<div dir="ltr"><div><div><div>Hello Daniel,<br><br></div>The whole point of the FASTQ APIs in biojava is to support conversions as you are trying to do, so you shouldn't have to do it yourself.<br><br></div>I would also be interested in seeing (some of) your input data. If you've found a historical edge case, or something that otherwise bends the rules, we could add it to the repo as another test case.<br><br></div> michael<br><div><div><br><br><div><div><div class="gmail_extra"><div class="gmail_quote">On Wed, Sep 16, 2015 at 2:22 AM, Peter Cock <span dir="ltr"><<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Daniel,<br>
<br>
I can't help you on the BioJava specifics, but do your input files really<br>
have Illumina's old FASTQ quality encoding? Can you show use the<br>
first couple of records which is usually enough to guess.<br>
<br>
<a href="http://dx.doi.org/10.1093/nar/gkp1137" rel="noreferrer" target="_blank">http://dx.doi.org/10.1093/nar/gkp1137</a><br>
<br>
Peter<br>
<div><div class="h5"><br>
On Wed, Sep 16, 2015 at 4:28 AM, Daniel Katzel <<a href="mailto:dkatzel@gmail.com">dkatzel@gmail.com</a>> wrote:<br>
> Sorry if this has been asked many times, but I couldn't find it when<br>
> searching the mailing list or popular forums. When I follow the BioJava<br>
> cookbook to convert a Sanger fastq file into an illumina fastq I get<br>
> validation errors.<br>
><br>
> The cookbook<br>
><br>
> <a href="http://biojava.org/wiki/BioJava:CookBook3:FASTQ#Convert_between_FASTQ_variants_using_streaming_API" rel="noreferrer" target="_blank">http://biojava.org/wiki/BioJava:CookBook3:FASTQ#Convert_between_FASTQ_variants_using_streaming_API</a><br>
><br>
> says this will work:<br>
><br>
> FastqReader fastqReader = new IlluminaFastqReader();<br>
> final FastqWriter fastqWriter = new SangerFastqWriter();<br>
> final FileWriter fileWriter = new FileWriter(new File("sanger.fastq"))));<br>
> InputStream in = ...<br>
><br>
> fastqReader.stream(in, new StreamListener()<br>
> {<br>
> @Override<br>
> public void fastq(final Fastq fastq)<br>
> {<br>
> fastqWriter.append(fileWriter, fastq);<br>
> }<br>
> });<br>
><br>
><br>
> But instead it throws this error:<br>
><br>
> Caused by: java.io.IOException: sequence SRR062634.1<br>
> HWI-EAS110_103327062:6:1:1092:8469/1 not fastq-illumina format, was<br>
> fastq-sanger<br>
> at<br>
> org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriter.validate(IlluminaFastqWriter.java:43)<br>
> at<br>
> org.biojava.nbio.sequencing.io.fastq.AbstractFastqWriter.append(AbstractFastqWriter.java:62)<br>
> at<br>
> org.biojava.nbio.sequencing.io.fastq.AbstractFastqWriter.append(AbstractFastqWriter.java:46)<br>
><br>
><br>
> My workaround was to create a new Fastq instance inside the<br>
> StreamListener#fastq() method to manually convert the quality chars<br>
><br>
><br>
> char[] oldQual = fastq.getQuality().toCharArray();<br>
> char[] newQual = new char[oldQual.length];<br>
> for(int i=0; i< oldQual.length; i++){<br>
> newQual[i] =<br>
> FastqVariant.FASTQ_ILLUMINA.quality(FastqVariant.FASTQ_SANGER.qualityScore(oldQual[i]));<br>
> }<br>
><br>
> Fastq newFastq = new<br>
> FastqBuilder().withDescription(fastq.getDescription())<br>
> .withSequence(fastq.getSequence())<br>
> .withQuality(new String(newQual))<br>
><br>
> .withVariant(FastqVariant.FASTQ_ILLUMINA)<br>
> .build();<br>
> try {<br>
> fastqWriter.append(writer, newFastq);<br>
> } catch (IOException e) {<br>
> throw new UncheckedIOException(e);<br>
> }<br>
><br>
><br>
> Is that the correct way to do it? Is there a better way?<br>
><br>
> Thanks<br>
><br>
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</blockquote></div><br></div></div></div></div></div></div>