From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 2 Nov 2011 09:46:06 +0000 (+0000)
Subject: added length check to bowtie_seq
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=12bb05ba3197c8e0ccb478d4b634f5555da14752;p=biopieces.git

added length check to bowtie_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1610 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/bowtie_seq b/bp_bin/bowtie_seq
index cf25188..57b6731 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";