1 files changed, 59 insertions, 0 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
new file mode 100644
index 000000000000..8e7250c51736
--- /dev/null
+++ b/dev-perl/Bio-SamTools/files/Bio-SamTools-1.390.0-samtools-1.patch
@@ -0,0 +1,59 @@
+ 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
+