From 5cb0665d936b0f477b82de87a772e6356fc736f3 Mon Sep 17 00:00:00 2001
From: Alexis CRISCUOLO <alexis.criscuolo@pasteur.fr>
Date: Thu, 12 Nov 2020 17:27:48 +0100
Subject: [PATCH] v2.0
---
src/AlienTrimmer.java | 30 +++++++++++++++---------------
1 file changed, 15 insertions(+), 15 deletions(-)
diff --git a/src/AlienTrimmer.java b/src/AlienTrimmer.java
index 36a6f8d..1466bd8 100644
--- a/src/AlienTrimmer.java
+++ b/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 ######################################################
--
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