@Override public String toString() { return "SAMSequenceDictionary:( sequences:"+ size()+ " length:"+ getReferenceLength()+" "+ " md5:"+md5()+")"; }
@Override public String toString() { return "SAMSequenceDictionary:( sequences:"+ size()+ " length:"+ getReferenceLength()+" "+ " md5:"+md5()+")"; }
@DataProvider public Object[][] actionAndTotalBasesWithInvertData() { final long totalBasesInDict = IntervalList.fromFile(secondInput).getHeader().getSequenceDictionary().getReferenceLength(); final int totalContigsInDict = IntervalList.fromFile(secondInput).getHeader().getSequenceDictionary().size(); return new Object[][]{ {IntervalListTools.Action.CONCAT, totalBasesInDict - 201, 2 + totalContigsInDict}, {IntervalListTools.Action.UNION, totalBasesInDict - 201, 2 + totalContigsInDict}, {IntervalListTools.Action.INTERSECT, totalBasesInDict - 140, 2 + totalContigsInDict}, {IntervalListTools.Action.SUBTRACT, totalBasesInDict - 60, 2 + totalContigsInDict}, {IntervalListTools.Action.SYMDIFF, totalBasesInDict - 61, 3 + totalContigsInDict}, {IntervalListTools.Action.OVERLAPS, totalBasesInDict - 150, 2 + totalContigsInDict}, }; }
if (genomeBaseCount == 0) { // Don't count the reference length more than once. intervalsSamSequenceDictionary = tmpIntervalList.getHeader().getSequenceDictionary(); genomeBaseCount = intervalsSamSequenceDictionary.getReferenceLength(); final long baseCount = (intervals != null) ? intervals.getBaseCount() : truthReader.getFileHeader().getSequenceDictionary().getReferenceLength(); addMissingTruthAndMissingCallStates(snpCounter.getCounterSize(), baseCount, snpCounter); addMissingTruthAndMissingCallStates(indelCounter.getCounterSize(), baseCount, indelCounter);
if (genomeBaseCount == 0) { // Don't count the reference length more than once. intervalsSamSequenceDictionary = tmpIntervalList.getHeader().getSequenceDictionary(); genomeBaseCount = intervalsSamSequenceDictionary.getReferenceLength(); final long baseCount = (intervals != null) ? intervals.getBaseCount() : truthReader.getFileHeader().getSequenceDictionary().getReferenceLength(); addMissingTruthAndMissingCallStates(snpCounter.getCounterSize(), baseCount, snpCounter); addMissingTruthAndMissingCallStates(indelCounter.getCounterSize(), baseCount, indelCounter);
long totalRefLength = header.getSequenceDictionary().getReferenceLength(); long totalRecordRange = ((BAMFileSpan)reader.indexing().getFilePointerSpanningReads()).toCoordinateArray()[1]; chunk = new Chunk(totalRefLength, totalRecordRange);