Fix build against newer protocol buffers library.

Regenerate source from missing protocol description fetched from:
https://bitbucket.org/statgen/plinkseq/raw/976c492c6e11e81aa798e2c4c20bcf17ea4073a1/lib/variant.proto
https://bitbucket.org/statgen/plinkseq/raw/976c492c6e11e81aa798e2c4c20bcf17ea4073a1/lib/pp.proto

Bump PKGREVISION.

3 files changed, 80 insertions, 1 deletions

diff --git a/biology/plinkseq/Makefile b/biology/plinkseq/Makefile
index 2578471abd2..93b002a32a1 100644
--- a/biology/plinkseq/Makefile
+++ b/biology/plinkseq/Makefile
@@ -1,6 +1,7 @@
-# $NetBSD: Makefile,v 1.1 2012/11/01 04:06:21 asau Exp $
+# $NetBSD: Makefile,v 1.2 2013/03/26 20:11:19 asau Exp $
 
 DISTNAME=	plinkseq-0.08
+PKGREVISION=	1
 CATEGORIES=	biology
 MASTER_SITES=	http://atgu.mgh.harvard.edu/plinkseq/dist/version-0.08/
 
@@ -21,5 +22,15 @@ REPLACE_BASH=	browser/pbrowse.in index/index.in
 BUILDLINK_TRANSFORM=	rm:-ldl
 .endif
 
+# Put missing protocol description files in place:
+post-extract:
+	$(CP) $(FILESDIR)/pp.proto $(WRKSRC)/lib/
+	$(CP) $(FILESDIR)/variant.proto $(WRKSRC)/lib/
+
+# Regenerate:
+pre-build:
+	cd $(WRKSRC)/lib && protoc --cpp_out=. pp.proto && mv pp.pb.cc pp.pb.cpp
+	cd $(WRKSRC)/lib && protoc --cpp_out=. variant.proto && mv variant.pb.cc variant.pb.cpp
+
 .include "../../devel/protobuf/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/plinkseq/files/pp.proto b/biology/plinkseq/files/pp.proto
new file mode 100644
index 00000000000..b425a4de1dc
--- /dev/null
+++ b/biology/plinkseq/files/pp.proto
@@ -0,0 +1,15 @@
+
+message PolyPhen2Buffer {
+
+	enum pred_t { UNKNOWN = 0; BENIGN = 1; POSS = 2; PROB = 3; }
+
+	required string transcript_name     = 1;
+	required string protein_name        = 2;
+
+	repeated int32  position    = 3 [packed=true];
+	repeated string reference   = 4;
+	repeated string alternate   = 5;
+	repeated double score       = 6 [packed=true];
+	repeated pred_t prediction  = 7 [packed=true];
+
+}
diff --git a/biology/plinkseq/files/variant.proto b/biology/plinkseq/files/variant.proto
new file mode 100644
index 00000000000..9fc8698d37e
--- /dev/null
+++ b/biology/plinkseq/files/variant.proto
@@ -0,0 +1,53 @@
+
+message VariantMetaUnit {
+	enum Type { INT = 1; FLOAT = 2; TEXT = 3; BOOL = 4; }
+	     	
+        required Type   type = 1;
+	required string name = 2;
+
+	repeated int32   int_value     = 3 [packed=true];
+	repeated double  double_value  = 4 [packed=true];
+	repeated string  string_value  = 5;
+	repeated bool    bool_value    = 6 [packed=true];
+}
+
+
+message GenotypeMetaUnit {
+
+	enum Type { INT = 1; FLOAT = 2; TEXT = 3; BOOL = 4; }
+	     	
+        required Type    type          = 1;
+	required string  name          = 2;
+	
+        optional int32   fixed_len     = 3;
+	repeated int32   len           = 4 [packed=true];
+
+	repeated int32   int_value     = 5 [packed=true];
+	repeated double  double_value  = 6 [packed=true];
+	repeated string  string_value  = 7;
+	repeated bool    bool_value    = 8 [packed=true];
+
+        optional int32   fixed_indiv   = 9;
+	repeated int32   indiv_index   = 10 [packed=true];
+	repeated int32   missing_index = 11 [packed=true];
+}
+
+
+message VariantBuffer {
+	optional string ref = 1;
+	optional string alt = 2;
+	optional double quality = 3;
+	repeated string filter  = 4;
+}
+
+message VariantMetaBuffer { 	
+	repeated VariantMetaUnit vmeta = 1;
+}
+
+message GenotypeBuffer {
+	repeated uint32  geno     = 1 [packed=true];
+}
+
+message GenotypeMetaBuffer {
+	repeated GenotypeMetaUnit gmeta = 1;
+}