From f8d937faec5c0c8166e81c8c806fe79a87897e12 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 25 Aug 2008 05:48:07 +0000
Subject: [PATCH] added --verbose run option for blast_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@221 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_c/Maasha/src/lib/ucsc.c       |  2 +-
 code_c/Maasha/src/repeat-O-matic.c |  4 ++--
 code_perl/Maasha/Biopieces.pm      | 36 +++++++++++++++++++++++++++++-
 3 files changed, 38 insertions(+), 4 deletions(-)

diff --git a/code_c/Maasha/src/lib/ucsc.c b/code_c/Maasha/src/lib/ucsc.c
index b349c94..92ec4d9 100644
--- a/code_c/Maasha/src/lib/ucsc.c
+++ b/code_c/Maasha/src/lib/ucsc.c
@@ -89,7 +89,7 @@ void bed_split( char *string, struct bed_entry12 *bed, int cols )
         } else if ( i == 3 ) {
             bed->q_id = mem_clone( ( char * ) field, field_len );
         } else if ( i == 4 ) {
-            bed->score = strtof( field, &pt );
+//            bed->score = strtof( field, &pt );
         } else if ( i == 5 ) {
             bed->strand = field[ 0 ];
         } else if ( i == 6 ) {
diff --git a/code_c/Maasha/src/repeat-O-matic.c b/code_c/Maasha/src/repeat-O-matic.c
index 765b4ef..9821129 100644
--- a/code_c/Maasha/src/repeat-O-matic.c
+++ b/code_c/Maasha/src/repeat-O-matic.c
@@ -18,8 +18,8 @@
 #include "fasta.h"
 
 
-// #define OLIGO_SIZE 15
-#define OLIGO_SIZE 5
+#define OLIGO_SIZE 15
+//#define OLIGO_SIZE 5
 #define SIZE ( 1 << ( OLIGO_SIZE * 2 ) )
 
 #define T 3   /* 11 on the rightmost two bits of bin. */
diff --git a/code_perl/Maasha/Biopieces.pm b/code_perl/Maasha/Biopieces.pm
index ce308a3..072846c 100644
--- a/code_perl/Maasha/Biopieces.pm
+++ b/code_perl/Maasha/Biopieces.pm
@@ -3473,7 +3473,41 @@ sub script_blast_seq
         }
     }
 
-    Maasha::Common::run( "blastall", "-p $options->{ 'program' } -e $options->{ 'e_val' } -a $options->{ 'cpus' } -m 8 -i $tmp_in -d $options->{ 'database' } -F $options->{ 'filter' } -o $tmp_out > /dev/null 2>&1", 1 );
+    if ( $options->{ 'verbose' } )
+    {
+        Maasha::Common::run(
+            "blastall",
+            join( " ",
+                "-p $options->{ 'program' }",
+                "-e $options->{ 'e_val' }",
+                "-a $options->{ 'cpus' }",
+                "-m 8",
+                "-i $tmp_in",
+                "-d $options->{ 'database' }",
+                "-F $options->{ 'filter' }",
+                "-o $tmp_out",
+            ),
+            1
+        );
+    }
+    else
+    {
+        Maasha::Common::run(
+            "blastall",
+            join( " ",
+                "-p $options->{ 'program' }",
+                "-e $options->{ 'e_val' }",
+                "-a $options->{ 'cpus' }",
+                "-m 8",
+                "-i $tmp_in",
+                "-d $options->{ 'database' }",
+                "-F $options->{ 'filter' }",
+                "-o $tmp_out",
+                "> /dev/null 2>&1"
+            ),
+            1
+        );
+    }
 
     unlink $tmp_in;
 
-- 
2.39.5