;
- 
diff --git a/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch
deleted file mode 100644
index 158e9b1262e4..000000000000
--- a/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch
+++ /dev/null
@@ -1,18 +0,0 @@
- configure.ac | 4 ++++
- 1 file changed, 4 insertions(+)
-
-diff --git a/configure.ac b/configure.ac
-index 9d4bb66..aa94364 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -12,6 +12,10 @@ AC_PROG_CPP
- AC_PROG_CXX
- AC_PROG_INSTALL
- AC_PROG_RANLIB
-+AN_MAKEVAR([AR], [AC_PROG_AR])
-+AN_PROGRAM([ar], [AC_PROG_AR])
-+AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)])
-+AC_PROG_AR
- AC_CHECK_TOOL(GHC, ghc)
- AM_CONDITIONAL([HAVE_GHC], [test "$GHC"])
- 
diff --git a/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch
deleted file mode 100644
index c2cc35c31d98..000000000000
--- a/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- ParseAligns/abyss-fixmate.cc |    1 +
- 1 files changed, 1 insertions(+), 0 deletions(-)
-
-diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc
-index 1a169cf..36cc05b 100644
---- a/ParseAligns/abyss-fixmate.cc
-+++ b/ParseAligns/abyss-fixmate.cc
-@@ -16,6 +16,7 @@
- #include <iterator>
- #include <sstream>
- #include <string>
-+#include <unistd.h>
- 
- using namespace std;
- 
diff --git a/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch b/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch
deleted file mode 100644
index cb7dfb08a84d..000000000000
--- a/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-Hello,
-
-I see Shaun Jackmans' (abyss-)sam2afg script is available within the 
-Amos source repository. I find this very useful for coercing output from 
-assemblers which which don't track read location into amos by remapping 
-reads against the assembly and converting to afg - not ideal but better 
-than nothing when you don't have the 'real' read locations to work with.
-
-This fails, however when reads are aligned with 'bwa mem', which can 
-output multi-part alignments. sam2afg checks for reuse of the same read 
-id (presumably to prevent the generation of non-unique eid values), 
-consequently encountering multiple alignments for a read causes it to die.
-
-The following one-line patch allows sam2afg to skip these secondary 
-alignments present in 'bwa mem' output, provided bwa mem has been run 
-with the '-M' argument which sets the SAM 'secondary alignment' flag on 
-the alignments in question.
-
-Hopefully this will also be of use to others...
-
-Best Regards,
-James
-
--- 
-Dr. James Abbott
-Lead Bioinformatician
-Bioinformatics Support Service
-Imperial College, London
-
-
---- abyss-1.3.6/bin/abyss-samtoafg.ori	2015-05-23 23:43:46.797747928 +0200
-+++ abyss-1.3.6/bin/abyss-samtoafg	2015-05-23 23:44:09.227747743 +0200
-@@ -105,6 +105,7 @@
- 	die unless defined $qqual;
- 
- 	$tstart--; # convert to zero-based coordinate
-+        next if $flag & 0x100; # secondary alignment
- 	$qid .= "/1" if $flag & 0x40; #FREAD1
- 	$qid .= "/2" if $flag & 0x80; #FREAD2
- 
diff --git a/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch
deleted file mode 100644
index 158e9b1262e4..000000000000
--- a/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch
+++ /dev/null
@@ -1,18 +0,0 @@
- configure.ac | 4 ++++
- 1 file changed, 4 insertions(+)
-
-diff --git a/configure.ac b/configure.ac
-index 9d4bb66..aa94364 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -12,6 +12,10 @@ AC_PROG_CPP
- AC_PROG_CXX
- AC_PROG_INSTALL
- AC_PROG_RANLIB
-+AN_MAKEVAR([AR], [AC_PROG_AR])
-+AN_PROGRAM([ar], [AC_PROG_AR])
-+AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)])
-+AC_PROG_AR
- AC_CHECK_TOOL(GHC, ghc)
- AM_CONDITIONAL([HAVE_GHC], [test "$GHC"])
- 
diff --git a/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch b/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch
deleted file mode 100644
index 49a30f993478..000000000000
--- a/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-diff --git a/DataBase/db-csv.cc b/DataBase/db-csv.cc
-index 05cac19..48e3b44 100644
---- a/DataBase/db-csv.cc
-+++ b/DataBase/db-csv.cc
-@@ -18,11 +18,11 @@ static const char TABLE_LIST[] =
- typedef vector<string> vs;
- 
- static bool existFile(const char* f)
- {
- 	ifstream file(f);
--	return file;
-+	return bool(file);
- }
- 
- template <typename D>
- static bool existTable(
- 		D& db, const string& t)
-diff --git a/SimpleGraph/SimpleGraph.cpp b/SimpleGraph/SimpleGraph.cpp
-index 373ec70..0a9ebd3 100644
---- a/SimpleGraph/SimpleGraph.cpp
-+++ b/SimpleGraph/SimpleGraph.cpp
-@@ -645,11 +645,11 @@ static void* worker(void* pArg)
- 	for (;;) {
- 		/** Lock the input stream. */
- 		static pthread_mutex_t inMutex = PTHREAD_MUTEX_INITIALIZER;
- 		pthread_mutex_lock(&inMutex);
- 		EstimateRecord er;
--		bool good = (*arg.in) >> er;
-+		bool good = bool((*arg.in) >> er);
- 		pthread_mutex_unlock(&inMutex);
- 		if (!good)
- 			break;
- 
- 		// Flip the anterior distance estimates.