Index: samtools.debian/Makefile
===================================================================
--- samtools.debian.orig/Makefile	2012-12-19 15:16:35.947509197 -0800
+++ samtools.debian/Makefile	2012-12-19 15:18:01.359506182 -0800
@@ -2,15 +2,17 @@
 CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
 DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
 KNETFILE_O=	knetfile.o
-LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
-			bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \
-			$(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-AOBJS=		bam_tview.o bam_plcmd.o sam_view.o	\
-			bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o	\
-			bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
-			cut_target.o phase.o bam2depth.o
+LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam_view.o sam.o bam_index.o \
+			bam_mate.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o \
+			bedidx.o $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o \
+			kprobaln.o bam_cat.o errmod.o phase.o bam_rmdup.o bam_rmdupse.o bam_stat.o \
+			cut_target.o bam2depth.o bam_plcmd.o bam2bcf.o bam2bcf_indel.o \
+			bcftools/bcf.o bcftools/bcfutils.o bcftools/fet.o sample.o
+AOBJS=		bam_tview.o \
+			bam_color.o \
+			bamtk.o kaln.o
 PROG=		samtools
-INCLUDES=	-I.
+INCLUDES=	-I. -Ibcftools
 SUBDIRS=	. bcftools misc
 LIBPATH=
 LIBCURSES=	-lcurses # -lXCurses