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Update BioJava_CookBook3_FASTQ.md
Update for API changes
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‎_wiki/BioJava_CookBook3_FASTQ.md‎

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@@ -6,7 +6,7 @@ permalink: wiki/BioJava%3ACookBook3%3AFASTQ
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How do I work with nextgen sequencing reads in FASTQ format?
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------------------------------------------------------------
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9-
The org.biojava3.sequencing.io.fastq package provides support for
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The org.biojava.nbio.genome.io.fastq package provides support for
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reading and writing nextgen sequencing reads in FASTQ format
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(FastqReader and FastqWriter, respectively) and for converting FASTQ
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sequences into proper biojava3 DNASequences for analysis purposes
@@ -44,29 +44,29 @@ for (Fastq fastq : fastqReader.read(new File("illumina.fastq"))) {
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```java
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FastqReader fastqReader = new IlluminaFastqReader();
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InputSupplier inputSupplier = Files.newReaderSupplier(new File("illumina.fastq"));
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BufferedReader reader = new BufferedReader(new FileReader(new File("illumina.fastq")));
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final FastqWriter fastqWriter = new SangerFastqWriter();
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final FileWriter fileWriter = new FileWriter(new File("sanger.fastq"))));
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fastqReader.stream(inputSupplier, new StreamListener()
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fastqReader.stream(reader, new StreamListener()
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{
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  @Override
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  public void fastq(final Fastq fastq)
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  {
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    fastqWriter.append(fileWriter, fastq);
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  }
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@Override
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public void fastq(final Fastq fastq)
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{
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   fastqWriter.append(fileWriter, fastq);
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}
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});
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```
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### Convert only long sequences using streaming API
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```java
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FastqReader fastqReader = new IlluminaFastqReader();
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InputSupplier inputSupplier = Files.newReaderSupplier(new File("illumina.fastq"));
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BufferedReader reader = new BufferedReader(new FileReader(new File("illumina.fastq")));
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FastqWriter fastqWriter = new SangerFastqWriter();
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FileWriter fileWriter = new FileWriter(new File("sanger.fastq"))));
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fastqReader.stream(inputSupplier, new StreamListener()
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fastqReader.stream(reader, new StreamListener()
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{
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  @Override
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  public void fastq(final Fastq fastq)
@@ -95,11 +95,10 @@ System.out.println(count);
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```java
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FastqReader fastqReader = new IlluminaFastqReader();
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InputSupplier inputSupplier = Files.newReaderSupplier(new
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File("illumina.fastq"));
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BufferedReader reader = new BufferedReader(new FileReader(new File("illumina.fastq")));
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final AtomicInteger count = new AtomicInteger();
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fastqReader.stream(inputSupplier, new StreamListener()
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fastqReader.stream(reader, new StreamListener()
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{
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  @Override
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  public void fastq(final Fastq fastq)
@@ -115,11 +114,10 @@ System.out.println(count.get());
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```java
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FastqReader fastqReader = new IlluminaFastqReader();
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InputSupplier inputSupplier = Files.newReaderSupplier(new
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File("illumina.fastq"));
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BufferedReader reader = new BufferedReader(new FileReader(new File("illumina.fastq")));
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final AtomicInteger count = new AtomicInteger();
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fastqReader.parse(inputSupplier, new ParseAdapter()
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fastqReader.parse(reader, new ParseAdapter()
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{
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  @Override
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  public void complete() throws IOException
@@ -136,9 +134,9 @@ System.out.println(count.get());
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```java
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final Pattern pattern = Pattern.compile("^HWUSI-EAS100R:.\*$");
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FastqReader fastqReader = new IlluminaFastqReader();
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InputSupplier inputSupplier = Files.newReaderSupplier(new File("illumina.fastq"));
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BufferedReader reader = new BufferedReader(new FileReader(new File("illumina.fastq")));
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fastqReader.parse(inputSupplier, new ParseAdapter()
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fastqReader.parse(reader, new ParseAdapter()
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{
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  @Override
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  public void description(final String description) throws IOException
@@ -155,7 +153,7 @@ fastqReader.parse(inputSupplier, new ParseAdapter()
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```java
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FastqReader fastqReader = new SangerFastqReader();
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List<DNASequence> sequences = new LinkedList<DNASequence>();
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List<DNASequence> sequences = new ArrayList<DNASequence>();
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for (Fastq fastq : fastqReader.read(new File("sanger.fastq"))) {
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sequences.add(FastqTools.createDNASequence(fastq));
@@ -166,7 +164,7 @@ for (Fastq fastq : fastqReader.read(new File("sanger.fastq"))) {
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```java
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FastqReader fastqReader = new SangerFastqReader();
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List<DNASequence> sequences = new LinkedList<DNASequence>();
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List<DNASequence> sequences = new ArrayList<DNASequence>();
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for (Fastq fastq : fastqReader.read(new File("sanger.fastq"))) {
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sequences.add(FastqTools.createDNASequenceWithQualityScores(fastq));
@@ -177,7 +175,7 @@ for (Fastq fastq : fastqReader.read(new File("sanger.fastq"))) {
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```java
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FastqReader fastqReader = new SangerFastqReader();
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List<DNASequence> sequences = new LinkedList<DNASequence>();
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List<DNASequence> sequences = new ArrayList<DNASequence>();
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for (Fastq fastq : fastqReader.read(new File("sanger.fastq"))) {
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sequences.add(FastqTools.createDNASequenceWithQualityScoresAndErrorProbabilities(fastq));
@@ -188,10 +186,10 @@ for (Fastq fastq : fastqReader.read(new File("sanger.fastq"))) {
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```java
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FastqReader fastqReader = new SangerFastqReader();
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InputSupplier inputSupplier = Files.newReaderSupplier(new File("sanger.fastq"));
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List<DNASequence> sequences = new LinkedList<DNASequence>();
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BufferedReader reader = new BufferedReader(new FileReader(new File("sanger.fastq")));
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List<DNASequence> sequences = new ArrayList<DNASequence>();
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fastqReader.stream(inputSupplier, new StreamListener()
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fastqReader.stream(reader, new StreamListener()
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{
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  @Override
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  public void fastq(final Fastq fastq)
@@ -205,8 +203,8 @@ fastqReader.stream(inputSupplier, new StreamListener()
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```java
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FastqReader fastqReader = new SangerFastqReader();
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InputSupplier inputSupplier = Files.newReaderSupplier(new File("sanger.fastq"));
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List<DNASequence> sequences = new LinkedList<DNASequence>();
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BufferedReader reader = new BufferedReader(new FileReader(new File("sanger.fastq")));
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List<DNASequence> sequences = new ArrayList<DNASequence>();
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fastqReader.stream(inputSupplier, new StreamListener()
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{
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```java
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FastqReader fastqReader = new SangerFastqReader();
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InputSupplier inputSupplier = Files.newReaderSupplier(new File("sanger.fastq"));
226-
List<DNASequence> sequences = new LinkedList<DNASequence>();
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BufferedReader reader = new BufferedReader(new FileReader(new File("sanger.fastq")));
224+
List<DNASequence> sequences = new ArrayList<DNASequence>();
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228-
fastqReader.stream(inputSupplier, new StreamListener()
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fastqReader.stream(reader, new StreamListener()
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{
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  @Override
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  public void fastq(final Fastq fastq)
@@ -239,11 +237,11 @@ fastqReader.stream(inputSupplier, new StreamListener()
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240238
```java
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FastqReader fastqReader = new SangerFastqReader();
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InputSupplier inputSupplier = Files.newReaderSupplier(new File("sanger.fastq"));
240+
BufferedReader reader = new BufferedReader(new FileReader(new File("sanger.fastq")));
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SummaryStatistics stats = new SummaryStatistics();
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StringBuilder sb = new StringBuilder(512);
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246-
fastqReader.stream(inputSupplier, new StreamListener()
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fastqReader.stream(reader, new StreamListener()
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{
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  @Override
249247
  public void fastq(final Fastq fastq)
@@ -268,11 +266,11 @@ fastqReader.stream(inputSupplier, new StreamListener()
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269267
```java
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FastqReader fastqReader = new SangerFastqReader();
271-
InputSupplier inputSupplier = Files.newReaderSupplier(new File("sanger.fastq"));
269+
BufferedReader reader = new BufferedReader(new FileReader(new File("sanger.fastq")));
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SummaryStatistics stats = new SummaryStatistics();
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StringBuilder sb = new StringBuilder(512);
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275-
fastqReader.stream(inputSupplier, new StreamListener()
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fastqReader.stream(reader, new StreamListener()
276274
{
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  @Override
278276
  public void fastq(final Fastq fastq)

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