Pysam wants several functions not included in the library

[samtools.git] / debian / patches / phase-in-so

diff --git a/debian/patches/phase-in-so b/debian/patches/phase-in-so
new file mode 100644 (file)
index 0000000..64f44be
--- /dev/null
+++ b/debian/patches/phase-in-so
@@ -0,0 +1,30 @@
+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