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			ERROR CORRECTION TOOLS
			  Author: Y. Liu 
				  Y. Li
			  Version: 1.0
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1. Introduction

Here we provide a small tool for counting kmers in the error correction.
We implemented the tools in java and this tools can be successfully compil-
ed using Java JDK > 1.7_0_65. We provide several different versions of kmer
counting implementations in our tools. We support a stand-alone version
and the hadoop mapreduce version of k-mer counting.

2. How to compile the code

Our implementations use several external libraries to compile. You MUST add
those libraries to your classpath to compile. Here is the list of libraries:

a) guava-18.0.jar
b) junit-4.12-beta-3.jar
c) hadoop-common-2.5.2.jar
d) hadoop-hdfs-2.5.2.jar
e) hadoop-mapreduce-client-core-2.5.2.jar
f) hadoop-annotations-2.5.2.jar

We provide those libraries in our lib folder. 

TO COMPILE THE CODE:

e.g.:

   mkdir bin2
   
   javac -classpath lib/hadoop-mapreduce-client-core-2.5.2.jar: \
   lib/hadoop-hdfs-2.5.2.jar:lib/hadoop-common-2.5.2.jar: \
   lib/hadoop-annotations-2.5.2.jar:lib/guava-18.0.jar
   :lib/junit-4.12-beta-3.jar \ 
   -d bin2 \
   `find ./src -type f | grep java`
   
You can select different packages to compile. But please make sure you have
all the classpath set. If you have difficulties to compile the code, please
use the binary file we provided in the bin folder.


3. How to run the code

The classes that can be executed in our project is:

a) edu.jhu.cs.cs439.project.exactcount.ExactCountSerial
b) edu.jhu.cs.cs439.project.exactcount.ExactCountHadoop
c) edu.jhu.cs.cs439.project.kmercountwithcmsketch.CountKMersWithCountMinSerial
d) edu.jhu.cs.cs439.project.kmercountwithcmsketch.CountKMersWithCMSHadoop

For a) c), you can run the code by
java -classpath lib/guava-18.0.jar <class> <command line options>

For example:
  java -classpath lib/guava-18.0.jar \
  edu.jhu.cs.cs439.project.exactcount.ExactCountSerial \
  ../data/Hiv/hiv_sim_80_1.fq output
  
For b) d), you can run the code if you have hadoop environment setup.
For example:
  jar -cvf ExactCount1.jar -C bin/ .
  hadoop jar ExactCount1.jar \
  edu.jhu.cs.cs439.project.exactcount.ExactCountHadoop \
  <input data> <output data>
  
  If you hit a error, please see the usage for adding command line options.
  

4. How to run the script

First, make sure you have change mod to +x.
then call the script.
For example:
  script/evaluate
  
5. Please use the data we provided in the data folder

6. For source code details, please see our javadoc in the ./doc

7. This tool is under Apache License.

If you have any questions, please contact:

yliu120@jhmi.edu
yli86@jhmi.edu

Enjoy the tool!