* added BED support to samtools view and mpileup and bcftools view

[samtools.git] / Makefile

diff --git a/Makefile b/Makefile
index e28822eabfa7499e5cb8d5a1a5198360e73630ee..2cfa085b82789d321d103f18c1de1819af6cec37 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -1,13 +1,14 @@
 CC=                    gcc
 CFLAGS=                -g -Wall -O2 #-m64 #-arch ppc
-DFLAGS=                -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1
+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 glf.o razf.o faidx.o \
-                       $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o
+                       bam_pileup.o bam_lpileup.o bam_md.o glf.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_maqcns.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
+                       bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
+                       cut_target.o phase.o
 PROG=          samtools
 INCLUDES=      -I.
 SUBDIRS=       . bcftools misc
@@ -66,6 +67,8 @@ bcf.o:bcftools/bcf.h
 bam2bcf.o:bam2bcf.h errmod.h bcftools/bcf.h
 bam2bcf_indel.o:bam2bcf.h
 errmod.o:errmod.h
+phase.o:bam.h khash.h ksort.h
+bamtk.o:bam.h
 
 faidx.o:faidx.h razf.h khash.h
 faidx_main.o:faidx.h razf.h