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josemduartejosemduarte
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Merge pull request biojava#736 from josemduarte/issue536
Merging sequencing module into genome module
2 parents e42757a + a61fb75 commit 65326fa

113 files changed

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‎biojava-genome/pom.xml‎

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<groupId>com.google.guava</groupId>
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<artifactId>guava</artifactId>
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<scope>compile</scope>
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<version>19.0</version>
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<version>24.0-jre</version>
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</dependency>
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<dependency>
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<groupId>junit</groupId>

biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/AbstractFastqReader.java renamed to biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/AbstractFastqReader.java

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* http://www.biojava.org/
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*
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*/
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package org.biojava.nbio.sequencing.io.fastq;
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package org.biojava.nbio.genome.io.fastq;
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import com.google.common.collect.Iterables;
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import com.google.common.collect.Lists;

biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/AbstractFastqWriter.java renamed to biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/AbstractFastqWriter.java

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* http://www.biojava.org/
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*
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*/
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package org.biojava.nbio.sequencing.io.fastq;
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package org.biojava.nbio.genome.io.fastq;
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import java.io.BufferedWriter;
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import java.io.File;

biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/Fastq.java renamed to biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/Fastq.java

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* http://www.biojava.org/
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*
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*/
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package org.biojava.nbio.sequencing.io.fastq;
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package org.biojava.nbio.genome.io.fastq;
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/**
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* FASTQ formatted sequence.

biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/FastqBuilder.java renamed to biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqBuilder.java

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* http://www.biojava.org/
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*
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*/
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package org.biojava.nbio.sequencing.io.fastq;
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package org.biojava.nbio.genome.io.fastq;
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/**
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* Fluent builder API for creating FASTQ formatted sequences.

biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/FastqParser.java renamed to biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqParser.java

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* http://www.biojava.org/
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*
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*/
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package org.biojava.nbio.sequencing.io.fastq;
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package org.biojava.nbio.genome.io.fastq;
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import com.google.common.io.CharStreams;
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import com.google.common.io.LineProcessor;

biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/FastqReader.java renamed to biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqReader.java

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* http://www.biojava.org/
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*
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*/
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package org.biojava.nbio.sequencing.io.fastq;
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package org.biojava.nbio.genome.io.fastq;
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import java.io.File;
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import java.io.IOException;

biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/FastqTools.java renamed to biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqTools.java

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* http://www.biojava.org/
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*
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*/
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package org.biojava.nbio.sequencing.io.fastq;
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package org.biojava.nbio.genome.io.fastq;
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import com.google.common.collect.ImmutableList;
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import com.google.common.collect.Lists;

biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/FastqVariant.java renamed to biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqVariant.java

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* http://www.biojava.org/
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*
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*/
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package org.biojava.nbio.sequencing.io.fastq;
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package org.biojava.nbio.genome.io.fastq;
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import java.util.HashMap;
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import java.util.Map;

biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/FastqWriter.java renamed to biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqWriter.java

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* http://www.biojava.org/
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*
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*/
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package org.biojava.nbio.sequencing.io.fastq;
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package org.biojava.nbio.genome.io.fastq;
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import java.io.File;
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import java.io.IOException;

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