fixed solexa/phred code

git-svn-id: http://biopieces.googlecode.com/svn/trunk@654 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/read_fastq b/bp_bin/read_fastq
index 5173aba2ce35dd8b05400fe339b7b0a5e6d9e6aa..eb926618efdeae2dff7bd5ddc50fab0fd1771b43 100755 (executable)
--- a/bp_bin/read_fastq
+++ b/bp_bin/read_fastq
@@ -66,6 +66,7 @@ if ( $options->{ 'data_in' } )
         if ( $record = Maasha::Fastq::fastq2biopiece( $entry ) )
         {
             Maasha::Fastq::softmask_phred_str( $record->{ 'SEQ' }, $record->{ 'SCORES' }, $options->{ 'cutoff' } ) if $options->{ 'soft_mask' };
+            $record->{ 'SCORES' } = Maasha::Fastq::phred_str2dec_str( $record->{ 'SCORES' } ) if $options->{ 'convert2dec' };
 
             Maasha::Biopieces::put_record( $record, $out );
         }

diff --git a/bp_bin/read_solexa b/bp_bin/read_solexa
index b7a56396ed9393033fcfd34458aeb5ec6cd1de2e..f594d8079427432e644f1e2674cbe39461a20ca8 100755 (executable)
--- a/bp_bin/read_solexa
+++ b/bp_bin/read_solexa
@@ -68,6 +68,7 @@ if ( $options->{ 'data_in' } )
         if ( $record = Maasha::Fastq::fastq2biopiece( $entry ) )
         {
             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 );
         }

diff --git a/code_perl/Maasha/Fastq.pm b/code_perl/Maasha/Fastq.pm
index 3a8ed4332763d8155183570c8104c2ac240e7a5a..402720923fc35ed239d37c73d68cd4b4ea6ec3b8 100644 (file)
--- a/code_perl/Maasha/Fastq.pm
+++ b/code_perl/Maasha/Fastq.pm
@@ -257,6 +257,42 @@ END_C
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+sub solexa_str2dec_str
+{
+    # Martin A. Hansen, September 2009
+
+    # Converts a string of Solexa octal scores to a ; separated
+    # string of decimal scores.
+
+    my ( $scores,   # Solexa scores
+       ) = @_;
+    
+    # Returns a string.
+
+    $scores =~ s/(.)/ solexa2dec( $1 ) . ";"/eg;
+
+    return $scores;
+}
+
+
+sub phred_str2dec_str
+{
+    # Martin A. Hansen, September 2009
+
+    # Converts a string of Phred octal scores to a ; separated
+    # string of decimal scores.
+
+    my ( $scores,   # Phred scores
+       ) = @_;
+    
+    # Returns a string.
+
+    $scores =~ s/(.)/ phred2dec( $1 ) . ";"/eg;
+
+    return $scores;
+}
+
+
 sub get_entry
 {
     # Martin A. Hansen, July 2009.