public static Container convert(List<SAMRecord> samRecords, CramContext cramContext) throws IllegalArgumentException, IllegalAccessException, IOException { return convert(samRecords, cramContext, getSpans(samRecords)); }
public static Container convert(List<SAMRecord> samRecords, SAMFileHeader samFileHeader, ReferenceSource source, CramLossyOptions lossyOptions) throws IllegalArgumentException, IllegalAccessException, IOException { CramContext context = new CramContext(samFileHeader, source, lossyOptions); Map<Integer, AlignmentSpan> spans = getSpans(samRecords); return convert(samRecords, context, spans); }
public static Container convertLossless(List<SAMRecord> samRecords, SAMFileHeader samFileHeader, ReferenceSource source) throws IllegalArgumentException, IllegalAccessException, IOException { CramContext context = new CramContext(samFileHeader, source, CramLossyOptions.lossless()); Map<Integer, AlignmentSpan> spans = getSpans(samRecords); return convert(samRecords, context, spans); }