v2.0

src/AlienTrimmer.java

@@ -299,7 +299,7 @@ public class AlienTrimmer {
 	    outS = ( gz ) ? new BufferedWriter(new OutputStreamWriter(new GZIPOutputStream(Files.newOutputStream(Path.of(filename + ".gz")), BUFFER_SIZE)), BUFFER_SIZE) : Files.newBufferedWriter(Path.of(filename));
 	}
 	else {
-	    filename = basename + "fastq";
+	    filename = basename + ".fastq";
 	    out1 = ( gz ) ? new BufferedWriter(new OutputStreamWriter(new GZIPOutputStream(Files.newOutputStream(Path.of(filename + ".gz")), BUFFER_SIZE)), BUFFER_SIZE) : Files.newBufferedWriter(Path.of(filename));
 	}
 	//## counters
@@ -509,14 +509,14 @@ public class AlienTrimmer {
 		    //## assessing R1 length  ##########################################################
 		    l = e1 - s1;                  //## NOTE: l = length of trimmed read
 		    discard1 = ( l < minLgt );
+		    //## assessing R1 composition  #####################################################
+		    if ( ! discard1 ) {
+			i = e1; x = 0; while ( --i >= s1 ) x += bad[i];
+			discard1 = ( 100 * x > l * prop );  //## NOTE: x/l > prop/100, where x is the no. 'bad' bases in the trimmeed read
+		    }
+		    
+		    if ( verbose && l != lgt1 ) display(l1_1, l1_2, l1_4, cov, bad, lgt1, s1, e1, discard1);
 		}
-		//## assessing R1 composition  #####################################################
-		if ( ! discard1 ) {
-		    i = e1; x = 0; while ( --i >= s1 ) x += bad[i];
-		    discard1 = ( 100 * x > l * prop );  //## NOTE: x/l > prop/100, where x is the no. 'bad' bases in the trimmeed read
-		}
-		
-		if ( verbose && l != lgt1 ) display(l1_1, l1_2, l1_4, cov, bad, lgt1, s1, e1, discard1);
 	    }
 
 	    //## writing single-end outfile  #######################################################
@@ -649,14 +649,14 @@ public class AlienTrimmer {
 		    //## assessing R2 length  ##########################################################
 		    l = e2 - s2;                  //## NOTE: l = length of trimmed read
 		    discard2 = ( l < minLgt );
-		}
-		//## assessing R2 composition  #####################################################
-		if ( ! discard2 ) {
-		    i = e2; x = 0; while ( --i >= s2 ) x += bad[i];
-		    discard2 = ( 100 * x > l * prop );  //## NOTE: x/l > prop/100, where x is the no. 'bad' bases in the trimmed read
-		}
+		    //## assessing R2 composition  #####################################################
+		    if ( ! discard2 ) {
+			i = e2; x = 0; while ( --i >= s2 ) x += bad[i];
+			discard2 = ( 100 * x > l * prop );  //## NOTE: x/l > prop/100, where x is the no. 'bad' bases in the trimmed read
+		    }
 		
-		if ( verbose && l != lgt2 ) display(l2_1, l2_2, l2_4, cov, bad, lgt2, s2, e2, discard2);
+		    if ( verbose && l != lgt2 ) display(l2_1, l2_2, l2_4, cov, bad, lgt2, s2, e2, discard2);
+		}
 	    }
 
 	    //## writing paired-end outfiles  ######################################################