/**
* Main method for the program. Checks that all input files are present and readable and that the
* output file can be written to. Then iterates through all the records generating a BAM Index,
* then writes the bai file.
*/
protected int doWork() {
try {
inputUrl = new URL(INPUT);
} catch (java.net.MalformedURLException e) {
inputFile = new File(INPUT);
}
// set default output file - input-file.bai
if (OUTPUT == null) {
final String baseFileName;
if (inputUrl != null) {
String path = inputUrl.getPath();
int lastSlash = path.lastIndexOf("/");
baseFileName = path.substring(lastSlash + 1, path.length());
} else {
baseFileName = inputFile.getAbsolutePath();
}
if (baseFileName.endsWith(BamFileIoUtils.BAM_FILE_EXTENSION)) {
final int index = baseFileName.lastIndexOf(".");
OUTPUT = new File(baseFileName.substring(0, index) + BAMIndex.BAMIndexSuffix);
} else {
OUTPUT = new File(baseFileName + BAMIndex.BAMIndexSuffix);
}
}
IOUtil.assertFileIsWritable(OUTPUT);
final SAMFileReader bam;
if (inputUrl != null) {
// remote input
bam = new SAMFileReader(inputUrl, null, false);
} else {
// input from a normal file
IOUtil.assertFileIsReadable(inputFile);
bam = new SAMFileReader(inputFile);
}
if (!bam.isBinary()) {
throw new SAMException("Input file must be bam file, not sam file.");
}
if (!bam.getFileHeader().getSortOrder().equals(SAMFileHeader.SortOrder.coordinate)) {
throw new SAMException("Input bam file must be sorted by coordinates");
}
BAMIndexer.createIndex(bam, OUTPUT);
log.info("Successfully wrote bam index file " + OUTPUT);
CloserUtil.close(bam);
return 0;
}
/**
* Generates a BAM index file from an input BAM file
*
* @param reader SAMFileReader for input BAM file
* @param output File for output index file
*/
public static void createIndex(SAMFileReader reader, File output) {
createIndex(reader, output, null);
}