65 lines
2.8 KiB
Java
65 lines
2.8 KiB
Java
/*
|
|
* The Broad Institute
|
|
* SOFTWARE COPYRIGHT NOTICE AGREEMENT
|
|
* This software and its documentation are copyright 2009 by the
|
|
* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
|
|
*
|
|
* This software is supplied without any warranty or guaranteed support whatsoever. Neither
|
|
* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
|
|
*/
|
|
package edu.mit.broad.sam;
|
|
|
|
import java.io.File;
|
|
|
|
/**
|
|
* Create a SAMFileWriter for writing SAM or BAM.
|
|
*/
|
|
public class SAMFileWriterFactory {
|
|
|
|
/**
|
|
* Create a BAMFileWriter that is ready to receive SAMRecords
|
|
* @param header entire header. Sort order is determined by the sortOrder property of this arg
|
|
* @param presorted if true, SAMRecords must be added to the SAMFileWriter in order that agrees with header.sortOrder
|
|
* @param outputFile where to write the output.
|
|
* @return
|
|
*/
|
|
public SAMFileWriter makeBAMWriter(final SAMFileHeader header, final boolean presorted, final File outputFile) {
|
|
final BAMFileWriter ret = new BAMFileWriter(outputFile);
|
|
ret.setSortOrder(header.getSortOrder(), presorted);
|
|
ret.setHeader(header);
|
|
return ret;
|
|
}
|
|
|
|
/**
|
|
* Create a SAMTextWriter that is ready to receive SAMRecords
|
|
* @param header entire header. Sort order is determined by the sortOrder property of this arg
|
|
* @param presorted if true, SAMRecords must be added to the SAMFileWriter in order that agrees with header.sortOrder
|
|
* @param outputFile where to write the output.
|
|
* @return
|
|
*/
|
|
public SAMFileWriter makeSAMWriter(final SAMFileHeader header, final boolean presorted, final File outputFile) {
|
|
final SAMTextWriter ret = new SAMTextWriter(outputFile);
|
|
ret.setSortOrder(header.getSortOrder(), presorted);
|
|
ret.setHeader(header);
|
|
return ret;
|
|
}
|
|
|
|
/**
|
|
* Create either a SAM or a BAM writer based on examination of the outputFile
|
|
* @param header entire header. Sort order is determined by the sortOrder property of this arg
|
|
* @param presorted presorted if true, SAMRecords must be added to the SAMFileWriter in order that agrees with header.sortOrder
|
|
* @param outputFile
|
|
* @return outputFile where to write the output. Must end with .sam or .bam
|
|
*/
|
|
public SAMFileWriter makeSAMOrBAMWriter(final SAMFileHeader header, final boolean presorted, final File outputFile) {
|
|
final String filename = outputFile.getName();
|
|
if (filename.endsWith(".bam")) {
|
|
return makeBAMWriter(header, presorted, outputFile);
|
|
}
|
|
if (filename.endsWith(".sam")) {
|
|
return makeSAMWriter(header, presorted, outputFile);
|
|
}
|
|
throw new IllegalArgumentException("SAM/BAM file should end with .sam or .bam: " + outputFile);
|
|
}
|
|
}
|