From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 24 Nov 2009 17:26:35 +0000 (+0000)
Subject: kiss_sort()
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=631f074917d4608da0553c8d7d68c4bd676e7fe0;p=biopieces.git

kiss_sort()

git-svn-id: http://biopieces.googlecode.com/svn/trunk@769 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/upload_to_KISS b/bp_bin/upload_to_KISS
index cbf88fe..bb5c208 100755
--- a/bp_bin/upload_to_KISS
+++ b/bp_bin/upload_to_KISS
@@ -118,6 +118,7 @@ if ( $options->{ 'track_name' } )
 
         Maasha::Filesys::file_copy( "$tmp_dir/$key", "$dst_dir/track_data.kiss" );
 
+        Maasha::KISS::IO::kiss_sort( "$dst_dir/track_data.kiss" );
         Maasha::KISS::IO::kiss_index( "$dst_dir/track_data.kiss" );
 
         unlink "$tmp_dir/$key";
diff --git a/code_perl/Maasha/KISS/IO.pm b/code_perl/Maasha/KISS/IO.pm
index f013d2f..f64af41 100644
--- a/code_perl/Maasha/KISS/IO.pm
+++ b/code_perl/Maasha/KISS/IO.pm
@@ -154,13 +154,30 @@ sub kiss_sql_get
 }
 
 
+sub kiss_sort
+{
+    # Martin A. Hansen, November 2009.
+
+    # Sorts a KISS file on S_BEG and S_END
+
+    my ( $file,   # KISS file
+       ) = @_;
+
+    # Returns nothing.
+
+    `sort -k 2,2n -k 3,3n > $file.sort`;
+
+    rename "$file.sort" $file;
+}
+
+
 sub kiss_index
 {
     # Martin A, Hansen, November 2009.
 
     # Creates an index of a sorted KISS file.
 
-    my ( $file,   # KISS file to index
+    my ( $file,   # KISS file
        ) = @_;
 
     # Returns a hashref.