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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;
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