Follow in better way the alientrimmer style

conda_inst/build.sh

 #!/bin/bash
 BINDIR="$PREFIX/bin"
 echo "$BINDIR"
-cd $SRC_DIR/alientrimmerapp/src/
+cd $SRC_DIR/src/
 ./JarMaker.sh
 mv AlienTrimmer.jar $BINDIR/
 echo -e "#!/bin/bash\nSCRIPTPATH=\$(dirname \"\${BASH_SOURCE[0]}\")\njava -jar \$SCRIPTPATH/AlienTrimmer.jar \$@" > $BINDIR/AlienTrimmer

src/AlienTrimmer.java

@@ -212,6 +212,7 @@ public class AlienTrimmer {
     static String fid1, fseq, fid2, fqsc, rid1, rseq, rid2, rqsc;
     static byte[] score;
 
+
     // stuffs
     static byte cpt, b, bq, k_1, k2;
     static short i, j, x, lgt, l, start0, start, end0, end, n, scount;
@@ -220,7 +221,7 @@ public class AlienTrimmer {
     static long t, cur;
     static int imsk, iptn;
     static long lmsk, lptn, nptn, lkm, lpt;
-    static String line, seq;
+    static String line, seq, finfilename, rinfilename, foutfilename, routfilename, finext, rinext, foutext, routext;
     static ArrayList<String> contaminant;
     static TreeSet<Long> lts;
     static StringBuffer sb;
@@ -338,14 +339,14 @@ public class AlienTrimmer {
 		System.exit(0);
 	    }
 	}
-  String finfilename = finfile.toString();
-  String rinfilename = rinfile.toString();
-  String foutfilename = foutfile.toString();
-  String routfilename = routfile.toString();
-  String finext = finfilename.substring(finfilename.lastIndexOf(".") + 1, finfilename.length());
-  String rinext = rinfilename.substring(rinfilename.lastIndexOf(".") + 1, rinfilename.length());
-  String foutext = foutfilename.substring(foutfilename.lastIndexOf(".") + 1, foutfilename.length());
-  String routext = routfilename.substring(routfilename.lastIndexOf(".") + 1, routfilename.length());
+  finfilename = finfile.toString();
+  rinfilename = rinfile.toString();
+  foutfilename = foutfile.toString();
+  routfilename = routfile.toString();
+  finext = finfilename.substring(finfilename.lastIndexOf(".") + 1, finfilename.length());
+  rinext = rinfilename.substring(rinfilename.lastIndexOf(".") + 1, rinfilename.length());
+  foutext = foutfilename.substring(foutfilename.lastIndexOf(".") + 1, foutfilename.length());
+  routext = routfilename.substring(routfilename.lastIndexOf(".") + 1, routfilename.length());
 	//### testing default variables ##############################################################################
 	if ( finfile.toString().equals("no.file") ) { System.out.println("  no input file"); System.exit(1); }
 	if ( foutfile.toString().equals("no.file") ) foutfile = new File(finfile + ".at.fq");