Created
December 15, 2015 11:15
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Example Scala reading FastQ
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import net.sf.picard.fastq.FastqReader | |
import java.io.File | |
import scala.collection.JavaConversions._ | |
object Reader extends App { | |
val file = new File(args(0)) | |
val fr = new FastqReader(file) | |
printToFile(new File(args(1)))(p => { | |
for (seq <- fr.iterator()) { | |
val header = seq.getReadHeader.split(" ") | |
if ((header.takeRight(2)(0)) != "/") { | |
p.println(">"+header(0)+"/"+header(1)(0)+"\n"+seq.getReadString) | |
} | |
} | |
}) |
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import scala.collection.JavaConversions.asScalaIterator
val reader = new FastqReader(new java.io.File(forward))
for(read <- reader){
println(read.getReadHeader())
}