/**
* Checks for null object(s).
*
* @param input Object(s) to check.
* @param isToThrow True to throw IAE on null, false otherwise.
* @return True if null, false otherwise.
*/
public static boolean checkNullObject(final boolean isToThrow, final Object... input) {
// first, check array itself
boolean result = BaseUtils.checkNullObject(input, isToThrow);
// then, check elements
if (!result) {
for (final Object item : input) {
result = BaseUtils.checkNullObject(item, isToThrow);
if (result) {
break;
}
}
}
return result;
}
private Map<String, AlignmentContext> getFilteredAndStratifiedContexts(
UnifiedArgumentCollection UAC,
ReferenceContext refContext,
AlignmentContext rawContext,
final GenotypeLikelihoodsCalculationModel.Model model) {
if (!BaseUtils.isRegularBase(refContext.getBase())) return null;
Map<String, AlignmentContext> stratifiedContexts = null;
if (model.name().contains("INDEL")) {
final ReadBackedPileup pileup =
rawContext.getBasePileup().getMappingFilteredPileup(UAC.MIN_BASE_QUALTY_SCORE);
// don't call when there is no coverage
if (pileup.getNumberOfElements() == 0 && UAC.OutputMode != OUTPUT_MODE.EMIT_ALL_SITES)
return null;
// stratify the AlignmentContext and cut by sample
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup);
} else if (model.name().contains("SNP")) {
// stratify the AlignmentContext and cut by sample
stratifiedContexts =
AlignmentContextUtils.splitContextBySampleName(rawContext.getBasePileup());
if (!(UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES
&& UAC.GenotypingMode
!= GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES)) {
int numDeletions = 0;
for (final PileupElement p : rawContext.getBasePileup()) {
if (p.isDeletion()) numDeletions++;
}
if (((double) numDeletions) / ((double) rawContext.getBasePileup().getNumberOfElements())
> UAC.MAX_DELETION_FRACTION) {
return null;
}
}
}
return stratifiedContexts;
}
@Override
public CallableBaseState map(
RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
CalledState state;
if (BaseUtils.isNBase(ref.getBase())) {
state = CalledState.REF_N;
} else {
// count up the depths of all and QC+ bases
int rawDepth = 0, QCDepth = 0, lowMAPQDepth = 0;
for (PileupElement e : context.getBasePileup()) {
rawDepth++;
if (e.getMappingQual() <= maxLowMAPQ) lowMAPQDepth++;
if (e.getMappingQual() >= minMappingQuality
&& (e.getQual() >= minBaseQuality || e.isDeletion())) {
QCDepth++;
}
}
// System.out.printf("%s rawdepth = %d QCDepth = %d lowMAPQ = %d%n", context.getLocation(),
// rawDepth, QCDepth, lowMAPQDepth);
if (rawDepth == 0) {
state = CalledState.NO_COVERAGE;
} else if (rawDepth >= minDepthLowMAPQ
&& MathUtils.ratio(lowMAPQDepth, rawDepth) >= maxLowMAPQFraction) {
state = CalledState.POOR_MAPPING_QUALITY;
} else if (QCDepth < minDepth) {
state = CalledState.LOW_COVERAGE;
} else if (rawDepth >= maxDepth && maxDepth != -1) {
state = CalledState.EXCESSIVE_COVERAGE;
} else {
state = CalledState.CALLABLE;
}
}
return new CallableBaseState(getToolkit().getGenomeLocParser(), context.getLocation(), state);
}
/**
* Checks for null object.
*
* @param input Object to check.
* @param isToThrow True to throw IAE on null, false otherwise.
* @return True if null, false otherwise.
*/
public static boolean checkNullObject(final Object input, final boolean isToThrow) {
return BaseUtils.checkNullObject(input, isToThrow, null);
}
private static void loadOtherImages() {
BaseUtils.readIcon("/com/fr/design/images/m_report/reportWriteAttr.png");
BaseUtils.readIcon("/com/fr/design/images/m_report/linearAttr.png");
BaseUtils.readIcon("/com/fr/design/images/m_insert/bindColumn.png");
BaseUtils.readIcon("/com/fr/design/images/m_insert/text.png");
BaseUtils.readIcon("/com/fr/design/images/m_insert/chart.png");
BaseUtils.readIcon("/com/fr/design/images/m_insert/image.png");
BaseUtils.readIcon("/com/fr/design/images/m_insert/bias.png");
BaseUtils.readIcon("/com/fr/design/images/m_insert/subReport.png");
BaseUtils.readIcon("/com/fr/design/images/m_insert/insertRow.png");
BaseUtils.readIcon("/com/fr/design/images/m_insert/insertColumn.png");
BaseUtils.readIcon("/com/fr/design/images/m_format/highlight.png");
BaseUtils.readIcon("/com/fr/design/images/m_insert/hyperLink.png");
BaseUtils.readIcon("/com/fr/design/images/m_edit/merge.png");
BaseUtils.readIcon("/com/fr/design/images/m_edit/unmerge.png");
BaseUtils.readIcon("/com/fr/design/images/m_file/export.png");
BaseUtils.readIcon("/com/fr/design/images/m_insert/cell.png");
BaseUtils.readIcon("/com/fr/design/images/m_insert/float.png");
BaseUtils.readIcon("/com/fr/design/images/m_edit/undo.png");
BaseUtils.readIcon("/com/fr/design/images/m_edit/redo.png");
BaseUtils.readIcon("/com/fr/design/images/m_edit/cut.png");
BaseUtils.readIcon("/com/fr/design/images/m_edit/paste.png");
BaseUtils.readIcon("/com/fr/design/images/m_format/cellstyle/leftAlignment.png");
BaseUtils.readIcon("/com/fr/design/images/m_format/cellstyle/centerAlignment.png");
BaseUtils.readIcon("/com/fr/design/images/m_format/cellstyle/rightAlignment.png");
BaseUtils.readIcon("/com/fr/design/images/m_format/noboder.png");
BaseUtils.readIcon("/com/fr/design/images/gui/color/background.png");
BaseUtils.readIcon("/com/fr/design/images/m_insert/floatPop.png");
}
/** 预加载 */
public static void preLoadingImages() {
BaseUtils.readIcon("com/fr/design/images/custombtn/baobiaozhuti.png");
BaseUtils.readIcon("com/fr/design/images/custombtn/baobiaozhuti_hover.png");
BaseUtils.readIcon("com/fr/design/images/custombtn/baobiaozhuti_click.png");
BaseUtils.readIcon("com/fr/design/images/custombtn/canshujiemian.png");
BaseUtils.readIcon("com/fr/design/images/custombtn/canshujiemian_hover.png");
BaseUtils.readIcon("com/fr/design/images/custombtn/canshujiemian_click.png");
BaseUtils.readIcon("com/fr/design/images/custombtn/setting.png");
BaseUtils.readIcon("com/fr/design/images/custombtn/setting_hover.png");
BaseUtils.readIcon("com/fr/design/images/custombtn/setting_click.png");
BaseUtils.readIcon("com/fr/design/images/custombtn/page.png");
BaseUtils.readIcon("com/fr/design/images/custombtn/page_hover.png");
BaseUtils.readIcon("com/fr/design/images/custombtn/page_click.png");
BaseUtils.readIcon("com/fr/design/images/custombtn/form.png");
BaseUtils.readIcon("com/fr/design/images/custombtn/form_hover.png");
BaseUtils.readIcon("com/fr/design/images/custombtn/form_click.png");
BaseUtils.readIcon("com/fr/design/images/custombtn/edit.png");
BaseUtils.readIcon("com/fr/design/images/custombtn/edit_hover.png");
BaseUtils.readIcon("com/fr/design/images/custombtn/edit_click.png");
BaseUtils.readIcon("com/fr/base/images/oem/addworksheet.png");
BaseUtils.readIcon("com/fr/design/images/sheet/addpolysheet.png");
BaseUtils.readIcon("com/fr/base/images/oem/worksheet.png");
BaseUtils.readIcon("com/fr/design/images/sheet/polysheet.png");
BaseUtils.readIcon("com/fr/design/images/sheet/left_right_btn.png");
BaseUtils.readIcon("/com/fr/design/images/m_insert/cellPop.png");
BaseUtils.readIcon("/com/fr/design/images/docking/right.gif");
BaseUtils.readIcon("/com/fr/design/images/docking/left.gif");
BaseUtils.readIcon("/com/fr/design/images/m_file/save.png");
BaseUtils.readIcon("/com/fr/design/images/m_file/excel.png");
BaseUtils.readIcon("/com/fr/design/images/m_file/pdf.png");
BaseUtils.readIcon("/com/fr/design/images/m_file/word.png");
BaseUtils.readIcon("/com/fr/design/images/m_file/svg.png");
BaseUtils.readIcon("/com/fr/design/images/m_file/csv.png");
BaseUtils.readIcon("/com/fr/design/images/m_file/text.png");
BaseUtils.readIcon("/com/fr/design/images/m_web/datasource.png");
BaseUtils.readIcon("/com/fr/design/images/m_report/webreportattribute.png");
BaseUtils.readIcon("/com/fr/design/images/m_file/pageSetup.png");
BaseUtils.readIcon("/com/fr/design/images/m_report/header.png");
BaseUtils.readIcon("/com/fr/design/images/m_report/footer.png");
BaseUtils.readIcon("/com/fr/design/images/m_file/saveAs.png");
BaseUtils.readIcon("/com/fr/design/images/m_report/background.png");
loadOtherImages();
}
