[Genabel-commits] r1915 - in pkg/OmicABEL: . src src/float2double
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Jan 18 21:35:31 CET 2015
Author: dfabregat
Date: 2015-01-18 21:35:31 +0100 (Sun, 18 Jan 2015)
New Revision: 1915
Added:
pkg/OmicABEL/src/METADATA.h
Modified:
pkg/OmicABEL/Makefile
pkg/OmicABEL/src/CLAK_GWAS.c
pkg/OmicABEL/src/GWAS.c
pkg/OmicABEL/src/GWAS.h
pkg/OmicABEL/src/REML.c
pkg/OmicABEL/src/REML.h
pkg/OmicABEL/src/blas.h
pkg/OmicABEL/src/databel.c
pkg/OmicABEL/src/databel.h
pkg/OmicABEL/src/double_buffering.c
pkg/OmicABEL/src/double_buffering.h
pkg/OmicABEL/src/fgls_chol.c
pkg/OmicABEL/src/fgls_chol.h
pkg/OmicABEL/src/fgls_eigen.c
pkg/OmicABEL/src/fgls_eigen.h
pkg/OmicABEL/src/float2double/float2double.c
pkg/OmicABEL/src/lapack.h
pkg/OmicABEL/src/ooc_BLAS.c
pkg/OmicABEL/src/ooc_BLAS.h
pkg/OmicABEL/src/optimization.c
pkg/OmicABEL/src/optimization.h
pkg/OmicABEL/src/options.h
pkg/OmicABEL/src/statistics.c
pkg/OmicABEL/src/statistics.h
pkg/OmicABEL/src/timing.c
pkg/OmicABEL/src/timing.h
pkg/OmicABEL/src/utils.c
pkg/OmicABEL/src/utils.h
pkg/OmicABEL/src/wrappers.c
pkg/OmicABEL/src/wrappers.h
Log:
Added version number to improve packaging, bug tracking, etc.
Starting from 0.8.0 as suggested by Yurii in:
http://lists.r-forge.r-project.org/pipermail/genabel-devel/2015-January/001252.html
Also, updated year ranges in copyright headers.
Modified: pkg/OmicABEL/Makefile
===================================================================
--- pkg/OmicABEL/Makefile 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/Makefile 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,9 +1,11 @@
include ./make.inc
+VERSION=0.8.0
+
SRCDIR = ./src
RESH_SRCDIR = ./src/reshuffle
F2D_SRCDIR = ./src/float2double
-CLAKGWAS = ./bin/CLAK-GWAS
+CLAKGWAS = ./bin/OmicABEL
RESHUFFLE = ./bin/reshuffle
F2D = ./bin/float2double
@@ -41,7 +43,7 @@
# Dirty, improve
platform=Linux
-bindistDir=OmicABEL-$(platform)-bin
+bindistDir=OmicABEL-$(VERSION)-$(platform)-bin
bindist: ./bin/ $(CLAKGWAS) $(RESHUFFLE) $(F2D)
rm -rf $(bindistDir)
mkdir $(bindistDir)
@@ -64,13 +66,9 @@
$(RM) $(F2D)
-src/CLAK_GWAS.o: src/CLAK_GWAS.c src/wrappers.h src/utils.h src/GWAS.h \
- src/databel.h src/timing.h src/REML.h src/fgls_chol.h src/fgls_eigen.h \
- src/double_buffering.h
-src/GWAS.o: src/GWAS.c src/utils.h src/GWAS.h src/databel.h src/wrappers.h
-src/REML.o: src/REML.c src/options.h src/blas.h src/lapack.h src/ooc_BLAS.h \
- src/wrappers.h src/utils.h src/GWAS.h src/databel.h src/statistics.h \
- src/optimization.h src/REML.h
+src/CLAK_GWAS.o: src/CLAK_GWAS.c src/METADATA.h src/wrappers.h src/utils.h \
+ src/GWAS.h src/databel.h src/timing.h src/REML.h src/fgls_chol.h \
+ src/fgls_eigen.h src/double_buffering.h
src/databel.o: src/databel.c src/databel.h src/wrappers.h
src/double_buffering.o: src/double_buffering.c src/GWAS.h src/databel.h \
src/wrappers.h src/double_buffering.h
@@ -80,12 +78,15 @@
src/fgls_eigen.o: src/fgls_eigen.c src/blas.h src/lapack.h src/options.h \
src/GWAS.h src/databel.h src/wrappers.h src/timing.h \
src/double_buffering.h src/ooc_BLAS.h src/utils.h src/fgls_eigen.h
+src/GWAS.o: src/GWAS.c src/utils.h src/GWAS.h src/databel.h src/wrappers.h
src/ooc_BLAS.o: src/ooc_BLAS.c src/blas.h src/lapack.h src/options.h \
src/GWAS.h src/databel.h src/wrappers.h src/utils.h \
src/double_buffering.h src/ooc_BLAS.h
src/optimization.o: src/optimization.c src/optimization.h
+src/REML.o: src/REML.c src/options.h src/blas.h src/lapack.h src/ooc_BLAS.h \
+ src/wrappers.h src/utils.h src/GWAS.h src/databel.h src/statistics.h \
+ src/optimization.h src/REML.h
src/statistics.o: src/statistics.c src/statistics.h
src/timing.o: src/timing.c src/timing.h
-src/utils.o: src/utils.c \
- src/GWAS.h src/databel.h src/wrappers.h src/utils.h
+src/utils.o: src/utils.c src/GWAS.h src/databel.h src/wrappers.h src/utils.h
src/wrappers.o: src/wrappers.c src/GWAS.h src/databel.h src/wrappers.h
Modified: pkg/OmicABEL/src/CLAK_GWAS.c
===================================================================
--- pkg/OmicABEL/src/CLAK_GWAS.c 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/CLAK_GWAS.c 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
@@ -28,6 +28,7 @@
#include <sys/stat.h>
+#include "METADATA.h"
#include "wrappers.h"
#include "utils.h"
#include "timing.h"
@@ -63,6 +64,8 @@
FGLS_config_t cf;
struct timeval start, end;
+ print_banner();
+
status = parse_input( argc, argv, var,
cov_base, phi_base, snp_base, pheno_base, out_base,
&nths, &thres, &xtile, &ytile, &xb, &yb, &write_output );
@@ -488,6 +491,14 @@
cf->y_tile = ytile;
}
+void print_banner( void )
+{
+ printf("\n* This is OmicABEL version %s.\n", OMICABEL_VERSION);
+ printf("* Copyright (C) 2010-2015 Diego Fabregat-Traver, Paolo Bientinesi.\n");
+ printf("* OmicABEL is distributed under the GNU GPL version 3 or later (see LICENSE).\n");
+ printf("* For a tutorial and more, see http://www.genabel.org/packages/OmicABEL.\n\n\n");
+}
+
void print_info( FGLS_config_t *cf )
{
printf( "\nRunning a Genome-Wide Association Study of the following size:\n" );
Modified: pkg/OmicABEL/src/GWAS.c
===================================================================
--- pkg/OmicABEL/src/GWAS.c 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/GWAS.c 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/GWAS.h
===================================================================
--- pkg/OmicABEL/src/GWAS.h 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/GWAS.h 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Added: pkg/OmicABEL/src/METADATA.h
===================================================================
--- pkg/OmicABEL/src/METADATA.h (rev 0)
+++ pkg/OmicABEL/src/METADATA.h 2015-01-18 20:35:31 UTC (rev 1915)
@@ -0,0 +1 @@
+#define OMICABEL_VERSION "0.8.0"
Modified: pkg/OmicABEL/src/REML.c
===================================================================
--- pkg/OmicABEL/src/REML.c 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/REML.c 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/REML.h
===================================================================
--- pkg/OmicABEL/src/REML.h 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/REML.h 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/blas.h
===================================================================
--- pkg/OmicABEL/src/blas.h 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/blas.h 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/databel.c
===================================================================
--- pkg/OmicABEL/src/databel.c 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/databel.c 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/databel.h
===================================================================
--- pkg/OmicABEL/src/databel.h 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/databel.h 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/double_buffering.c
===================================================================
--- pkg/OmicABEL/src/double_buffering.c 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/double_buffering.c 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/double_buffering.h
===================================================================
--- pkg/OmicABEL/src/double_buffering.h 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/double_buffering.h 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/fgls_chol.c
===================================================================
--- pkg/OmicABEL/src/fgls_chol.c 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/fgls_chol.c 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/fgls_chol.h
===================================================================
--- pkg/OmicABEL/src/fgls_chol.h 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/fgls_chol.h 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/fgls_eigen.c
===================================================================
--- pkg/OmicABEL/src/fgls_eigen.c 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/fgls_eigen.c 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/fgls_eigen.h
===================================================================
--- pkg/OmicABEL/src/fgls_eigen.h 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/fgls_eigen.h 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/float2double/float2double.c
===================================================================
--- pkg/OmicABEL/src/float2double/float2double.c 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/float2double/float2double.c 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2013, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/lapack.h
===================================================================
--- pkg/OmicABEL/src/lapack.h 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/lapack.h 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/ooc_BLAS.c
===================================================================
--- pkg/OmicABEL/src/ooc_BLAS.c 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/ooc_BLAS.c 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/ooc_BLAS.h
===================================================================
--- pkg/OmicABEL/src/ooc_BLAS.h 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/ooc_BLAS.h 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/optimization.c
===================================================================
--- pkg/OmicABEL/src/optimization.c 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/optimization.c 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/optimization.h
===================================================================
--- pkg/OmicABEL/src/optimization.h 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/optimization.h 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/options.h
===================================================================
--- pkg/OmicABEL/src/options.h 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/options.h 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/statistics.c
===================================================================
--- pkg/OmicABEL/src/statistics.c 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/statistics.c 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/statistics.h
===================================================================
--- pkg/OmicABEL/src/statistics.h 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/statistics.h 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/timing.c
===================================================================
--- pkg/OmicABEL/src/timing.c 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/timing.c 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/timing.h
===================================================================
--- pkg/OmicABEL/src/timing.h 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/timing.h 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/utils.c
===================================================================
--- pkg/OmicABEL/src/utils.c 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/utils.c 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/utils.h
===================================================================
--- pkg/OmicABEL/src/utils.h 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/utils.h 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/wrappers.c
===================================================================
--- pkg/OmicABEL/src/wrappers.c 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/wrappers.c 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
Modified: pkg/OmicABEL/src/wrappers.h
===================================================================
--- pkg/OmicABEL/src/wrappers.h 2015-01-14 09:28:26 UTC (rev 1914)
+++ pkg/OmicABEL/src/wrappers.h 2015-01-18 20:35:31 UTC (rev 1915)
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2012, Diego Fabregat-Traver and Paolo Bientinesi.
+ * Copyright (c) 2010-2015, Diego Fabregat-Traver and Paolo Bientinesi.
* All rights reserved.
*
* This file is part of OmicABEL.
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