com.milaboratory.MiStatic Maven / Gradle / Ivy

Go to download

Show more of this group Show more artifacts with this name
Show all versions of mitcr-groovy Show documentation

MiTCR is an open source software package aimed at extraction of information on repertoire of T-cell clones from Next Generation Sequencing (NGS) data. It is designed with the knowledge of the critical challenges arising in everyday processing of immunological data.

There is a newer version: 1.0.3

Show newest version

package com.milaboratory;

import cc.redberry.pipe.OutputPort;
import com.milaboratory.core.sequencing.io.fastq.SFastqReader;
import com.milaboratory.core.sequencing.io.fastq.quality.QualityStringFormat;
import com.milaboratory.core.sequencing.read.SSequencingRead;
import com.milaboratory.util.CompressionType;

import java.io.IOException;

public class MiStatic {
    static OutputPort fastq(String fileName) throws IOException {
        CompressionType ct = CompressionType.None;
        if (fileName.endsWith(".gz"))
            ct = CompressionType.GZIP;
        if (fileName.endsWith(".bz2"))
            ct = CompressionType.BZIP2;
        return new SFastqReader(fileName, QualityStringFormat.Illumina18u, ct);
    }
}