SamFiles.java

package htsjdk.samtools;

import java.io.File;

/**
 * @author mccowan
 */
public class SamFiles {
    /**
     * Finds the index file associated with the provided SAM file.  The index file must exist and be reachable to be found. 
     *
     * @return The index for the provided SAM, or null if one was not found.
     */
    public static File findIndex(final File samFile) {
        // If input is foo.bam, look for foo.bai
        File indexFile;
        final String fileName = samFile.getName();
        if (fileName.endsWith(BamFileIoUtils.BAM_FILE_EXTENSION)) {
            final String bai = fileName.substring(0, fileName.length() - BamFileIoUtils.BAM_FILE_EXTENSION.length()) + BAMIndex.BAMIndexSuffix;
            indexFile = new File(samFile.getParent(), bai);
            if (indexFile.isFile()) {
                return indexFile;
            }
        }

        // If foo.bai doesn't exist look for foo.bam.bai
        indexFile = new File(samFile.getParent(), samFile.getName() + BAMIndex.BAMIndexSuffix);
        if (indexFile.isFile()) {
            return indexFile;
        } else {
            return null;
        }
    }
}