1 files changed, 0 insertions, 59 deletions
diff --git a/dev-perl/Bio-SamTools/files/Bio-SamTools-1.390.0-samtools-1.patch b/dev-perl/Bio-SamTools/files/Bio-SamTools-1.390.0-samtools-1.patch
deleted file mode 100644
index 8e7250c51736..000000000000
--- a/dev-perl/Bio-SamTools/files/Bio-SamTools-1.390.0-samtools-1.patch
+++ /dev/null
@@ -1,59 +0,0 @@
- Build.PL          | 2 +-
- c_bin/makefile    | 6 +++---
- lib/Bio/DB/Sam.xs | 9 ++++++---
- 3 files changed, 10 insertions(+), 7 deletions(-)
-
-diff --git a/Build.PL b/Build.PL
-index 1393e03..cf97ad5 100644
---- a/Build.PL
-+++ b/Build.PL
-@@ -38,7 +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','-lhts','-lpthread','-lz'],
- 
-     extra_compiler_flags=>[
- 
-diff --git a/c_bin/makefile b/c_bin/makefile
-index 9aef917..96a30f2 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 -lhts -lpthread -lm -lz
- 
- clean:
- 	rm -f *.o $(PROG)
-diff --git a/lib/Bio/DB/Sam.xs b/lib/Bio/DB/Sam.xs
-index 5ca303b..7f92860 100644
---- a/lib/Bio/DB/Sam.xs
-+++ b/lib/Bio/DB/Sam.xs
-@@ -571,9 +571,12 @@ bama_l_aux(b,...)
-     Bio::DB::Bam::Alignment b
- PROTOTYPE: $;$
- CODE:
--    if (items > 1)
--      b->l_aux = SvIV(ST(1));
--    RETVAL=b->l_aux;
-+    if (items > 1) {
-+      RETVAL = SvIV(ST(1));
-+      }
-+    else {
-+      RETVAL=bam_get_l_aux(b);
-+    }
- OUTPUT:
-     RETVAL
-