From aedce509b5cab1f098968b04550fabc8dafd251c Mon Sep 17 00:00:00 2001
From: Amine GHOZLANE <amine.ghozlane@pasteur.fr>
Date: Thu, 24 Sep 2020 11:42:04 +0200
Subject: [PATCH] Follow in better way the alientrimmer style
---
conda_inst/build.sh | 2 +-
src/AlienTrimmer.java | 19 ++++++++++---------
2 files changed, 11 insertions(+), 10 deletions(-)
diff --git a/conda_inst/build.sh b/conda_inst/build.sh
index eb519ee..37ee3e3 100644
--- a/conda_inst/build.sh
+++ b/conda_inst/build.sh
@@ -1,7 +1,7 @@
#!/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
diff --git a/src/AlienTrimmer.java b/src/AlienTrimmer.java
index 1b5eba7..c35cc61 100644
--- a/src/AlienTrimmer.java
+++ b/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");
--
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