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POD update

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1 parent 367d38a commit d8bfc634b953bc371c229f4e4647742e3fc7c183 @fangly fangly committed Dec 13, 2012
Showing with 12 additions and 6 deletions.
  1. +12 −6 lib/Bio/Tools/Run/Alignment/Blat.pm
@@ -11,9 +11,8 @@ Bio::Tools::Run::Alignment::Blat
=head1 SYNOPSIS
use Bio::Tools::Run::Alignment::Blat;
-
my $factory = Bio::Tools::Run::Alignment::Blat->new(-db => $database);
- # $report is a SearchIO-compliant object
+ # $report is a Bio::SearchIO-compliant object
my $report = $factory->run($seqobj);
=head1 DESCRIPTION
@@ -240,7 +239,6 @@ sub db {
Function : pass in a B<UCSC-compliant> string for the query sequence(s)
Returns : string
Args : string
- Status : New
Note : Requires the sequence(s) in question be 2bit or nib format
Reminder : UCSC segment/regions coordinates are 0-based half-open (sequence
begins at 0, but start isn't counted with length), whereas BioPerl
@@ -265,7 +263,6 @@ sub qsegment {
Function : pass in a B<UCSC-compliant> string for the target sequence(s)
Returns : string
Args : string
- Status : New
Note : Requires the sequence(s) in question be 2bit or nib format
Reminder : UCSC segment/regions coordinates are 0-based half-open (sequence
begins at 0, but start isn't counted with length), whereas BioPerl
@@ -283,6 +280,16 @@ sub tsegment {
}
+=head2 outfile_name
+
+ Title : outfile_name
+ Usage : $obj->outfile_name('out.blat')
+ Function : Get or set the name for the BLAT output file
+ Returns : string
+ Args : string
+
+=cut
+
# override this, otherwise one gets a default of 'mlc'
sub outfile_name {
my $self = shift;
@@ -298,7 +305,6 @@ sub outfile_name {
Function : Pass in additional parameters to the returned Bio::SearchIO parser
Returns : Hash reference with Bio::SearchIO parameters
Args : Hash reference
- Status : New
Note : Currently, this implementation overrides any passed -format
parameter based on whether the output is changed ('out'). This
may change if requested, but we can't see the utility of doing so,
@@ -503,7 +509,7 @@ sub to_exe_string {
my $string = "$exe ".join(' ',@params);
- $string;
+ return $string;
}

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