1 files changed, 0 insertions, 110 deletions
diff --git a/dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy-r1.patch b/dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy-r1.patch
deleted file mode 100644
index ee9bde8fe3d0..000000000000
--- a/dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy-r1.patch
+++ /dev/null
@@ -1,110 +0,0 @@
-From 82942523b2db5143a9da0f9d2f8ec83a26c8d5b0 Mon Sep 17 00:00:00 2001
-From: Kent Fredric <kentfredric@gmail.com>
-Date: Sun, 10 Sep 2017 13:33:32 +1200
-Subject: Fix linking/compiling for bam-0.1-legacy
-
----
- Build.PL             | 14 +++++++-------
- c_bin/bam2bedgraph.c |  2 +-
- c_bin/makefile       |  6 +++---
- lib/Bio/DB/Sam.xs    |  6 +++---
- 4 files changed, 14 insertions(+), 14 deletions(-)
-
-diff --git a/Build.PL b/Build.PL
-index 685815f..882f231 100644
---- a/Build.PL
-+++ b/Build.PL
-@@ -4,11 +4,10 @@ use strict;
- use Module::Build;
- use Module::Load::Conditional qw(can_load);
- 
--my $HeaderFile = "bam.h";
--my $LibFile    = "libbam.a";
--my $ReadLine;
--
--my ($sam_include,$sam_lib) = find_sam(); # may exit with error here
-+my ($sam_include,$sam_lib) = do {
-+  ($ENV{"SAM_INCLUDE"} || die "SAM_INCLUDE not set"),
-+  ($ENV{"SAM_LIB"} || die "SAM_LIB not set")
-+};
- 
- my $class = Module::Build->subclass(code=><<EOF);
-     sub process_c_bin_files {
-@@ -39,7 +38,7 @@ my $build = $class->new(
-     dist_abstract      => 'Perl interface to SamTools library for DNA sequencing',
-     license            => 'perl',
-     include_dirs       => [$sam_include],
--    extra_linker_flags => ["-L$sam_lib",'-lbam','-lpthread','-lz'],
-+    extra_linker_flags => ["-L$sam_lib",'-lbam-0.1-legacy','-lpthread','-lz'],
- 
-     extra_compiler_flags=>[
- 
-@@ -67,7 +66,7 @@ $build->add_build_element('c_bin');
- $build->create_build_script;
- 
- exit 0;
--
-+=for non-gentoo
- sub find_sam {
-     my ($sam_include,$sam_lib);
- 
-@@ -162,6 +161,7 @@ sub prompt {
-     $ReadLine->addhistory($in) if $in =~ /\S/;
-     return $in;
- }
-+=cut
- 
- sub _samtools {
-     $ENV{SAMTOOLS} ||
-diff --git a/c_bin/bam2bedgraph.c b/c_bin/bam2bedgraph.c
-index 298e9a8..91218fa 100644
---- a/c_bin/bam2bedgraph.c
-+++ b/c_bin/bam2bedgraph.c
-@@ -1,5 +1,5 @@
- #include <stdio.h>
--#include "sam.h"
-+#include "bam-0.1-legacy/sam.h"
- 
- typedef struct {
-   uint32_t ltid;
-diff --git a/c_bin/makefile b/c_bin/makefile
-index 9aef917..0abbb4c 100644
---- a/c_bin/makefile
-+++ b/c_bin/makefile
-@@ -1,5 +1,5 @@
--CC=		gcc
--CFLAGS=		-g -Wall -O2 -fPIC
-+CC?=		gcc
-+CFLAGS?=		-g -Wall -O2 -fPIC
- DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
- INCLUDES=
- LIBPATH=
-@@ -14,7 +14,7 @@ PROG=		bam2bedgraph
- all:$(PROG)
- 
- bam2bedgraph: bam2bedgraph.o
--	$(CC) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LIBPATH) -lbam -lpthread -lm -lz
-+	$(CC) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LIBPATH) -lbam-0.1-legacy -lpthread -lm -lz
- 
- clean:
- 	rm -f *.o $(PROG)
-diff --git a/lib/Bio/DB/Sam.xs b/lib/Bio/DB/Sam.xs
-index 023f655..86410fb 100644
---- a/lib/Bio/DB/Sam.xs
-+++ b/lib/Bio/DB/Sam.xs
-@@ -25,9 +25,9 @@
- 
- #include <unistd.h>
- #include <math.h>
--#include "bam.h"
--#include "khash.h"
--#include "faidx.h"
-+#include "bam-0.1-legacy/bam.h"
-+#include "bam-0.1-legacy/khash.h"
-+#include "bam-0.1-legacy/faidx.h"
- 
- /* stolen from bam_aux.c */
- #define MAX_REGION 1<<29
--- 
-2.26.2
-