IOUtil.assertFileIsReadable(INPUT);
IOUtil.assertFileIsWritable(OUTPUT);
final boolean sanitizing = SANITIZE;
final SamReader in = SamReaderFactory.makeDefault().validationStringency(VALIDATION_STRINGENCY).open(INPUT);
final SAMFileHeader inHeader = in.getFileHeader();
// If we are going to override SAMPLE_ALIAS or LIBRARY_NAME, make sure all the read
// groups have the same values.
final List<SAMReadGroupRecord> rgs = inHeader.getReadGroups();
if (SAMPLE_ALIAS != null || LIBRARY_NAME != null) {
boolean allSampleAliasesIdentical = true;
boolean allLibraryNamesIdentical = true;
for (int i = 1; i < rgs.size(); i++) {
if (!rgs.get(0).getSample().equals(rgs.get(i).getSample())) {
allSampleAliasesIdentical = false;
}
if (!rgs.get(0).getLibrary().equals(rgs.get(i).getLibrary())) {
allLibraryNamesIdentical = false;
}
}
if (SAMPLE_ALIAS != null && !allSampleAliasesIdentical) {
throw new PicardException("Read groups have multiple values for sample. " +
"A value for SAMPLE_ALIAS cannot be supplied." );
}
if (LIBRARY_NAME != null && !allLibraryNamesIdentical) {
throw new PicardException("Read groups have multiple values for library name. " +
"A value for library name cannot be supplied." );
}
}
////////////////////////////////////////////////////////////////////////////
// Build the output writer with an appropriate header based on the options
////////////////////////////////////////////////////////////////////////////
final boolean presorted = (inHeader.getSortOrder() == SORT_ORDER) || (SORT_ORDER == SortOrder.queryname && SANITIZE);
final SAMFileHeader outHeader = new SAMFileHeader();
for (final SAMReadGroupRecord rg : inHeader.getReadGroups()) {
if (SAMPLE_ALIAS != null) {
rg.setSample(SAMPLE_ALIAS);
}
if (LIBRARY_NAME != null) {
rg.setLibrary(LIBRARY_NAME);
}
outHeader.addReadGroup(rg);
}
outHeader.setSortOrder(SORT_ORDER);
if (!REMOVE_ALIGNMENT_INFORMATION) {
outHeader.setSequenceDictionary(inHeader.getSequenceDictionary());
outHeader.setProgramRecords(inHeader.getProgramRecords());
}
final SAMFileWriter out = new SAMFileWriterFactory().makeSAMOrBAMWriter(outHeader, presorted, OUTPUT);
////////////////////////////////////////////////////////////////////////////