/** * Adds an interval to the list of intervals. */ public void add(final Interval interval) { if (header.getSequence(interval.getContig()) == null) { throw new IllegalArgumentException(String.format("Cannot add interval %s, contig not in header", interval.toString())); } this.intervals.add(interval); }
/** * Adds an interval to the list of intervals. */ public void add(final Interval interval) { if (header.getSequence(interval.getContig()) == null) { throw new IllegalArgumentException(String.format("Cannot add interval %s, contig not in header", interval.toString())); } this.intervals.add(interval); }
public String toString() { if (toInterval == null) { // Matched a chain, but entirely within a gap. return fromInterval.toString() + " (len " + fromInterval.length() + ")=>null using chain " + chainId; } final String strand = toInterval.isNegativeStrand()? "-": "+"; return fromInterval.toString() + " (len " + fromInterval.length() + ")=>" + toInterval + "(" + strand + ") using chain " + chainId + " ; pct matched " + percentLiftedOver; } }
public String toString() { if (toInterval == null) { // Matched a chain, but entirely within a gap. return fromInterval.toString() + " (len " + fromInterval.length() + ")=>null using chain " + chainId; } final String strand = toInterval.isNegativeStrand()? "-": "+"; return fromInterval.toString() + " (len " + fromInterval.length() + ")=>" + toInterval + "(" + strand + ") using chain " + chainId + " ; pct matched " + percentLiftedOver; } }
public String toString() { if (toInterval == null) { // Matched a chain, but entirely within a gap. return fromInterval.toString() + " (len " + fromInterval.length() + ")=>null using chain " + chainId; } final String strand = toInterval.isNegativeStrand()? "-": "+"; return fromInterval.toString() + " (len " + fromInterval.length() + ")=>" + toInterval + "(" + strand + ") using chain " + chainId + " ; pct matched " + percentLiftedOver; } }
itv = new Interval(itv.getContig(), 1, end); iter = vcfReader.query(itv.getContig(), itv.getStart(), itv.getEnd()); System.err.println("Will read interval " + itv.toString()); } else { System.err.println("Will read full input file");