polished read_454 and added tests

[biopieces.git] / bp_bin / read_454

diff --git a/bp_bin/read_454 b/bp_bin/read_454
index 012bc3391525e83b1a7ecd958c2c9476e6265302..ae2f4b0ce239a2468b982d33bbaf7aea857d4399 100755 (executable)
--- a/bp_bin/read_454
+++ b/bp_bin/read_454
@@ -42,13 +42,9 @@ my ( $options, $in, $out, $record, $data_in, $qual_in, $num, $fasta, $qual, @seq
 
 $options = Maasha::Biopieces::parse_options(
     [
-        { long => 'data_in',     short => 'i', type => 'file!',  mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
-        { long => 'qual_in',     short => 'q', type => 'file!',  mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
-        { long => 'num',         short => 'n', type => 'uint',   mandatory => 'no',  default => undef, allowed => undef, disallowed => '0' },
-        { long => 'convert2dec', short => 'c', type => 'flag',   mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
-        { long => 'cutoff',      short => 'C', type => 'int',    mandatory => 'no',  default => 20,    allowed => undef, disallowed => undef },
-        { long => 'soft_mask',   short => 's', type => 'flag',   mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
-        { long => 'mean',        short => 'm', type => 'flag',   mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
+        { long => 'data_in', short => 'i', type => 'file!',  mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+        { long => 'qual_in', short => 'q', type => 'file!',  mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+        { long => 'num',     short => 'n', type => 'uint',   mandatory => 'no',  default => undef, allowed => undef, disallowed => '0' },
     ]   
 );
 
@@ -79,11 +75,6 @@ if ( $options->{ 'data_in' } )
             SCORES      => $qual->[ 1 ],
         };
 
-        $record->{ 'SCORES_MEAN' } = sprintf "%.2f", Maasha::Fastq::solexa_str_mean( $qual->[ 1 ] ) if $options->{ 'mean' };
-        
-        Maasha::Fastq::softmask_solexa_str( $record->{ 'SEQ' }, $record->{ 'SCORES' }, $options->{ 'cutoff' } ) if $options->{ 'soft_mask' };
-        $record->{ 'SCORES' } = Maasha::Fastq::solexa_str2dec_str( $record->{ 'SCORES' } ) if $options->{ 'convert2dec' };
-
         Maasha::Biopieces::put_record( $record, $out );
 
         last if $options->{ "num" } and $num == $options->{ "num" };