Commit 1a4582bc authored by Amine  GHOZLANE's avatar Amine GHOZLANE
Browse files

Remove deprecated warning and debug short length reads

parent 18103127
Pipeline #40424 passed with stage
in 6 minutes and 16 seconds
...@@ -2,6 +2,7 @@ ...@@ -2,6 +2,7 @@
BINDIR="$PREFIX/bin" BINDIR="$PREFIX/bin"
echo "$BINDIR" echo "$BINDIR"
cd $SRC_DIR/src/ cd $SRC_DIR/src/
javac AlienTrimmer.java
./JarMaker.sh ./JarMaker.sh
mv AlienTrimmer.jar $BINDIR/ mv AlienTrimmer.jar $BINDIR/
echo -e "#!/bin/bash\nSCRIPTPATH=\$(dirname \"\${BASH_SOURCE[0]}\")\njava -jar \$SCRIPTPATH/AlienTrimmer.jar \$@" > $BINDIR/AlienTrimmer echo -e "#!/bin/bash\nSCRIPTPATH=\$(dirname \"\${BASH_SOURCE[0]}\")\njava -jar \$SCRIPTPATH/AlienTrimmer.jar \$@" > $BINDIR/AlienTrimmer
......
...@@ -509,7 +509,7 @@ public class AlienTrimmer { ...@@ -509,7 +509,7 @@ public class AlienTrimmer {
case 'A': lptn |= B1; break; case 'C': iptn |= B1; lptn |= B2; break; case 'A': lptn |= B1; break; case 'C': iptn |= B1; lptn |= B2; break;
case 'G': iptn |= B2; lptn |= B4; break; case 'T': iptn |= B3; lptn |= B8; break; case 'G': iptn |= B2; lptn |= B4; break; case 'T': iptn |= B3; lptn |= B8; break;
} }
bsfkmer.set((iptn &= imsk)); lts.add( new Long((lptn &= lmsk)) ); bsfkmer.set((iptn &= imsk)); lts.add( Long.valueOf((lptn &= lmsk)) );
} }
} }
lfkmer = new long[(lfkmerLgt=(o=lts.size()))]; while ( --o >= 0 ) lfkmer[o] = lts.pollLast().longValue(); lfkmer = new long[(lfkmerLgt=(o=lts.size()))]; while ( --o >= 0 ) lfkmer[o] = lts.pollLast().longValue();
...@@ -532,11 +532,11 @@ public class AlienTrimmer { ...@@ -532,11 +532,11 @@ public class AlienTrimmer {
//## displaying info ## //## displaying info ##
if ( ++pcpt % 1000000 == 0 ) if ( ++pcpt % 1000000 == 0 )
System.out.println("[" + String.format(Locale.US, "%02d", new Long((cur=(System.currentTimeMillis()-t)/1000)/60)) System.out.println("[" + String.format(Locale.US, "%02d", Long.valueOf((cur=(System.currentTimeMillis()-t)/1000)/60))
+ ":" + (line="0"+(cur%60)).substring(line.length()-2) + "]" + ":" + (line="0"+(cur%60)).substring(line.length()-2) + "]"
+ String.format(Locale.US, "%,12d", new Integer(pcpt)) + " reads processed:" + String.format(Locale.US, "%,12d", Integer.valueOf(pcpt)) + " reads processed:"
+ String.format(Locale.US, "%,12d", new Integer(ftcpt)) + " trimmed" + String.format(Locale.US, "%,12d", Integer.valueOf(ftcpt)) + " trimmed"
+ String.format(Locale.US, "%,12d", new Integer(frcpt)) + " removed"); + String.format(Locale.US, "%,12d", Integer.valueOf(frcpt)) + " removed");
//## matching k-mers... ## //## matching k-mers... ##
if ( (lgt=(short)fseq.length()) < minLgt ) { ++frcpt; continue; } // too small read if ( (lgt=(short)fseq.length()) < minLgt ) { ++frcpt; continue; } // too small read
if ( lgt >= score.length ) { score = new byte[++lgt]; --lgt; } else Arrays.fill(score, B0); if ( lgt >= score.length ) { score = new byte[++lgt]; --lgt; } else Arrays.fill(score, B0);
...@@ -696,11 +696,11 @@ public class AlienTrimmer { ...@@ -696,11 +696,11 @@ public class AlienTrimmer {
System.out.println(""); System.out.println(""); System.out.println(""); System.out.println("");
} }
fout.close(); fout.close();
System.out.println("[" + String.format(Locale.US, "%02d", new Long((cur=(System.currentTimeMillis()-t)/1000)/60)) System.out.println("[" + String.format(Locale.US, "%02d", Long.valueOf((cur=(System.currentTimeMillis()-t)/1000)/60))
+ ":" + (line="0"+(cur%60)).substring(line.length()-2) + "]" + ":" + (line="0"+(cur%60)).substring(line.length()-2) + "]"
+ String.format(Locale.US, "%,12d", new Integer(pcpt)) + " reads processed:" + String.format(Locale.US, "%,12d", Integer.valueOf(pcpt)) + " reads processed:"
+ String.format(Locale.US, "%,12d", new Integer(ftcpt)) + " trimmed" + String.format(Locale.US, "%,12d", Integer.valueOf(ftcpt)) + " trimmed"
+ String.format(Locale.US, "%,12d", new Integer(frcpt)) + " removed"); + String.format(Locale.US, "%,12d", Integer.valueOf(frcpt)) + " removed");
} }
...@@ -836,7 +836,7 @@ public class AlienTrimmer { ...@@ -836,7 +836,7 @@ public class AlienTrimmer {
case 'A': lptn |= B1; break; case 'C': iptn |= B1; lptn |= B2; break; case 'A': lptn |= B1; break; case 'C': iptn |= B1; lptn |= B2; break;
case 'G': iptn |= B2; lptn |= B4; break; case 'T': iptn |= B3; lptn |= B8; break; case 'G': iptn |= B2; lptn |= B4; break; case 'T': iptn |= B3; lptn |= B8; break;
} }
bsfkmer.set((iptn &= imsk)); lts.add( new Long((lptn &= lmsk)) ); bsfkmer.set((iptn &= imsk)); lts.add( Long.valueOf((lptn &= lmsk)) );
} }
} }
lfkmer = new long[(lfkmerLgt=(o=lts.size()))]; while ( --o >= 0 ) lfkmer[o] = lts.pollLast().longValue(); lfkmer = new long[(lfkmerLgt=(o=lts.size()))]; while ( --o >= 0 ) lfkmer[o] = lts.pollLast().longValue();
...@@ -965,7 +965,7 @@ public class AlienTrimmer { ...@@ -965,7 +965,7 @@ public class AlienTrimmer {
case 'A': lptn |= B1; break; case 'C': iptn |= B1; lptn |= B2; break; case 'A': lptn |= B1; break; case 'C': iptn |= B1; lptn |= B2; break;
case 'G': iptn |= B2; lptn |= B4; break; case 'T': iptn |= B3; lptn |= B8; break; case 'G': iptn |= B2; lptn |= B4; break; case 'T': iptn |= B3; lptn |= B8; break;
} }
bsrkmer.set((iptn &= imsk)); lts.add( new Long((lptn &= lmsk)) ); bsrkmer.set((iptn &= imsk)); lts.add( Long.valueOf((lptn &= lmsk)) );
} }
} }
lrkmer = new long[(lrkmerLgt=(o=lts.size()))]; while ( --o >= 0 ) lrkmer[o] = lts.pollLast().longValue(); lrkmer = new long[(lrkmerLgt=(o=lts.size()))]; while ( --o >= 0 ) lrkmer[o] = lts.pollLast().longValue();
...@@ -997,15 +997,15 @@ public class AlienTrimmer { ...@@ -997,15 +997,15 @@ public class AlienTrimmer {
//## displaying info ## //## displaying info ##
if ( ++pcpt % 1000000 == 0 ) if ( ++pcpt % 1000000 == 0 )
System.out.println("[" + String.format(Locale.US, "%02d", new Long((cur=(System.currentTimeMillis()-t)/1000)/60)) System.out.println("[" + String.format(Locale.US, "%02d", Long.valueOf((cur=(System.currentTimeMillis()-t)/1000)/60))
+ ":" + (line="0"+(cur%60)).substring(line.length()-2) + "]" + ":" + (line="0"+(cur%60)).substring(line.length()-2) + "]"
+ String.format(Locale.US, "%,12d", new Integer(pcpt)) + " read pairs processed:" + String.format(Locale.US, "%,12d", Integer.valueOf(pcpt)) + " read pairs processed:"
+ String.format(Locale.US, "%,12d", new Integer(ftcpt+rtcpt)) + " trimmed" + String.format(Locale.US, "%,12d", Integer.valueOf(ftcpt+rtcpt)) + " trimmed"
+ " (fwd:" + String.format(Locale.US, "%,12d", new Integer(ftcpt)) + " (fwd:" + String.format(Locale.US, "%,12d", Integer.valueOf(ftcpt))
+ " rev:" + String.format(Locale.US, "%,12d", new Integer(rtcpt)) + ")" + " rev:" + String.format(Locale.US, "%,12d", Integer.valueOf(rtcpt)) + ")"
+ String.format(Locale.US, "%,12d", new Integer(frcpt+rrcpt)) + " removed" + String.format(Locale.US, "%,12d", Integer.valueOf(frcpt+rrcpt)) + " removed"
+ " (fwd:" + String.format(Locale.US, "%,12d", new Integer(frcpt)) + " (fwd:" + String.format(Locale.US, "%,12d", Integer.valueOf(frcpt))
+ " rev:" + String.format(Locale.US, "%,12d", new Integer(rrcpt)) + ")"); + " rev:" + String.format(Locale.US, "%,12d", Integer.valueOf(rrcpt)) + ")");
//## matching k-mers (fwd) ## //## matching k-mers (fwd) ##
if ( (lgt=(short)fseq.length()) >= score.length ) { score = new byte[++lgt]; --lgt; } else Arrays.fill(score, B0); if ( (lgt=(short)fseq.length()) >= score.length ) { score = new byte[++lgt]; --lgt; } else Arrays.fill(score, B0);
...@@ -1067,8 +1067,8 @@ public class AlienTrimmer { ...@@ -1067,8 +1067,8 @@ public class AlienTrimmer {
} }
else { else {
//## ... with no degenerate nucleotide ## //## ... with no degenerate nucleotide ##
while ( ++j < k_1 ) { while ( ++j < k_1 && ++j < fseq.length()) {
iptn <<= B2; iptn <<= B2;
switch ( fseq.charAt(j) ) { case 'C': case 'c': iptn |= B1; break; case 'G': case 'g': iptn |= B2; break; case 'T': case 't': iptn |= B3; break; } switch ( fseq.charAt(j) ) { case 'C': case 'c': iptn |= B1; break; case 'G': case 'g': iptn |= B2; break; case 'T': case 't': iptn |= B3; break; }
} }
while ( j < lgt ) { while ( j < lgt ) {
...@@ -1280,15 +1280,15 @@ public class AlienTrimmer { ...@@ -1280,15 +1280,15 @@ public class AlienTrimmer {
} }
} }
fout.close(); rout.close(); sout.close(); fout.close(); rout.close(); sout.close();
System.out.println("[" + String.format(Locale.US, "%02d", new Long((cur=(System.currentTimeMillis()-t)/1000)/60)) System.out.println("[" + String.format(Locale.US, "%02d", Long.valueOf((cur=(System.currentTimeMillis()-t)/1000)/60))
+ ":" + (line="0"+(cur%60)).substring(line.length()-2) + "]" + ":" + (line="0"+(cur%60)).substring(line.length()-2) + "]"
+ String.format(Locale.US, "%,12d", new Integer(pcpt)) + " read pairs processed:" + String.format(Locale.US, "%,12d", Integer.valueOf(pcpt)) + " read pairs processed:"
+ String.format(Locale.US, "%,12d", new Integer(ftcpt+rtcpt)) + " trimmed" + String.format(Locale.US, "%,12d", Integer.valueOf(ftcpt+rtcpt)) + " trimmed"
+ " (fwd:" + String.format(Locale.US, "%,12d", new Integer(ftcpt)) + " (fwd:" + String.format(Locale.US, "%,12d", Integer.valueOf(ftcpt))
+ " rev:" + String.format(Locale.US, "%,12d", new Integer(rtcpt)) + ")" + " rev:" + String.format(Locale.US, "%,12d", Integer.valueOf(rtcpt)) + ")"
+ String.format(Locale.US, "%,12d", new Integer(frcpt+rrcpt)) + " removed" + String.format(Locale.US, "%,12d", Integer.valueOf(frcpt+rrcpt)) + " removed"
+ " (fwd:" + String.format(Locale.US, "%,12d", new Integer(frcpt)) + " (fwd:" + String.format(Locale.US, "%,12d", Integer.valueOf(frcpt))
+ " rev:" + String.format(Locale.US, "%,12d", new Integer(rrcpt)) + ")"); + " rev:" + String.format(Locale.US, "%,12d", Integer.valueOf(rrcpt)) + ")");
} }
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment