#!/usr/bin/perl -w

# fixContigEnd.perl

# used by consed for fixing a contig end.  It is called by consed
# when the user runs consed as:
# consed -ace (acefile) -fixContigEnds
#


$szUsage = "fixContigEnd.perl (fasta file of reads for input) (fof for ace file, output)";

$szRelease = "100714";

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

$szPhrapExe = $szConsedHome . "/bin/phrap";

if ( $#ARGV == 0 ) {
    if ( $ARGV[0] eq "-v" || $ARGV[1] eq "-V" ) {
        print "$szRelease\n";
        exit( 0 );
    }
}

if ( $#ARGV != 1 ) {
    die "$szUsage";
}


$szFasta = $ARGV[0];
$szAceFOF = $ARGV[1];


open( filAceFOF, ">$szAceFOF" ) || die "couldn't open $szAceFOF for output";


( $szPhrapOut = $szFasta ) =~ s/\.fasta//;
$szPhrapErr = $szPhrapOut;
$szPhrapOut .= ".phrap.out";
$szPhrapErr .= ".phrap.err";


if ( -e "$szPhrapOut" ) {
    unlink( $szPhrapOut ) || die "couldn't delete $szPhrapOut $!";
}

if ( -e "$szPhrapErr" ) {
    unlink( $szPhrapErr ) || die "couldn't delete $szPhrapErr $!";
}


$szCommand = "$szPhrapExe $szFasta -new_ace -minscore 20 -retain_duplicates -vector_bound 0 -max_group_size 0 >$szPhrapOut 2>$szPhrapErr";
print "about to run: $szCommand\n";
!system( $szCommand ) || die "couldn't run $szCommand $!";

$szAceFile = $szFasta . ".ace";
print filAceFOF "$szAceFile\n";
close( filAceFOF );


# clean up is done by consed