copyright updates, prep for release

DerrickWood · Jan 4, 2014 · 54af206 · 54af206
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Showing 26 changed files with 33 additions and 33 deletions.
diff --git a/README b/README
@@ -172,12 +172,12 @@ have multi-threading enabled) in December 2013:
 
   10m50s  *Step 1 (create set)
      n/a   Step 2 (reduce database, optional and skipped)
-  21m24s  *Step 3 (sort set)
-   0m47s   Step 4 (GI number to file map)
-   0m58s   Step 5 (File to taxon map)
-  39m10s  *Step 6 (set LCA values)
+  24m10s  *Step 3 (sort set)
+   1m28s   Step 4 (GI number to file map)
+   1m10s   Step 5 (File to taxon map)
+  47m08s  *Step 6 (set LCA values)
   ------
-  73m10s   Total build time
+  84m47s   Total build time
 
 To create a custom database, or to use a database from another
 source, see CUSTOM DATABASES.

diff --git a/install_kraken.sh b/install_kraken.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+# Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
 #
 # This file is part of the Kraken taxonomic classification system.
 #

diff --git a/scripts/add_to_library.sh b/scripts/add_to_library.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+# Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

diff --git a/scripts/build_kraken_db.sh b/scripts/build_kraken_db.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+# Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

diff --git a/scripts/clean_db.sh b/scripts/clean_db.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+# Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

diff --git a/scripts/download_genomic_library.sh b/scripts/download_genomic_library.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+# Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

diff --git a/scripts/download_taxonomy.sh b/scripts/download_taxonomy.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+# Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

diff --git a/scripts/kraken-build.broken b/scripts/kraken-build.broken
@@ -1,6 +1,6 @@
 #!/usr/bin/perl
 
-# Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+# Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #
@@ -235,7 +235,7 @@ sub display_help {
 
 sub display_version {
   print "Kraken version #####=VERSION=#####\n";
-  print "Copyright 2013, Derrick Wood (dwood\@cs.umd.edu)\n";
+  print "Copyright 2013-2014, Derrick Wood (dwood\@cs.umd.edu)\n";
   exit 0;
 }
 

diff --git a/scripts/kraken-report.broken b/scripts/kraken-report.broken
@@ -1,6 +1,6 @@
 #!/usr/bin/perl
 
-# Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+# Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #
@@ -42,7 +42,7 @@ sub display_help {
 
 sub display_version {
   print "Kraken version #####=VERSION=#####\n";
-  print "Copyright 2013, Derrick Wood (dwood\@cs.umd.edu)\n";
+  print "Copyright 2013-2014, Derrick Wood (dwood\@cs.umd.edu)\n";
   exit 0;
 }
 

diff --git a/scripts/kraken.broken b/scripts/kraken.broken
@@ -1,6 +1,6 @@
 #!/usr/bin/perl
 
-# Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+# Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #
@@ -128,6 +128,6 @@ sub display_help {
 
 sub display_version {
   print "Kraken version #####=VERSION=#####\n";
-  print "Copyright 2013, Derrick Wood (dwood\@cs.umd.edu)\n";
+  print "Copyright 2013-2014, Derrick Wood (dwood\@cs.umd.edu)\n";
   exit 0;
 }
diff --git a/scripts/shrink_db.sh b/scripts/shrink_db.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+# Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

diff --git a/scripts/standard_installation.sh b/scripts/standard_installation.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+# Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

diff --git a/scripts/upgrade_db.sh b/scripts/upgrade_db.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+# Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

diff --git a/src/classify.cpp b/src/classify.cpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+ * Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/db_shrink.cpp b/src/db_shrink.cpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+ * Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/db_sort.cpp b/src/db_sort.cpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+ * Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/krakendb.cpp b/src/krakendb.cpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+ * Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/krakendb.hpp b/src/krakendb.hpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+ * Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/krakenutil.cpp b/src/krakenutil.cpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+ * Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/krakenutil.hpp b/src/krakenutil.hpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+ * Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/make_file_to_taxon_map.cpp b/src/make_file_to_taxon_map.cpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+ * Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/quickfile.cpp b/src/quickfile.cpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+ * Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/quickfile.hpp b/src/quickfile.hpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+ * Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/seqreader.cpp b/src/seqreader.cpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+ * Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/seqreader.hpp b/src/seqreader.hpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+ * Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/set_lcas.cpp b/src/set_lcas.cpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013, Derrick Wood <dwood@cs.umd.edu>
+ * Copyright 2013-2014, Derrick Wood <dwood@cs.umd.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *