From 0cb2f40c3090c3b930637802c1fc5afa48d7642f Mon Sep 17 00:00:00 2001 From: martinahansen Date: Mon, 8 Jun 2009 13:53:54 +0000 Subject: [PATCH] fixed minor bugs git-svn-id: http://biopieces.googlecode.com/svn/trunk@513 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/get_genome_seq | 2 +- code_perl/Maasha/Biopieces.pm | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/bp_bin/get_genome_seq b/bp_bin/get_genome_seq index b5ea5a7..737469d 100755 --- a/bp_bin/get_genome_seq +++ b/bp_bin/get_genome_seq @@ -68,7 +68,7 @@ if ( $options->{ "genome" } ) map { $lookup_hash{ $_->[ 0 ] } = [ $_->[ 1 ], $_->[ 2 ] ] } @{ $index }; - if ( exists $lookup_hash{ $options->{ "chr" } } and defined $options->{ "beg" } and ( defined $options->{ "end" } or defined $options->{ "len" } ) ) + if ( defined $options->{ "chr" } and exists $lookup_hash{ $options->{ "chr" } } and defined $options->{ "beg" } and ( defined $options->{ "end" } or defined $options->{ "len" } ) ) { ( $index_beg, $index_len ) = @{ $lookup_hash{ $options->{ "chr" } } }; diff --git a/code_perl/Maasha/Biopieces.pm b/code_perl/Maasha/Biopieces.pm index 44b589b..09218a6 100644 --- a/code_perl/Maasha/Biopieces.pm +++ b/code_perl/Maasha/Biopieces.pm @@ -302,10 +302,10 @@ sub parse_options push @{ $arg_list }, ( - { long => 'help', short => '?', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'stream_in', short => 'I', type => 'file!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'stream_out', short => 'O', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'verbose', short => 'v', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'help', short => '?', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'stream_in', short => 'I', type => 'file!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'stream_out', short => 'O', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'verbose', short => 'v', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, ); check_duplicates_args( $arg_list ); -- 2.39.5