if (slice.isMappedSingleRef()) { start = Math.min(start, slice.alignmentStart); end = Math.max(end, slice.alignmentStart + slice.alignmentSpan); if (firstSlice.isMappedSingleRef()) { alignmentStart = start; alignmentSpan = end - start;
slice.sequenceId = MULTI_REFERENCE; else if (slice.isMappedSingleRef()) { if (slice.isMappedSingleRef()) { slice.alignmentStart = minAlStart; slice.alignmentSpan = maxAlEnd - minAlStart + 1;