#!/usr/bin/perl -w


use File::Basename;


$szUsage = "filter454Reads.perl (fasta file of 454 reads) (linker fasta) (puc19 fasta) (cross_match output file for linker) (cross_match output for puc19)";

if ( $#ARGV >= 0 ) {
   if ( lc( $ARGV[0]) eq "-v" ) {
      print "081028\n";
      exit(0);
   }
}


if ( $#ARGV != 4 ) {
   die "usage: $szUsage\n";
}


$sz454Reads = $ARGV[0];
$szLinker = $ARGV[1];
$szPuc = $ARGV[2];
$szLinkerOutput = $ARGV[3];
$szPucOutput = $ARGV[4];

defined( $szConsedHome = $ENV{'CONSED_HOME'} ) ||
    ( $szConsedHome = "/usr/local/genome" );

if ( !-r $szConsedHome ) {
    die "Could not find $szConsedHome for the root of the consed programs.  Is the
 environment variable CONSED_HOME set correctly?";
}

$szCrossMatch = $szConsedHome . "/bin/cross_match";

if ( -e "$szLinkerOutput" ) {
   unlink( $szLinkerOutput );
}

if ( -e "$szPucOutput" ) {
   unlink( $szPucOutput );
}


# warning--$sz454Reads must come before $szLinker
$szCommand = "$szCrossMatch -tags -minscore 16 $sz454Reads $szLinker >$szLinkerOutput";

!system( $szCommand ) || die "couldn't execute $szCommand";



# $szPuc may be in a write-only directory.  So copy it to your local directory

$szPucBasename = basename( $szPuc );

$szCommand = "cp $szPuc $szPucBasename";
!system( $szCommand ) || die "couldn't execute $szCommand";


# warning $szPuc must come before $sz454Reads 
$szCommand = "$szCrossMatch -masklevel 101 -tags $szPucBasename $sz454Reads >$szPucOutput";

!system( $szCommand ) || die "couldn't execute $szCommand";


# these can be commented-out for troubleshooting
unlink( $sz454Reads );
unlink( $szPucBasename );
unlink( $szPucBasename . ".log" );