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