use Maasha::Fasta;
use Maasha::Calc;
+use constant {
+ SEQ_NAME => 0,
+ SEQ => 1,
+ SCORES => 2,
+};
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
if ( $entry = Maasha::Fastq::biopiece2fastq( $record ) )
{
Maasha::Common::error( "Mixed FASTA and FASTQ entries in stream" ) if defined $type and $type ne "FASTQ";
+ Maasha::Common::error( "Sequence longer than 1024 not allowed") if length( $entry->[ SEQ ] ) > 1024;
Maasha::Fastq::put_entry( $entry, $fh_out );
$type = "FASTQ";
elsif ( $entry = Maasha::Fasta::biopiece2fasta( $record ) )
{
Maasha::Common::error( "Mixed FASTA and FASTQ entries in stream" ) if defined $type and $type ne "FASTA";
+ Maasha::Common::error( "Sequence longer than 1024 not allowed") if length( $entry->[ SEQ ] ) > 1024;
Maasha::Fasta::put_entry( $entry, $fh_out );
$type = "FASTA";
push @args, "-v $options->{ 'mismatches' }"; # DANGER: using seed mismatches as alignment mismatches - may work, may not!
push @args, "-f" if $type eq "FASTA";
push @args, "-p $options->{ 'cpus' }";
-push @args, "--phred64-quals";
+push @args, "--phred64-quals" unless $type eq "FASTA";
if ( defined $options->{ 'max_hits' } ) {
push @args, "-k $options->{ 'max_hits' }";