X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fbowtie_seq;h=07374216593d0a6f24d7fd858f6de3b21c6377ec;hb=5de6112b70b59420b245ce636a8b2e3c90acbe00;hp=cf25188e6e42019ae131ee23fbd10837b3adf9af;hpb=acd65310e4cf43ad3fb8af7810cbc246301b3b87;p=biopieces.git

diff --git a/bp_bin/bowtie_seq b/bp_bin/bowtie_seq
index cf25188..0737421 100755
--- a/bp_bin/bowtie_seq
+++ b/bp_bin/bowtie_seq
@@ -35,6 +35,11 @@ use Maasha::Fastq;
 use Maasha::Fasta;
 use Maasha::Calc;
 
+use constant {
+    SEQ_NAME => 0,
+    SEQ      => 1,
+    SCORES   => 2,
+};
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
@@ -75,6 +80,7 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     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";
@@ -82,6 +88,7 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     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";
@@ -96,7 +103,7 @@ push @args, "-n $options->{ 'mismatches' }";
 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" unless $type eq "FASTA";
+push @args, "--phred33-quals" unless $type eq "FASTA";
 
 if ( defined $options->{ 'max_hits' } ) {
     push @args, "-k $options->{ 'max_hits' }";