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/**
* Copyright Copyright 2010-15 Simon Andrews
*
* This file is part of FastQC.
*
* FastQC is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option) any later version.
*
* FastQC is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with FastQC; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package uk.ac.babraham.FastQC.Sequence;
import java.io.File;
import java.io.IOException;
import uk.ac.babraham.FastQC.FastQCConfig;
import uk.ac.babraham.FastQC.Utilities.CasavaBasename;
import uk.ac.babraham.FastQC.Utilities.NameFormatException;
public class SequenceFactory {
/**
*
* This option is used when multiple files are to be treated as a group to produce
* a single output. This is currently used for groups of files generated by casava
*
* @param files
* @return
* @throws SequenceFormatException
* @throws IOException
*/
public static SequenceFile getSequenceFile (File [] files) throws SequenceFormatException, IOException {
/*
* We used to build a set of SequenceFile objects to make a sequence group, but we found that
* doing this caused too many files to be open simultaneously and caused crashes on large
* runs. We now just pass the files to the group and let it open them as and when they're needed.
*/
if (files.length == 1) {
if (FastQCConfig.getInstance().casava) {
try {
// We do this simply to find out if the casava basename is valid. If it is then the
// Sequencefilegroup is created at the end of this sub. If it's not then we do a
// simple creation without modifying the file name.
CasavaBasename.getCasavaBasename(files[0].getName());
}
catch (NameFormatException nfe) {
return getSequenceFile(files[0]);
}
}
else {
return getSequenceFile(files[0]);
}
}
return new SequenceFileGroup(files);
}
public static SequenceFile getSequenceFile(File file) throws SequenceFormatException, IOException {
FastQCConfig config = FastQCConfig.getInstance();
// System.err.println("Format is "+config.sequence_format);
if (config.sequence_format != null) {
// We're not autodetecting the format, but taking whatever they said
if (config.sequence_format.equals("bam") || config.sequence_format.equals("sam")) {
return new BAMFile(file,false);
}
else if (config.sequence_format.equals("bam_mapped") || config.sequence_format.equals("sam_mapped")) {
return new BAMFile(file,true);
}
else if (config.sequence_format.equals("fastq")) {
return new FastQFile(config,file);
}
else {
throw new SequenceFormatException("Didn't understand format name '"+config.sequence_format+"'");
}
}
// Otherwise we just use the extension on the end of the file name to try to determine
// the type
if (file.getName().toLowerCase().endsWith(".bam") || file.getName().toLowerCase().endsWith(".sam")) {
// We default to using all reads
return new BAMFile(file,false);
}
else {
return new FastQFile(config,file);
}
}
}
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