From 82942523b2db5143a9da0f9d2f8ec83a26c8d5b0 Mon Sep 17 00:00:00 2001
From: Kent Fredric <kentfredric@gmail.com>
Date: Sun, 10 Sep 2017 13:33:32 +1200
Subject: Fix linking/compiling for bam-0.1-legacy

---
 Build.PL             | 14 +++++++-------
 c_bin/bam2bedgraph.c |  2 +-
 c_bin/makefile       |  6 +++---
 lib/Bio/DB/Sam.xs    |  6 +++---
 4 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/Build.PL b/Build.PL
index 685815f..882f231 100644
--- a/Build.PL
+++ b/Build.PL
@@ -4,11 +4,10 @@ use strict;
 use Module::Build;
 use Module::Load::Conditional qw(can_load);
 
-my $HeaderFile = "bam.h";
-my $LibFile    = "libbam.a";
-my $ReadLine;
-
-my ($sam_include,$sam_lib) = find_sam(); # may exit with error here
+my ($sam_include,$sam_lib) = do {
+  ($ENV{"SAM_INCLUDE"} || die "SAM_INCLUDE not set"),
+  ($ENV{"SAM_LIB"} || die "SAM_LIB not set")
+};
 
 my $class = Module::Build->subclass(code=><<EOF);
     sub process_c_bin_files {
@@ -39,7 +38,7 @@ my $build = $class->new(
     dist_abstract      => 'Perl interface to SamTools library for DNA sequencing',
     license            => 'perl',
     include_dirs       => [$sam_include],
-    extra_linker_flags => ["-L$sam_lib",'-lbam','-lpthread','-lz'],
+    extra_linker_flags => ["-L$sam_lib",'-lbam-0.1-legacy','-lpthread','-lz'],
 
     extra_compiler_flags=>[
 
@@ -67,7 +66,7 @@ $build->add_build_element('c_bin');
 $build->create_build_script;
 
 exit 0;
-
+=for non-gentoo
 sub find_sam {
     my ($sam_include,$sam_lib);
 
@@ -162,6 +161,7 @@ sub prompt {
     $ReadLine->addhistory($in) if $in =~ /\S/;
     return $in;
 }
+=cut
 
 sub _samtools {
     $ENV{SAMTOOLS} ||
diff --git a/c_bin/bam2bedgraph.c b/c_bin/bam2bedgraph.c
index 298e9a8..91218fa 100644
--- a/c_bin/bam2bedgraph.c
+++ b/c_bin/bam2bedgraph.c
@@ -1,5 +1,5 @@
 #include <stdio.h>
-#include "sam.h"
+#include "bam-0.1-legacy/sam.h"
 
 typedef struct {
   uint32_t ltid;
diff --git a/c_bin/makefile b/c_bin/makefile
index 9aef917..0abbb4c 100644
--- a/c_bin/makefile
+++ b/c_bin/makefile
@@ -1,5 +1,5 @@
-CC=		gcc
-CFLAGS=		-g -Wall -O2 -fPIC
+CC?=		gcc
+CFLAGS?=		-g -Wall -O2 -fPIC
 DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
 INCLUDES=
 LIBPATH=
@@ -14,7 +14,7 @@ PROG=		bam2bedgraph
 all:$(PROG)
 
 bam2bedgraph: bam2bedgraph.o
-	$(CC) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LIBPATH) -lbam -lpthread -lm -lz
+	$(CC) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LIBPATH) -lbam-0.1-legacy -lpthread -lm -lz
 
 clean:
 	rm -f *.o $(PROG)
diff --git a/lib/Bio/DB/Sam.xs b/lib/Bio/DB/Sam.xs
index 023f655..86410fb 100644
--- a/lib/Bio/DB/Sam.xs
+++ b/lib/Bio/DB/Sam.xs
@@ -25,9 +25,9 @@
 
 #include <unistd.h>
 #include <math.h>
-#include "bam.h"
-#include "khash.h"
-#include "faidx.h"
+#include "bam-0.1-legacy/bam.h"
+#include "bam-0.1-legacy/khash.h"
+#include "bam-0.1-legacy/faidx.h"
 
 /* stolen from bam_aux.c */
 #define MAX_REGION 1<<29
-- 
2.26.2