debian/patches/phase-in-so

   1 Index: samtools.debian/Makefile
   2 ===================================================================
   3 --- samtools.debian.orig/Makefile       2012-12-19 15:16:35.947509197 -0800
   4 +++ samtools.debian/Makefile    2012-12-19 15:18:01.359506182 -0800
   5 @@ -2,15 +2,17 @@
   6  CFLAGS=                -g -Wall -O2 #-m64 #-arch ppc
   7  DFLAGS=                -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
   8  KNETFILE_O=    knetfile.o
   9 -LOBJS=         bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
  10 -                       bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \
  11 -                       $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
  12 -AOBJS=         bam_tview.o bam_plcmd.o sam_view.o      \
  13 -                       bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o     \
  14 -                       bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
  15 -                       cut_target.o phase.o bam2depth.o
  16 +LOBJS=         bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam_view.o sam.o bam_index.o \
  17 +                       bam_mate.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o \
  18 +                       bedidx.o $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o \
  19 +                       kprobaln.o bam_cat.o errmod.o phase.o bam_rmdup.o bam_rmdupse.o bam_stat.o \
  20 +                       cut_target.o bam2depth.o bam_plcmd.o bam2bcf.o bam2bcf_indel.o \
  21 +                       bcftools/bcf.o bcftools/bcfutils.o bcftools/fet.o sample.o
  22 +AOBJS=         bam_tview.o \
  23 +                       bam_color.o \
  24 +                       bamtk.o kaln.o
  25  PROG=          samtools
  26 -INCLUDES=      -I.
  27 +INCLUDES=      -I. -Ibcftools
  28  SUBDIRS=       . bcftools misc
  29  LIBPATH=
  30  LIBCURSES=     -lcurses # -lXCurses