bump version number to 1.7.0

fix #93
fix #94

Author: pmenzel

README.md

@@ -323,9 +323,9 @@ kaiju-mkfmi proteins
 This will create two intermediate files `proteins.bwt` and `proteins.sa`, and finally
 the file `proteins.fmi`, which is used by Kaiju.
 
-The option `-n` for `mkbwt` specifies the number of parallel threads. The more
+The option `-n` for `kaiju-mkbwt` specifies the number of parallel threads. The more
 threads are used, the higher the memory consumption becomes.  The option `-e`
-for `mkbwt` specifies the exponent of the suffix array checkpoint distances and
+for `kaiju-mkbwt` specifies the exponent of the suffix array checkpoint distances and
 therefore determines the trade-off between the size of the suffix array and the
 speed of the search. The default value is 5.
 

src/Config.hpp

@@ -1,4 +1,4 @@
-/* This file is part of Kaiju, Copyright 2015-2018 Peter Menzel and Anders Krogh,
+/* This file is part of Kaiju, Copyright 2015-2019 Peter Menzel and Anders Krogh,
  * Kaiju is licensed under the GPLv3, see the file LICENSE. */
 
 #ifndef CONFIG_H

src/ConsumerThread.hpp

@@ -1,4 +1,4 @@
-/* This file is part of Kaiju, Copyright 2015-2017 Peter Menzel and Anders Krogh,
+/* This file is part of Kaiju, Copyright 2015-2019 Peter Menzel and Anders Krogh,
  * Kaiju is licensed under the GPLv3, see the file LICENSE. */
 
 #ifndef CONSUMERTHREAD_H

src/version.hpp

@@ -4,6 +4,6 @@
 #ifndef KAIJU_VERSION_H
 #define KAIJU_VERSION_H
 
-#define KAIJUVERSION "1.6.3"
+#define KAIJUVERSION "1.7.0"
 
 #endif

util/kaiju-makedb

@@ -18,6 +18,10 @@ index_only=0
 
 
 usage() {
+	echo
+	echo kaiju-makedb
+	echo Copyright 2015-2019 Peter Menzel, Anders Krogh
+	echo License GPLv3+: GNU GPL version 3 or later, http://gnu.org/licenses/gpl.html
 	echo
 	echo This program creates a protein reference database and index for Kaiju.
 	echo
@@ -40,16 +44,16 @@ usage() {
 	echo
 	echo  " rvdb: Viral proteins from RVDB-prot"
 	echo
-	echo "For example: $0 -s nr will create the database file kaijud_db_nr.fmi"
+	echo "For example: $0 -s nr will create the database file kaiju_db_nr.fmi"
 	echo
 	echo Additional options:
 	echo
-	echo  "$s" -t X  Set number of parallel threads for index construction to X \(default:5\)
-	echo  "       The more threads are used, the higher the memory requirement becomes."
+	echo  "  -t X  Set number of parallel threads for index construction to X \(default:5\)"
+	echo  "        The more threads are used, the higher the memory requirement becomes."
 	echo
-	echo  "$s" --no-download  Do not download files, but use the existing files in the folder.
+	echo  "  --no-download   Do not download files, but use the existing files in the folder."
 	echo
-	echo  "$s" --index-only  Only create BWT and FMI from kaiju_db_*.faa files, implies --no-download.
+	echo  "  --index-only    Only create BWT and FMI from kaiju_db_*.faa files, implies --no-download."
 	echo
 }
 
@@ -118,7 +122,7 @@ command -v kaiju-mkfmi >/dev/null 2>/dev/null || { echo Error: kaiju-mkfmi not f
 command -v kaiju-mkbwt >/dev/null 2>/dev/null || { echo Error: kaiju-mkbwt not found in $PATH; exit 1; }
 command -v kaiju-convertNR >/dev/null 2>/dev/null || { echo Error: kaiju-convertNR not found in $PATH; exit 1; }
 
-[ -z "$DB" ] && { echo Error: Use option -s to select a source database; exit 1; }
+[ -z "$DB" ] && { echo Error: Use option -s to select a source database; usage; exit 1; }
 [ "$DB" = "mar" -o "$DB" = "mar_ref" -o "$DB" = "mar_db" -o "$DB" = "mar_mag" -o "$DB" = "nr" -o "$DB" = "nr_euk" -o "$DB" = "refseq" -o "$DB" = "progenomes" -o "$DB" = "viruses" -o "$DB" = "plasmids" -o "$DB" = "rvdb" ] || { echo Error: $DB is not a valid source database; usage; exit 1; }
 
 if [ "$DB" = "mar" -o "$DB" = "mar_ref" -o "$DB" = "mar_db" -o "$DB" = "mar_mag" ]