Commit aedce509 authored by Amine  GHOZLANE's avatar Amine GHOZLANE
Browse files

Follow in better way the alientrimmer style

parent 7c61c4aa
Pipeline #38193 failed with stage
in 5 minutes and 36 seconds
#!/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
......
......@@ -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");
......
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