/**
* Returns all supported sample rates.
*
* @return an array of sample rates, in Hertz, never <code>null</code>.
*/
public Integer[] getSampleRates() {
final String rawValue = this.properties.get(DEVICE_SAMPLERATES);
final String[] values = rawValue.split(",\\s*");
final SortedSet<Integer> result =
new TreeSet<Integer>(
NumberUtils.<Integer>createNumberComparator(false /* aSortAscending */));
for (String value : values) {
result.add(Integer.valueOf(value.trim()));
}
return result.toArray(new Integer[result.size()]);
}
public RecalibrationReport(final File recalFile, final SortedSet<String> allReadGroups) {
final GATKReport report = new GATKReport(recalFile);
argumentTable = report.getTable(RecalUtils.ARGUMENT_REPORT_TABLE_TITLE);
RAC = initializeArgumentCollectionTable(argumentTable);
GATKReportTable quantizedTable = report.getTable(RecalUtils.QUANTIZED_REPORT_TABLE_TITLE);
quantizationInfo = initializeQuantizationTable(quantizedTable);
Pair<ArrayList<Covariate>, ArrayList<Covariate>> covariates =
RecalUtils.initializeCovariates(RAC); // initialize the required and optional covariates
ArrayList<Covariate> requiredCovariates = covariates.getFirst();
ArrayList<Covariate> optionalCovariates = covariates.getSecond();
requestedCovariates = new Covariate[requiredCovariates.size() + optionalCovariates.size()];
optionalCovariateIndexes = new HashMap<String, Integer>(optionalCovariates.size());
int covariateIndex = 0;
for (final Covariate covariate : requiredCovariates)
requestedCovariates[covariateIndex++] = covariate;
for (final Covariate covariate : optionalCovariates) {
requestedCovariates[covariateIndex] = covariate;
final String covariateName =
covariate
.getClass()
.getSimpleName()
.split("Covariate")[
0]; // get the name of the covariate (without the "covariate" part of it) so we can
// match with the GATKReport
optionalCovariateIndexes.put(covariateName, covariateIndex - 2);
covariateIndex++;
}
for (Covariate cov : requestedCovariates)
cov.initialize(
RAC); // initialize any covariate member variables using the shared argument collection
recalibrationTables = new RecalibrationTables(requestedCovariates, allReadGroups.size());
initializeReadGroupCovariates(allReadGroups);
parseReadGroupTable(
report.getTable(RecalUtils.READGROUP_REPORT_TABLE_TITLE),
recalibrationTables.getReadGroupTable());
parseQualityScoreTable(
report.getTable(RecalUtils.QUALITY_SCORE_REPORT_TABLE_TITLE),
recalibrationTables.getQualityScoreTable());
parseAllCovariatesTable(
report.getTable(RecalUtils.ALL_COVARIATES_REPORT_TABLE_TITLE), recalibrationTables);
}
/**
* Prints one Unicode property value per line, along with its aliases, if any, for the given
* unicodeVersion.
*
* @param unicodeVersion The Unicode version to print property values and aliases for
* @throws UnicodeProperties.UnsupportedUnicodeVersionException if unicodeVersion is not supported
*/
private static void printUnicodePropertyValuesAndAliases(String unicodeVersion)
throws UnicodeProperties.UnsupportedUnicodeVersionException {
Pattern versionPattern = Pattern.compile("(\\d+)(?:\\.(\\d+))?(?:\\.\\d+)?");
Matcher matcher = versionPattern.matcher(unicodeVersion);
if (!matcher.matches()) {
throw new UnicodeProperties.UnsupportedUnicodeVersionException();
}
String underscoreVersion =
matcher.group(1) + (null == matcher.group(2) ? "_0" : "_" + matcher.group(2));
String[] propertyValues;
String[] propertyValueAliases;
try {
Class<?> clazz = Class.forName("jflex.unicode.data.Unicode_" + underscoreVersion);
Field field = clazz.getField("propertyValues");
propertyValues = (String[]) field.get(null);
field = clazz.getField("propertyValueAliases");
propertyValueAliases = (String[]) field.get(null);
} catch (Exception e) {
throw new UnicodeProperties.UnsupportedUnicodeVersionException();
}
SortedMap<String, SortedSet<String>> propertyValuesToAliases =
new TreeMap<String, SortedSet<String>>();
for (String value : propertyValues) {
propertyValuesToAliases.put(value, new TreeSet<String>());
}
for (int i = 0; i < propertyValueAliases.length; i += 2) {
String alias = propertyValueAliases[i];
String value = propertyValueAliases[i + 1];
SortedSet<String> aliases = propertyValuesToAliases.get(value);
if (null == aliases) {
aliases = new TreeSet<String>();
propertyValuesToAliases.put(value, aliases);
}
aliases.add(alias);
}
for (Map.Entry<String, SortedSet<String>> entry : propertyValuesToAliases.entrySet()) {
String value = entry.getKey();
SortedSet<String> aliases = entry.getValue();
Out.print(value);
if (aliases.size() > 0) {
for (String alias : aliases) {
Out.print(", " + alias);
}
}
Out.println("");
}
}
public static String getNext(SortedSet<String> slines, String num) {
String nxt = "";
SortedSet<String> candidates = new TreeSet<String>();
for (String s : slines) {
if (s.contains(num) && s.indexOf(num) < s.length() - 1) {
candidates.add(s.split("")[s.indexOf(num) + 1]);
}
}
// System.out.println(candidates);
if (candidates.size() == 0) return null;
nxt = candidates.first();
for (String s : slines) {
for (String c : candidates) {
if (s.contains(c) && s.contains(nxt) && s.indexOf(c) < s.indexOf(nxt)) nxt = c;
}
}
return nxt;
}
/** Create a new set of shared job state counters for all jobs in the given group. */
public void initCounters(TaskTimer timer, QueueJobGroup group) {
long groupID = group.getGroupID();
if (LogMgr.getInstance().isLoggable(LogMgr.Kind.Ops, LogMgr.Level.Finest))
LogMgr.getInstance()
.log(LogMgr.Kind.Ops, LogMgr.Level.Finest, "Init Job Counts for Group (" + groupID + ")");
SortedSet<Long> jobIDs = group.getJobIDs();
Counters counters = new Counters(jobIDs.size());
timer.acquire();
synchronized (pCountersByGroup) {
timer.resume();
if (pCountersByGroup.put(groupID, counters) != null)
LogMgr.getInstance()
.logAndFlush(
LogMgr.Kind.Ops,
LogMgr.Level.Warning,
"Somehow the job group ("
+ groupID
+ ") was already in the state "
+ "counts table!");
}
timer.acquire();
synchronized (pCountersByJob) {
timer.resume();
for (Long jobID : jobIDs) {
if (pCountersByJob.put(jobID, counters) != null)
LogMgr.getInstance()
.logAndFlush(
LogMgr.Kind.Ops,
LogMgr.Level.Warning,
"Somehow the job (" + jobID + ") was already in the state counts table!");
}
}
}
int getActiveThreadCount() {
return active_threads.size();
}