package global;

/**
 *
 * @author nick
 */
public class Data {

    // software info
    public static final String APP_NAME = "ATAV (Analysis Tool for Annotated Variants)";
    public static String VERSION = "trunk";
    public static String userName = System.getProperty("user.name");

    // atav home path
    public static final String ATAV_HOME = "/nfs/goldstein/software/atav_home/"; // location of compiled Jar file
//    public static final String ATAV_HOME = ""; // local testing

    // system config file path
    public static final String SYSTEM_CONFIG = Data.ATAV_HOME +  "config/atav.dragen.system.config.properties";
    public static final String SYSTEM_CONFIG_FOR_DEBUG = Data.ATAV_HOME +  "config/atav.dragen.debug.system.config.properties";

    // system default values
    public static final int NO_FILTER = Integer.MAX_VALUE;
    public static final String NO_FILTER_STR = "";

    public static final byte BYTE_NA = Byte.MIN_VALUE;
    public static final short SHORT_NA = Short.MIN_VALUE;
    public static final int INTEGER_NA = Integer.MIN_VALUE;
    public static final float FLOAT_NA = Float.MIN_VALUE;
    public static final double DOUBLE_NA = Double.MIN_VALUE;
    public static String STRING_NA = "NA";
    public static String STRING_NAN = "NaN";
}

@@ -307,125 +307,79 @@
 path
-%0A    public static final String ATAV_HOME = %22/nfs/goldstein/software/atav_home/%22; // location of compiled Jar file%0A//
+ (location of executable jar file, config dir, data dir, lib dir etc.)%0A
     
@@ -384,38 +384,32 @@
   public static 
-final 
 String ATAV_HOME
@@ -415,28 +415,54 @@
 E = 
-%22%22; // local testing
+System.getenv().getOrDefault(%22ATAV_HOME%22, %22%22);
 %0A%0A  
@@ -545,33 +545,32 @@
 Data.ATAV_HOME +
- 
  %22config/atav.dr
@@ -674,17 +674,16 @@
 V_HOME +
- 
  %22config

set atav home dir path as environment variable