Description: Using Fastq* classes from biojava6-live
Author: Pierre Gruet <pgt@debian.org>
Forwarded: not-needed
Last-Update: 2023-01-12

--- a/src/main/java/org/snpeff/Fastq2Fastq.java
+++ b/src/main/java/org/snpeff/Fastq2Fastq.java
@@ -1,7 +1,7 @@
 package org.snpeff;
 
-import org.snpeff.fastq.Fastq;
-import org.snpeff.fastq.FastqVariant;
+import org.biojava.nbio.genome.io.fastq.Fastq;
+import org.biojava.nbio.genome.io.fastq.FastqVariant;
 import org.snpeff.fileIterator.FastqFileIterator;
 import org.snpeff.util.GprSeq;
 import org.snpeff.util.Log;
--- a/src/main/java/org/snpeff/Qseq2Fastq.java
+++ b/src/main/java/org/snpeff/Qseq2Fastq.java
@@ -3,7 +3,7 @@
 import java.io.BufferedReader;
 import java.io.InputStreamReader;
 
-import org.snpeff.fastq.FastqVariant;
+import org.biojava.nbio.genome.io.fastq.FastqVariant;
 import org.snpeff.util.GprSeq;
 import org.snpeff.util.Log;
 
--- a/src/main/java/org/snpeff/binseq/DnaAndQualitySequence.java
+++ b/src/main/java/org/snpeff/binseq/DnaAndQualitySequence.java
@@ -8,8 +8,8 @@
 import org.snpeff.binseq.coder.Coder;
 import org.snpeff.binseq.coder.DnaCoder;
 import org.snpeff.binseq.coder.DnaQualityCoder;
-import org.snpeff.fastq.Fastq;
-import org.snpeff.fastq.FastqVariant;
+import org.biojava.nbio.genome.io.fastq.Fastq;
+import org.biojava.nbio.genome.io.fastq.FastqVariant;
 
 /**
  * Binary packed DNA sequence and base calling quality
--- a/src/main/java/org/snpeff/binseq/DnaAndQualitySequenceWithId.java
+++ b/src/main/java/org/snpeff/binseq/DnaAndQualitySequenceWithId.java
@@ -4,7 +4,7 @@
 import java.io.DataOutputStream;
 import java.io.IOException;
 
-import org.snpeff.fastq.FastqVariant;
+import org.biojava.nbio.genome.io.fastq.FastqVariant;
 
 /**
  * DnaAndQualitySequence with an ID
--- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesDnaOverlap.java
+++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesDnaOverlap.java
@@ -10,7 +10,7 @@
 import org.snpeff.binseq.coder.DnaCoder;
 import org.snpeff.binseq.comparator.DnaQualSubsequenceComparator;
 import org.snpeff.binseq.comparator.DnaSubsequenceComparator;
-import org.snpeff.fastq.FastqVariant;
+import org.biojava.nbio.genome.io.fastq.FastqVariant;
 import org.snpeff.util.Gpr;
 import org.snpeff.util.Log;
 
--- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesDnaSequence.java
+++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesDnaSequence.java
@@ -5,8 +5,8 @@
 import org.snpeff.binseq.DnaSequence;
 import org.snpeff.binseq.DnaSequencePe;
 import org.snpeff.binseq.coder.DnaCoder;
-import org.snpeff.fastq.Fastq;
-import org.snpeff.fastq.FastqVariant;
+import org.biojava.nbio.genome.io.fastq.Fastq;
+import org.biojava.nbio.genome.io.fastq.FastqVariant;
 import org.snpeff.fileIterator.FastqFileIterator;
 import org.snpeff.util.Gpr;
 import org.snpeff.util.Log;
--- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesSequenceIndexer.java
+++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesSequenceIndexer.java
@@ -8,8 +8,8 @@
 import org.snpeff.binseq.comparator.SequenceReference;
 import org.snpeff.binseq.indexer.SequenceIndexer;
 import org.snpeff.binseq.indexer.SuffixIndexerNmer;
-import org.snpeff.fastq.Fastq;
-import org.snpeff.fastq.FastqVariant;
+import org.biojava.nbio.genome.io.fastq.Fastq;
+import org.biojava.nbio.genome.io.fastq.FastqVariant;
 import org.snpeff.fileIterator.FastaFileIterator;
 import org.snpeff.fileIterator.FastqFileIterator;
 import org.snpeff.util.Gpr;
--- a/src/main/java/org/snpeff/fastq/FastqTools.java
+++ b/src/main/java/org/snpeff/fastq/FastqTools.java
@@ -1,5 +1,7 @@
 package org.snpeff.fastq;
 
+import org.biojava.nbio.genome.io.fastq.Fastq;
+
 /**
  * Simple maipulation of fastq sequences
  * @author pcingola
--- a/src/main/java/org/snpeff/fastq/FastqTrimmer.java
+++ b/src/main/java/org/snpeff/fastq/FastqTrimmer.java
@@ -1,5 +1,8 @@
 package org.snpeff.fastq;
 
+import org.biojava.nbio.genome.io.fastq.Fastq;
+import org.biojava.nbio.genome.io.fastq.FastqBuilder;
+
 /**
  * Trim fastq sequence when quality drops below a threshold
  * The resulting sequence has to ba at least 'minBases'
--- a/src/main/java/org/snpeff/fastq/FastqTrimmerAdrian.java
+++ b/src/main/java/org/snpeff/fastq/FastqTrimmerAdrian.java
@@ -3,6 +3,8 @@
 import java.util.Collections;
 import java.util.LinkedList;
 
+import org.biojava.nbio.genome.io.fastq.Fastq;
+
 /**
  * Trim fastq sequence when:
  * 	- Median quality drops below a threshold (mean is calculated every 2 bases instead of every base)
--- a/src/main/java/org/snpeff/fastq/FastqTrimmerMedian.java
+++ b/src/main/java/org/snpeff/fastq/FastqTrimmerMedian.java
@@ -3,6 +3,8 @@
 import java.util.Collections;
 import java.util.LinkedList;
 
+import org.biojava.nbio.genome.io.fastq.Fastq;
+
 /**
  * Trim fastq sequence when median quality drops below a threshold
  * 
--- a/pom.xml
+++ b/pom.xml
@@ -109,6 +109,11 @@
         <version>6.0.4</version>
     </dependency>
     <dependency>
+    	<groupId>org.biojava</groupId>
+    	<artifactId>biojava-genome</artifactId>
+    	<version>5.x</version>
+    </dependency>
+    <dependency>
       <groupId>com.github.samtools</groupId>
       <artifactId>htsjdk</artifactId>
       <version>2.24.1</version>
--- a/src/main/java/org/snpeff/fileIterator/FastqFileIterator.java
+++ b/src/main/java/org/snpeff/fileIterator/FastqFileIterator.java
@@ -9,9 +9,9 @@
 import java.io.InputStreamReader;
 import java.util.Iterator;
 
-import org.snpeff.fastq.Fastq;
-import org.snpeff.fastq.FastqBuilder;
-import org.snpeff.fastq.FastqVariant;
+import org.biojava.nbio.genome.io.fastq.Fastq;
+import org.biojava.nbio.genome.io.fastq.FastqBuilder;
+import org.biojava.nbio.genome.io.fastq.FastqVariant;
 import org.snpeff.util.Log;
 
 /**
--- a/src/main/java/org/snpeff/util/GprSeq.java
+++ b/src/main/java/org/snpeff/util/GprSeq.java
@@ -1,7 +1,7 @@
 package org.snpeff.util;
 
-import org.snpeff.fastq.Fastq;
-import org.snpeff.fastq.FastqVariant;
+import org.biojava.nbio.genome.io.fastq.Fastq;
+import org.biojava.nbio.genome.io.fastq.FastqVariant;
 
 import java.io.BufferedReader;
 import java.io.IOException;