From 12bb05ba3197c8e0ccb478d4b634f5555da14752 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Wed, 2 Nov 2011 09:46:06 +0000 Subject: [PATCH] added length check to bowtie_seq git-svn-id: http://biopieces.googlecode.com/svn/trunk@1610 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/bowtie_seq | 7 +++++++ 1 file changed, 7 insertions(+) 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"; -- 2.39.5