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|
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
|
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