/**
* Update the recalibration statistics using the information in recalInfo
*
* @param recalInfo data structure holding information about the recalibration values for a single
* read
*/
@Requires("recalInfo != null")
public void updateDataForRead(final ReadRecalibrationInfo recalInfo) {
final GATKSAMRecord read = recalInfo.getRead();
final ReadCovariates readCovariates = recalInfo.getCovariatesValues();
final RecalibrationTables tables = getUpdatableRecalibrationTables();
final NestedIntegerArray<RecalDatum> qualityScoreTable = tables.getQualityScoreTable();
for (int offset = 0; offset < read.getReadBases().length; offset++) {
if (!recalInfo.skip(offset)) {
for (final EventType eventType : EventType.values()) {
final int[] keys = readCovariates.getKeySet(offset, eventType);
final int eventIndex = eventType.ordinal();
final byte qual = recalInfo.getQual(eventType, offset);
final double isError = recalInfo.getErrorFraction(eventType, offset);
RecalUtils.incrementDatumOrPutIfNecessary(
qualityScoreTable, qual, isError, keys[0], keys[1], eventIndex);
for (int i = 2; i < covariates.length; i++) {
if (keys[i] < 0) continue;
RecalUtils.incrementDatumOrPutIfNecessary(
tables.getTable(i), qual, isError, keys[0], keys[1], keys[i], eventIndex);
}
}
}
}
}
public static EventType parse(String value) {
EventType[] v = EventType.values();
for (EventType val : v) {
if (val.toString().equals(value)) {
return val;
}
}
return null;
}
public EventTargets() {
final int EVENTS_COUNT = EventType.values().length;
mEvents = new ArrayList<>(EVENTS_COUNT);
for (int i = 0; i < EVENTS_COUNT; i++) {
mEvents.add(new ArrayList<CallType>(1));
}
//
initTargetCalls();
//
for (int i = 0; i < EVENTS_COUNT; i++) {
mEvents.set(i, Collections.unmodifiableList(mEvents.get(i)));
}
}
public void activateMetrics() {
// Activate Plugin Metrics
try {
Metrics metrics = new Metrics(this);
metrics.addCustomData(
new Metrics.Plotter("Total Number of Server Rules") {
@Override
public int getValue() {
return ruleset.ruleCount();
}
});
Metrics.Graph graph = metrics.createGraph("Rules by Event");
for (final EventType r : EventType.values()) {
graph.addPlotter(
new Metrics.Plotter(r.toString()) {
@Override
public int getValue() {
return ruleset.ruleCount(r); // Number of rules for this event type
}
});
}
Metrics.Graph matchGraph = metrics.createGraph("Matches");
matchTracker = new Tracker("Matches");
matchGraph.addPlotter(matchTracker);
metrics.start();
} catch (IOException e) {
logger.fine(e.getMessage());
}
}
/** Utility class to facilitate base quality score recalibration. */
public final class RecalibrationTables
implements Serializable, Iterable<NestedIntegerArray<RecalDatum>> {
private static final long serialVersionUID = 1L;
private final int qualDimension;
private final int eventDimension = EventType.values().length;
private final int numReadGroups;
final StandardCovariateList covariates; // save the covariates this was created with
// These two tables are special
private final NestedIntegerArray<RecalDatum> readGroupTable;
private final NestedIntegerArray<RecalDatum> qualityScoreTable;
private final List<NestedIntegerArray<RecalDatum>> additionalTables;
private final List<NestedIntegerArray<RecalDatum>> allTables; // special + additional
// bidirectional mappings
private final Map<Covariate, NestedIntegerArray<RecalDatum>> covariateToTable;
private final Map<NestedIntegerArray<RecalDatum>, Covariate> tableToCovariate;
public RecalibrationTables(final StandardCovariateList covariates) {
this(covariates, covariates.getReadGroupCovariate().maximumKeyValue() + 1);
}
public RecalibrationTables(StandardCovariateList covariates, final int numReadGroups) {
this.covariates = covariates;
this.additionalTables = new ArrayList<>();
this.allTables = new ArrayList<>();
this.covariateToTable = new LinkedHashMap<>();
this.tableToCovariate = new LinkedHashMap<>();
this.qualDimension = covariates.getQualityScoreCovariate().maximumKeyValue() + 1;
this.numReadGroups = numReadGroups;
// two special tables
this.readGroupTable = new NestedIntegerArray<>(numReadGroups, eventDimension);
allTables.add(readGroupTable);
covariateToTable.put(covariates.getReadGroupCovariate(), readGroupTable);
tableToCovariate.put(readGroupTable, covariates.getReadGroupCovariate());
this.qualityScoreTable = makeQualityScoreTable();
allTables.add(qualityScoreTable);
covariateToTable.put(covariates.getQualityScoreCovariate(), qualityScoreTable);
tableToCovariate.put(qualityScoreTable, covariates.getQualityScoreCovariate());
// Non-special tables
for (Covariate cov : covariates.getAdditionalCovariates()) {
final NestedIntegerArray<RecalDatum> table =
new NestedIntegerArray<>(
numReadGroups, qualDimension, cov.maximumKeyValue() + 1, eventDimension);
additionalTables.add(table);
allTables.add(table);
covariateToTable.put(cov, table);
tableToCovariate.put(table, cov);
}
}
public NestedIntegerArray<RecalDatum> getTableForCovariate(Covariate cov) {
return covariateToTable.get(cov);
}
public Covariate getCovariateForTable(NestedIntegerArray<RecalDatum> table) {
return tableToCovariate.get(table);
}
public boolean isReadGroupTable(NestedIntegerArray<RecalDatum> table) {
// Note: NestedIntegerArray does not implement equals so we use reference identity to check
// equality
// to explicitly check identity (and future-proof against an equals method in
// NestedIntegerArray).
return table == getReadGroupTable();
}
public boolean isQualityScoreTable(NestedIntegerArray<RecalDatum> table) {
// Note: NestedIntegerArray does not implement equals so we use reference identity to check
// equality
// to explicitly check identity (and future-proof against an equals method in
// NestedIntegerArray).
return table == getQualityScoreTable();
}
public boolean isAdditionalCovariateTable(NestedIntegerArray<RecalDatum> table) {
return additionalTables.contains(table);
}
public NestedIntegerArray<RecalDatum> getReadGroupTable() {
return readGroupTable;
}
public NestedIntegerArray<RecalDatum> getQualityScoreTable() {
return qualityScoreTable;
}
public int numTables() {
return allTables.size();
}
@Override
public Iterator<NestedIntegerArray<RecalDatum>> iterator() {
return allTables.iterator();
}
/** @return true if all the tables contain no RecalDatums */
public boolean isEmpty() {
for (final NestedIntegerArray<RecalDatum> table : allTables) {
if (!table.getAllValues().isEmpty()) {
return false;
}
}
return true;
}
/**
* Allocate a new quality score table, based on requested parameters in this set of tables,
* without any data in it. The return result of this table is suitable for acting as a
* thread-local cache for quality score values
*
* @return a newly allocated, empty read group x quality score table
*/
public NestedIntegerArray<RecalDatum> makeQualityScoreTable() {
return new NestedIntegerArray<>(numReadGroups, qualDimension, eventDimension);
}
/** Merge all of the tables from toMerge into into this set of tables */
public RecalibrationTables combine(final RecalibrationTables toMerge) {
if (numTables() != toMerge.numTables())
throw new IllegalArgumentException(
"Attempting to merge RecalibrationTables with different sizes");
for (int i = 0; i < numTables(); i++) {
final NestedIntegerArray<RecalDatum> myTable = this.allTables.get(i);
final NestedIntegerArray<RecalDatum> otherTable = toMerge.allTables.get(i);
RecalUtils.combineTables(myTable, otherTable);
}
return this;
}
/**
* Combines the two tables into a new table (allocating a new table in the process)
*
* @param left first table to combine
* @param right second table to combine
* @return a new table with the merged contents of left and right
*/
public static RecalibrationTables safeCombine(
final RecalibrationTables left, final RecalibrationTables right) {
Utils.nonNull(left);
Utils.nonNull(right);
final RecalibrationTables newTable =
new RecalibrationTables(left.covariates, left.numReadGroups);
newTable.combine(left);
newTable.combine(right);
return newTable;
}
/**
* Combines the right table into the left table, in-place (without making a copy)
*
* @param left first table to combine
* @param right second table to combine
* @return modified version of left with the contents of right incorporated into it
*/
public static RecalibrationTables inPlaceCombine(
final RecalibrationTables left, final RecalibrationTables right) {
Utils.nonNull(left);
Utils.nonNull(right);
return left.combine(right);
}
// XXX this should not be accessible by index
public NestedIntegerArray<RecalDatum> getTable(int index) {
return allTables.get(index);
}
public List<NestedIntegerArray<RecalDatum>> getAdditionalTables() {
return additionalTables;
}
}
public void configurePlugin() {
if (getConfig().getBoolean("logfile")) {
setupLogfile();
} else { // Needed during configuration reload to turn off logging if the option changes
if (logfileHandler != null) {
logfileHandler.close();
logger.removeHandler(logfileHandler);
logfileHandler = null;
}
}
try {
ruleLogLevel = Level.parse(getConfig().getString("loglevel", "info").toUpperCase());
} catch (IllegalArgumentException e) {
ruleLogLevel = Level.INFO;
}
decolor = getConfig().getBoolean("decolor");
try {
debugMode = DebugModes.valueOf(getConfig().getString("debug"));
} catch (IllegalArgumentException e) {
debugMode = DebugModes.off;
}
cmdlist = getConfig().getStringList("cmdlist");
cmdblist = getConfig().getStringList("cmdblist");
enabledEvents.clear(); // Reset the enabled event types.
for (EventType e : EventType.values()) {
switch (e) {
case CHAT:
chatPriority =
EventPriority.valueOf(getConfig().getString("chatpriority", "LOWEST").toUpperCase());
enabledEvents.add(EventType.CHAT);
break;
case COMMAND:
if (getConfig().getBoolean("commandfilter", false)) {
cmdPriority =
EventPriority.valueOf(getConfig().getString("cmdpriority", "LOWEST").toUpperCase());
enabledEvents.add(EventType.COMMAND);
}
break;
case SIGN:
if (getConfig().getBoolean("signfilter", false)) {
signPriority =
EventPriority.valueOf(
getConfig().getString("signpriority", "LOWEST").toUpperCase());
enabledEvents.add(EventType.SIGN);
}
break;
case ITEM:
if (getConfig().getBoolean("itemfilter", false)) {
invPriority =
EventPriority.valueOf(getConfig().getString("invpriority", "LOWEST").toUpperCase());
enabledEvents.add(EventType.ITEM);
}
break;
}
}
}