V1.3.0

CMakeLists.txt

@@ -6,8 +6,8 @@ cmake_minimum_required(VERSION 2.6)
 # The version number.
 ################################################################################
 SET (gatb-tool_VERSION_MAJOR 1)
-SET (gatb-tool_VERSION_MINOR 0)
-SET (gatb-tool_VERSION_PATCH 1)
+SET (gatb-tool_VERSION_MINOR 3)
+SET (gatb-tool_VERSION_PATCH 0)
 
 IF (DEFINED MAJOR)
     SET (gatb-tool_VERSION_MAJOR ${MAJOR})

README.md

@@ -87,6 +87,15 @@ For further instructions on using simka, see User Manual, below.
 
 #Changelog
 
+* version 1.3.0 July 29, 2016:
+	- Bray-Crutis computed by default
+	- Better k-mer statistics
+	- Fix bug in script for creating heatmaps
+	- Add "all in memory" k-mer counter when k <= 15
+	- Fine grain paralellization for computing distances
+	- Clean all memory leaks with valgrind
+	- Update help messages
+	- Redirect stdout and stderr of parallel processes in specific log files 
 * version 1.0.1  March 16, 2016: minor updates ang bug fixes, first release on Github
 * version 1  Feb 16, 2016: stable version
 * version 0.1  May 28, 2015: initial public release

example/simple_test.sh

@@ -15,7 +15,12 @@ else
 fi
 
 # run simka
-$bindir/simka -verbose 0 -in ../example/simka_input.txt -out output/ -out-tmp temp_output
+command="$bindir/simka -in ../example/simka_input.txt -out output/ -out-tmp temp_output"
+#printf "$command\n\n"
+
+$command
+
+printf "\n\n\n"
 var=$?
 if [ $var -eq 0 ]
 then
@@ -25,5 +30,11 @@ else
     exit 1
 fi
 
+#printf "\nremoving all created dirs\n"
 # clean temp files
-rm -rf output temp_output
+rm -rf temp_output
+
+printf "\nCommand used:\n" 
+printf "\t$command\n"
+printf "Command for creating heatmaps and dendrogram:\n"
+printf "\tpython ../scripts/create_heatmaps.py output/\n"