$qual =~ tr/ \n\r/;;;/;
$qual =~ s/;;/;/g;
- $scores = Maasha::Fastq::dec_str2solexa_str( $qual );
+ $scores = Maasha::Fastq::dec_str2phred_str( $qual );
$entry = [ $name, $scores ];
test_aux_program "blat"
test_aux_program "bwa"
test_aux_program "bowtie"
+test_aux_program "bowtie2"
test_aux_program "formatdb"
+test_aux_program "hmmsearch"
test_aux_program "gnuplot"
test_aux_program "idba"
test_aux_program "muscle"
return $scores;
}
+sub dec_str2phred_str
+{
+ # Martin A. Hansen, November 2013.
+
+ # Converts a ; separated string of decimal scores to a
+ # string of Phred scores.
+
+ my ( $scores, # Decimal score string
+ ) = @_;
+
+ # Returns a string.
+
+ $scores =~ s/(-\d{1,2})/0/g;
+ $scores =~ s/(\d{1,2});?/dec2phred( $1 )/eg;
+
+ return $scores;
+}
sub get_entry
{