m_vcf.sh.in

#! @SH@
#
#     Copyright (C) 2005  Brendan Cully <brendan@kublai.com>
#     Copyright (C) 2011  Jamey Sharp <jamey@minilop.net>
#                   2024  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@
libdir=@libdir@

m_vcf_query()
{
  VCQ=${USE_LOCAL_LIB:-$libdir}/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
}