Pysam wants several functions not included in the library

The default samtools makefile has that marked
as an application object, this patch moves it into
the shared library.

diff --git a/debian/patches/build-so b/debian/patches/build-so
index ffe66d297fe16b5de716ee2967ec7ca5edce828e..8d25673bb94893f30f2471e3c8e2e2c57f88184d 100644 (file)
--- a/debian/patches/build-so
+++ b/debian/patches/build-so
@@ -1,15 +1,15 @@
-diff --git a/Makefile b/Makefile
-index db18333..926059b 100644
---- a/Makefile
-+++ b/Makefile
+Index: samtools.debian/Makefile
+===================================================================
+--- samtools.debian.orig/Makefile      2012-12-19 14:23:16.799622129 -0800
++++ samtools.debian/Makefile   2012-12-19 14:23:21.839621951 -0800
 @@ -1,5 +1,5 @@
  CC=                   gcc
 -CFLAGS=               -g -Wall -O2 #-m64 #-arch ppc
 +CFLAGS=               -g -Wall -O2 -fPIC #-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 \
-@@ -35,13 +35,13 @@ all:$(PROG)
+ LOBJS=                bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam_view.o sam.o bam_index.o \
+@@ -36,13 +36,13 @@
  .PHONY:all lib clean cleanlocal
  .PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
  
@@ -25,7 +25,7 @@ index db18333..926059b 100644
  
  razip:razip.o razf.o $(KNETFILE_O)
                $(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz
-@@ -75,8 +75,9 @@ faidx_main.o:faidx.h razf.h
+@@ -76,8 +76,9 @@
  libbam.1.dylib-local:$(LOBJS)
                libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
  

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

diff --git a/debian/patches/series b/debian/patches/series
index 8310354bea296f4247336821aec0f21abfd2459d..2cbc0aa0f5347f18cf8a493ca7660f32d80348df 100644 (file)
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
+phase-in-so
 no-pileup-tests.patch
 razip-oom-check
 build-so