From af29b0a2a874e7650d521030289320dc9bc17a37 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 8 Mar 2010 16:00:51 +0000
Subject: [PATCH] tweaks to blat_seq to avoid introns in fastMap - still going
 nowhere

git-svn-id: http://biopieces.googlecode.com/svn/trunk@896 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/blat_seq | 24 +++++++++++++++---------
 1 file changed, 15 insertions(+), 9 deletions(-)

diff --git a/bp_bin/blat_seq b/bp_bin/blat_seq
index 073cfd8..0069302 100755
--- a/bp_bin/blat_seq
+++ b/bp_bin/blat_seq
@@ -68,14 +68,20 @@ if ( $options->{ 'database' } ) {
     $subject_file = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/fasta/$options->{ 'genome' }.fna";
 }
 
-$blat_args .= " -tileSize=$options->{ 'tile_size' }";
-$blat_args .= " -oneOff=$options->{ 'one_off' }";
-$blat_args .= " -minIdentity=$options->{ 'min_identity' }";
-$blat_args .= " -minScore=$options->{ 'min_score' }";
-$blat_args .= " -stepSize=$options->{ 'step_size' }";
-$blat_args .= " -maxIntron=$options->{ 'intron_max' }";
-$blat_args .= " -fastMap" if $options->{ 'fast_map' };
-# $blat_args .= " -ooc=" . Maasha::Config::genome_blat_ooc( $options->{ "genome" }, 11 ) if $options->{ 'ooc' };
+if ( $options->{ 'fast_map' } )
+{
+    $blat_args .= " -fastMap";
+}
+else
+{
+    $blat_args .= " -tileSize=$options->{ 'tile_size' }";
+    $blat_args .= " -oneOff=$options->{ 'one_off' }";
+    $blat_args .= " -minIdentity=$options->{ 'min_identity' }";
+    $blat_args .= " -minScore=$options->{ 'min_score' }";
+    $blat_args .= " -stepSize=$options->{ 'step_size' }";
+    $blat_args .= " -maxIntron=$options->{ 'intron_max' }";
+    # $blat_args .= " -ooc=" . Maasha::Config::genome_blat_ooc( $options->{ "genome" }, 11 ) if $options->{ 'ooc' };
+}
 
 $tmp_dir = Maasha::Biopieces::get_tmpdir();
 $query_file = "$tmp_dir/blat.seq";
@@ -95,7 +101,7 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
 close $fh_out;
 
-$blat_args .= " -t=dnax" if $type eq "protein";
+$blat_args .= " -t=dnax" if $type eq "PROTEIN";
 $blat_args .= " -q=$type";
 
 $result_file = "$tmp_dir/blat.psl";
-- 
2.39.5