X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fread_454;h=96c6a4f0f8bdec096e9b85530dd71055b6dd47c7;hb=27a34d675d07468851f2076a62ca2b8dbefb5923;hp=ae2f4b0ce239a2468b982d33bbaf7aea857d4399;hpb=64a0c0c83ce39727ba86091490f2586450cd2411;p=biopieces.git

diff --git a/bp_bin/read_454 b/bp_bin/read_454
index ae2f4b0..96c6a4f 100755
--- a/bp_bin/read_454
+++ b/bp_bin/read_454
@@ -67,6 +67,7 @@ if ( $options->{ 'data_in' } )
         $qual = get_qual( $qual_in );
         
         check_names( $fasta, $qual );
+        check_lengths( $fasta, $qual );
 
         $record = {
             SEQ_NAME    => $fasta->[ 0 ],
@@ -129,7 +130,7 @@ sub get_qual
     $qual =~ tr/ \n\r/;;;/;
     $qual =~ s/;;/;/g;
 
-    $scores = Maasha::Fastq::dec_str2solexa_str( $qual );
+    $scores = Maasha::Fastq::dec_str2phred_str( $qual );
 
     $entry = [ $name, $scores ];
 
@@ -164,6 +165,28 @@ sub check_names
 }
 
 
+sub check_lengths
+{
+    # Martin A. Hansen, April 2011.
+
+    # Check if the lengths of the fasta and qual strings are the same
+    # and raise an error if not.
+
+    my ( $fasta,    # fasta entry
+         $qual,     # qual entry
+       ) = @_;
+
+    # Returns nothing.
+
+    my ( $f_len, $q_len );
+
+    $f_len = length $fasta->[ 1 ];
+    $q_len = length $qual->[ 1 ];
+
+    Maasha::Common::error( qq(lengths don't match "$f_len" != "$q_len") ) if $f_len != $q_len;
+}
+
+
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<