-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
# Copyright (C) 2007-2009 Martin A. Hansen.
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+use warnings;
use strict;
use Maasha::Biopieces;
use Maasha::Common;
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $adaptor, $seq, $adaptor_len,
+my ( $options, $in, $out, $record, $adaptor, $seq, $adaptor_len,
$seq_len, $offset, $max_match, $max_mismatch, $pos );
$options = Maasha::Biopieces::parse_options(
{
if ( $options->{ "remove" } eq "after" )
{
- $record->{ "SEQ" } = substr $record->{ "SEQ" }, 0, $pos;
+ $record->{ "SEQ" } = substr $record->{ "SEQ" }, 0, $pos;
+ $record->{ "SCORES" } = substr $record->{ "SCORES" }, 0, $pos if $record->{ "SCORES" };
$record->{ "SEQ_LEN" } = $pos;
}
else
{
- $record->{ "SEQ" } = substr $record->{ "SEQ" }, $pos + $adaptor_len;
+ $record->{ "SEQ" } = substr $record->{ "SEQ" }, $pos + $adaptor_len;
+ $record->{ "SCORES" } = substr $record->{ "SCORES" }, $pos + $adaptor_len if $record->{ "SCORES" };
$record->{ "SEQ_LEN" } = length $record->{ "SEQ" };
}
}
}
}
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
BEGIN
{
- $run_time_beg = Maasha::Biopieces::run_time();
-
- Maasha::Biopieces::log_biopiece();
+ Maasha::Biopieces::status_set();
}
END
{
- Maasha::Biopieces::close_stream( $in );
- Maasha::Biopieces::close_stream( $out );
-
- $run_time_end = Maasha::Biopieces::run_time();
-
- Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+ Maasha::Biopieces::status_log();
}
__END__
-