/** generates the index file using the latest java index generating code */
private File createIndexFile(File bamFile) throws IOException {
final File bamIndexFile = File.createTempFile("Bai.", ".bai");
final SAMFileReader bam = new SAMFileReader(bamFile);
BuildBamIndex.createIndex(bam, bamIndexFile);
verbose("Wrote BAM Index file " + bamIndexFile);
return bamIndexFile;
}
@Test(enabled = true)
public void testWriteBinary() throws Exception {
// Compare java-generated bai file with c-generated and sorted bai file
final File javaBaiFile = File.createTempFile("javaBai.", ".bai");
final SAMFileReader bam = new SAMFileReader(BAM_FILE);
BuildBamIndex.createIndex(bam, javaBaiFile);
verbose("Wrote binary java BAM Index file " + javaBaiFile);
final File cRegeneratedBaiFile = File.createTempFile("cBai.", ".bai");
BAMIndexer.createAndWriteIndex(BAI_FILE, cRegeneratedBaiFile, false);
verbose("Wrote sorted C binary BAM Index file " + cRegeneratedBaiFile);
// Binary compare of javaBaiFile and cRegeneratedBaiFile should be the same
verbose("diff " + javaBaiFile + " " + cRegeneratedBaiFile);
IoUtil.assertFilesEqual(javaBaiFile, cRegeneratedBaiFile);
javaBaiFile.deleteOnExit();
cRegeneratedBaiFile.deleteOnExit();
}
@Test(enabled = true)
public void testWriteText() throws Exception {
// Compare the text form of the c-generated bai file and a java-generated one
final File cBaiTxtFile = File.createTempFile("cBai.", ".bai.txt");
BAMIndexer.createAndWriteIndex(BAI_FILE, cBaiTxtFile, true);
verbose("Wrote textual C BAM Index file " + cBaiTxtFile);
final File javaBaiFile = File.createTempFile("javaBai.", "java.bai");
final File javaBaiTxtFile = new File(javaBaiFile.getAbsolutePath() + ".txt");
final SAMFileReader bam = new SAMFileReader(BAM_FILE);
BuildBamIndex.createIndex(bam, javaBaiFile);
verbose("Wrote binary Java BAM Index file " + javaBaiFile);
// now, turn the bai file into text
BAMIndexer.createAndWriteIndex(javaBaiFile, javaBaiTxtFile, true);
// and compare them
verbose("diff " + javaBaiTxtFile + " " + cBaiTxtFile);
IoUtil.assertFilesEqual(javaBaiTxtFile, cBaiTxtFile);
cBaiTxtFile.deleteOnExit();
javaBaiFile.deleteOnExit();
javaBaiTxtFile.deleteOnExit();
}