From f01c2a5b5fac8effb317dc226276e94410303c37 Mon Sep 17 00:00:00 2001
From: Diane Trout <diane@caltech.edu>
Date: Wed, 19 Dec 2012 13:24:28 -0800
Subject: [PATCH] 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.
---
 debian/patches/build-so    | 14 +++++++-------
 debian/patches/phase-in-so | 30 ++++++++++++++++++++++++++++++
 debian/patches/series      |  1 +
 3 files changed, 38 insertions(+), 7 deletions(-)
 create mode 100644 debian/patches/phase-in-so

diff --git a/debian/patches/build-so b/debian/patches/build-so
index ffe66d2..8d25673 100644
--- 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
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 8310354..2cbc0aa 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
+phase-in-so
 no-pileup-tests.patch
 razip-oom-check
 build-so
-- 
2.30.2