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 cbf88fe5b77111f05d0bc0d8bb6710466a9d8390..bb5c208b2947e3f7d95d1be6a205f351f9a52540 100755 (executable)
--- 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 f013d2fcdd39037d95137527a013986b625e9917..f64af41f0676a3634eb35616b58b62f7f9be904f 100644 (file)
--- 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.