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#! @SH@
#
# Copyright (C) 2005 Brendan Cully <brendan@kublai.com>
# Copyright (C) 2011 Jamey Sharp <jamey@minilop.net>
# 2024-2025 Roland Rosenfeld <roland@spinanker.de>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software Foundation,
# Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301,, USA.
prefix=@prefix@
exec_prefix=@exec_prefix@
libexecdir=@libexecdir@
m_vcf_query()
{
VCQ=${USE_LOCAL_LIB:-$libexecdir}/vcquery
QUERY="$1"
for file in ${OVERRIDE_VCF_FILES:-$VCF_FILES}
do
if test -r $file.cache -a $file.cache -nt $file
then
cmd="cat $file.cache"
else
if $VCQ $file > $file.cache
then
cmd="cat $file.cache"
else
cmd="$VCQ $file"
fi
fi
$cmd | grep -ie "$QUERY" | awk '
BEGIN { FS = OFS = "\t" }
$2 == "(null)" { $2 = " " }
{ NF = 2; $3 = "(VCF)"; print }'
done
}
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