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Merge pull request #180 from broadinstitute/mc_diagnosetargets_missing_targets 

DiagnoseTargets Global Refactor
This commit is contained in:
MauricioCarneiro 2013-04-24 14:54:55 -07:00
parent 3f52f55c55 367f0c0ac1
commit 45fec382e7
25 changed files with 1386 additions and 864 deletions
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2
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/BaseCoverageDistribution.java → protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/BaseCoverageDistribution.java
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@ -44,7 +44,7 @@
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
package org.broadinstitute.sting.gatk.walkers.diagnostics;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java → protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/FindCoveredIntervals.java
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@ -44,7 +44,7 @@
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
package org.broadinstitute.sting.gatk.walkers.diagnostics;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
@ -105,7 +105,7 @@ public class FindCoveredIntervals extends ActiveRegionWalker<GenomeLoc, Long> {
// Look to see if the region has sufficient coverage
public ActivityProfileState isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) {
int depth = ThresHolder.DEFAULTS.getFilteredCoverage(context.getBasePileup());
int depth = context.getBasePileup().getBaseFilteredPileup(coverageThreshold).depthOfCoverage();
// note the linear probability scale
return new ActivityProfileState(ref.getLocus(), Math.min(depth / coverageThreshold, 1));

150
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/AbstractStratification.java 100644
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@ -0,0 +1,150 @@
/*
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*
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*
* This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
*
* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
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* 3. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
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*
* 5. NO REPRESENTATIONS OR WARRANTIES
* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
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* 7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
* 7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
* 7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
* 7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
/**
* Generic code for Diagnose Target Statistics
*
* @author Mauricio Carneiro
* @since 4/23/13
*/
abstract class AbstractStratification {
private long preComputedTotalCoverage = -1;
private Map<CallableStatus, Integer> statusTally = null;
protected ThresHolder thresholds;
/**
* Calculates the average "good" coverage of this sample. Good means "passes the base and
* mapping quality requirements.
*
* @return the average "good" coverage
*/
public double averageCoverage(final int size) {
if (preComputedTotalCoverage < 0)
preComputedTotalCoverage = calculateTotalCoverage(getElements());
return (double) preComputedTotalCoverage / size;
}
/**
* Calculates the total "good" coverage of this sample. Good means "passes the base and
* mapping quality requirements.
*
* @return the total "good" coverage across the interval for this sample
*/
public long getCoverage() {
if (preComputedTotalCoverage < 0)
preComputedTotalCoverage = calculateTotalCoverage(getElements());
return preComputedTotalCoverage;
}
/**
* This is how the extending class will calculate it's own total coverage
*
* @return the total coverage
*/
private long calculateTotalCoverage(Iterable<AbstractStratification> elements) {
long cov = 0;
for (AbstractStratification element : elements) {
cov += element.getCoverage();
}
return cov;
}
/**
* What are the list of elements in your class? For example:
*
* IntervalStatistics => List<SampleStatistics>
* SampleStatistics => List<LocusStatistics>
*
* @return the corresponding list of elements of the extending class
*/
public abstract Iterable<AbstractStratification> getElements();
/**
* Calculates the Callable statuses for the statistic as a whole (interval, sample or locus)
*
* @return the callable status(es) for the whole object
*/
public abstract Iterable<CallableStatus> callableStatuses();
/**
* Tally up all the callable status of all the loci in this sample.
*
* @return a map of callable status and counts
*/
public Map<CallableStatus, Integer> getStatusTally() {
if (statusTally == null) {
statusTally = new HashMap<CallableStatus, Integer>(CallableStatus.values().length);
for (AbstractStratification stats : getElements()) {
for (CallableStatus status : stats.callableStatuses()) {
statusTally.put(status, !statusTally.containsKey(status) ? 1 : statusTally.get(status) + 1);
}
}
}
return statusTally;
}
public static List<CallableStatus> queryStatus(List<Metric> statList, AbstractStratification stratification) {
List<CallableStatus> output = new LinkedList<CallableStatus>();
for (Metric stat : statList) {
final CallableStatus status = stat.status(stratification);
if (status != null) {
output.add(status);
}
}
return output;
}
}

13
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/CallableStatus.java → protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/CallableStatus.java
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@ -44,7 +44,7 @@
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
/**
* Short one line description of the walker.
@ -52,9 +52,7 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
* @author Mauricio Carneiro
* @since 2/1/12
*/
public enum CallableStatus {
REF_N("the reference base was an N, which is not considered callable the GATK"),
enum CallableStatus {
PASS("the base satisfied the min. depth for calling but had less than maxDepth to avoid having EXCESSIVE_COVERAGE"),
@ -68,12 +66,7 @@ public enum CallableStatus {
BAD_MATE("the reads are not properly mated, suggesting mapping errors"),
NO_READS("there are no reads contained in the interval"),
//
// Interval-level statuses
//
LOW_MEDIAN_DEPTH("interval has insufficient median depth across samples");
NO_READS("there are no reads contained in the interval");
public final String description;

253
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java → protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java
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@ -44,10 +44,10 @@
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
import net.sf.picard.util.PeekableIterator;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.ArgumentCollection;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -56,13 +56,14 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.variant.variantcontext.*;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.vcf.*;
import java.util.*;
@ -110,79 +111,52 @@ import java.util.*;
@PartitionBy(PartitionType.INTERVAL)
public class DiagnoseTargets extends LocusWalker<Long, Long> {
@Output(doc = "File to which variants should be written")
private static final String AVG_INTERVAL_DP_KEY = "IDP";
@Output(doc = "File to which interval statistics should be written")
private VariantContextWriter vcfWriter = null;
@Argument(fullName = "minimum_base_quality", shortName = "BQ", doc = "The minimum Base Quality that is considered for calls", required = false)
private int minimumBaseQuality = 20;
@ArgumentCollection
private ThresHolder thresholds = new ThresHolder();
@Argument(fullName = "minimum_mapping_quality", shortName = "MQ", doc = "The minimum read mapping quality considered for calls", required = false)
private int minimumMappingQuality = 20;
private Map<GenomeLoc, IntervalStratification> intervalMap = null; // maps each interval => statistics
private PeekableIterator<GenomeLoc> intervalListIterator; // an iterator to go over all the intervals provided as we traverse the genome
private Set<String> samples = null; // all the samples being processed
private static final Allele SYMBOLIC_ALLELE = Allele.create("<DT>", false); // avoid creating the symbolic allele multiple times
private static final Allele UNCOVERED_ALLELE = Allele.create("A", true); // avoid creating the 'fake' ref allele for uncovered intervals multiple times
@Argument(fullName = "minimum_coverage", shortName = "min", doc = "The minimum allowable coverage, used for calling LOW_COVERAGE", required = false)
private int minimumCoverage = 5;
@Argument(fullName = "maximum_coverage", shortName = "max", doc = "The maximum allowable coverage, used for calling EXCESSIVE_COVERAGE", required = false)
private int maximumCoverage = 700;
@Argument(fullName = "minimum_median_depth", shortName = "med", doc = "The minimum allowable median coverage, used for calling LOW_MEDIAN_DEPTH", required = false)
private int minMedianDepth = 10;
@Argument(fullName = "maximum_insert_size", shortName = "ins", doc = "The maximum allowed distance between a read and its mate", required = false)
private int maxInsertSize = 500;
@Argument(fullName = "voting_status_threshold", shortName = "stV", doc = "The needed percentage of samples containing a call for the interval to adopt the call ", required = false)
private double votePercentage = 0.50;
@Argument(fullName = "low_median_depth_status_threshold", shortName = "stMED", doc = "The percentage of the loci needed for calling LOW_MEDIAN_DEPTH", required = false)
private double lowMedianDepthPercentage = 0.20;
@Argument(fullName = "bad_mate_status_threshold", shortName = "stBM", doc = "The percentage of the loci needed for calling BAD_MATE", required = false)
private double badMateStatusThreshold = 0.50;
@Argument(fullName = "coverage_status_threshold", shortName = "stC", doc = "The percentage of the loci needed for calling LOW_COVERAGE and COVERAGE_GAPS", required = false)
private double coverageStatusThreshold = 0.20;
@Argument(fullName = "excessive_coverage_status_threshold", shortName = "stXC", doc = "The percentage of the loci needed for calling EXCESSIVE_COVERAGE", required = false)
private double excessiveCoverageThreshold = 0.20;
@Argument(fullName = "quality_status_threshold", shortName = "stQ", doc = "The percentage of the loci needed for calling POOR_QUALITY", required = false)
private double qualityStatusThreshold = 0.50;
@Argument(fullName = "print_debug_log", shortName = "dl", doc = "Used only for debugging the walker. Prints extra info to screen", required = false)
private boolean debug = false;
private HashMap<GenomeLoc, IntervalStatistics> intervalMap = null; // maps each interval => statistics
private PeekableIterator<GenomeLoc> intervalListIterator; // an iterator to go over all the intervals provided as we traverse the genome
private Set<String> samples = null; // all the samples being processed
private final Allele SYMBOLIC_ALLELE = Allele.create("<DT>", false); // avoid creating the symbolic allele multiple times
private ThresHolder thresholds = null;
private static final int INITIAL_HASH_SIZE = 500000;
@Override
public void initialize() {
super.initialize();
if (getToolkit().getIntervals() == null)
throw new UserException("This tool only works if you provide one or more intervals. ( Use the -L argument )");
if (getToolkit().getIntervals() == null || getToolkit().getIntervals().isEmpty())
throw new UserException("This tool only works if you provide one or more intervals (use the -L argument). If you want to run whole genome, use -T DepthOfCoverage instead.");
thresholds = new ThresHolder(minimumBaseQuality, minimumMappingQuality, minimumCoverage, maximumCoverage, minMedianDepth, maxInsertSize, votePercentage, lowMedianDepthPercentage, badMateStatusThreshold, coverageStatusThreshold, excessiveCoverageThreshold, qualityStatusThreshold);
intervalMap = new HashMap<GenomeLoc, IntervalStatistics>();
intervalMap = new HashMap<GenomeLoc, IntervalStratification>(INITIAL_HASH_SIZE);
intervalListIterator = new PeekableIterator<GenomeLoc>(getToolkit().getIntervals().iterator());
samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader()); // get all of the unique sample names for the VCF Header
vcfWriter.writeHeader(new VCFHeader(ThresHolder.getHeaderInfo(), samples)); // initialize the VCF header
// get all of the unique sample names for the VCF Header
samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
vcfWriter.writeHeader(new VCFHeader(getHeaderInfo(), samples));
// pre load all the statistics classes because it is costly to operate on the JVM and we only want to do it once.
loadAllPlugins(thresholds);
}
@Override
public Long map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
GenomeLoc refLocus = ref.getLocus();
removePastIntervals(refLocus, ref.getBase()); // process and remove any intervals in the map that are don't overlap the current locus anymore
addNewOverlappingIntervals(refLocus); // add all new intervals that may overlap this reference locus
// process and remove any intervals in the map that are don't overlap the current locus anymore
// and add all new intervals that may overlap this reference locus
outputFinishedIntervals(refLocus, ref.getBase());
addNewOverlappingIntervals(refLocus);
for (IntervalStatistics intervalStatistics : intervalMap.values())
intervalStatistics.addLocus(context, ref, thresholds); // Add current locus to stats
// at this point, all intervals in intervalMap overlap with this locus, so update all of them
for (IntervalStratification intervalStratification : intervalMap.values())
intervalStratification.addLocus(context);
return 1L;
}
@ -212,53 +186,40 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
@Override
public void onTraversalDone(Long result) {
for (GenomeLoc interval : intervalMap.keySet())
outputStatsToVCF(intervalMap.get(interval), Allele.create("A", true));
}
outputStatsToVCF(intervalMap.get(interval), UNCOVERED_ALLELE);
private GenomeLoc getIntervalMapSpan() {
GenomeLoc loc = null;
for (GenomeLoc interval : intervalMap.keySet()) {
if (loc == null) {
loc = interval;
} else
loc = interval.union(loc);
GenomeLoc interval = intervalListIterator.peek();
while (interval != null) {
outputStatsToVCF(createIntervalStatistic(interval), UNCOVERED_ALLELE);
intervalListIterator.next();
interval = intervalListIterator.peek();
}
return loc;
}
private GenomeLoc getFinishedIntervalSpan(GenomeLoc pos) {
GenomeLoc loc = null;
for (GenomeLoc interval : intervalMap.keySet()) {
if (interval.isBefore(pos)) {
if (loc == null)
loc = interval;
else
loc = interval.union(loc);
}
}
return loc;
}
/**
* Removes all intervals that are behind the current reference locus from the intervalMap
* Outputs all intervals that are behind the current reference locus
*
* @param refLocus the current reference locus
* @param refBase the reference allele
*/
private void removePastIntervals(GenomeLoc refLocus, byte refBase) {
// if there are statistics to output/ check to see that we can output them in order
if (getFinishedIntervalSpan(refLocus) != null &&
getIntervalMapSpan().getStart() == getFinishedIntervalSpan(refLocus).getStart()) {
private void outputFinishedIntervals(final GenomeLoc refLocus, final byte refBase) {
GenomeLoc interval = intervalListIterator.peek();
for (GenomeLoc interval : intervalMap.keySet()) {
if (interval.isBefore(refLocus)) {
outputStatsToVCF(intervalMap.get(interval), Allele.create(refBase, true));
intervalMap.remove(interval);
}
// output empty statistics for uncovered intervals
while (interval != null && interval.isBefore(refLocus)) {
final IntervalStratification stats = intervalMap.get(interval);
outputStatsToVCF(stats != null ? stats : createIntervalStatistic(interval), UNCOVERED_ALLELE);
if (stats != null) intervalMap.remove(interval);
intervalListIterator.next();
interval = intervalListIterator.peek();
}
// remove any potential leftover interval in intervalMap (this will only happen when we have overlapping intervals)
for (GenomeLoc key : intervalMap.keySet()) {
if (key.isBefore(refLocus)) {
outputStatsToVCF(intervalMap.get(key), Allele.create(refBase, true));
intervalMap.remove(key);
}
}
}
@ -269,17 +230,9 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
*/
private void addNewOverlappingIntervals(GenomeLoc refLocus) {
GenomeLoc interval = intervalListIterator.peek();
// skip any intervals with no coverage that we have passed
while (interval != null && interval.isBefore(refLocus)) {
intervalListIterator.next(); // discard the interval (we've already added it to the map)
interval = intervalListIterator.peek();
}
// add any intervals that overlap this one
while (interval != null && !interval.isPast(refLocus)) {
intervalMap.put(interval, createIntervalStatistic(interval));
intervalListIterator.next(); // discard the interval (we've already added it to the map)
intervalListIterator.next();
interval = intervalListIterator.peek();
}
}
@ -290,7 +243,7 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
* @param stats The statistics of the interval
* @param refAllele the reference allele
*/
private void outputStatsToVCF(IntervalStatistics stats, Allele refAllele) {
private void outputStatsToVCF(IntervalStratification stats, Allele refAllele) {
GenomeLoc interval = stats.getInterval();
@ -302,37 +255,26 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
alleles.add(SYMBOLIC_ALLELE);
VariantContextBuilder vcb = new VariantContextBuilder("DiagnoseTargets", interval.getContig(), interval.getStart(), interval.getStop(), alleles);
vcb = vcb.log10PError(VariantContext.NO_LOG10_PERROR); // QUAL field makes no sense in our VCF
vcb.filters(new HashSet<String>(statusesToStrings(stats.callableStatuses(thresholds), true)));
vcb = vcb.log10PError(VariantContext.NO_LOG10_PERROR);
vcb.filters(new LinkedHashSet<String>(statusToStrings(stats.callableStatuses(), true)));
attributes.put(VCFConstants.END_KEY, interval.getStop());
attributes.put(ThresHolder.AVG_INTERVAL_DP_KEY, stats.averageCoverage());
attributes.put(AVG_INTERVAL_DP_KEY, stats.averageCoverage(interval.size()));
vcb = vcb.attributes(attributes);
if (debug) {
System.out.printf("Output -- Interval: %s, Coverage: %.2f%n", stats.getInterval(), stats.averageCoverage());
}
for (String sample : samples) {
final GenotypeBuilder gb = new GenotypeBuilder(sample);
SampleStatistics sampleStat = stats.getSample(sample);
gb.attribute(ThresHolder.AVG_INTERVAL_DP_KEY, sampleStat.averageCoverage());
gb.attribute("Q1", sampleStat.getQuantileDepth(0.25));
gb.attribute("MED", sampleStat.getQuantileDepth(0.50));
gb.attribute("Q3", sampleStat.getQuantileDepth(0.75));
SampleStratification sampleStat = stats.getSampleStatistics(sample);
gb.attribute(AVG_INTERVAL_DP_KEY, sampleStat.averageCoverage(interval.size()));
if (debug) {
System.out.printf("Found %d bad mates out of %d reads %n", sampleStat.getnBadMates(), sampleStat.getnReads());
}
gb.filters(statusesToStrings(stats.getSample(sample).getCallableStatuses(thresholds), false));
gb.filters(statusToStrings(stats.getSampleStatistics(sample).callableStatuses(), false));
genotypes.add(gb.make());
}
vcb = vcb.genotypes(genotypes);
vcfWriter.add(vcb.make());
}
/**
@ -341,17 +283,74 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
* @param statuses the set of statuses to be converted
* @return a matching set of strings
*/
private List<String> statusesToStrings(Set<CallableStatus> statuses, final boolean includePASS) {
List<String> output = new ArrayList<String>(statuses.size());
private List<String> statusToStrings(Iterable<CallableStatus> statuses, final boolean isInfoField) {
List<String> output = new LinkedList<String>();
for (CallableStatus status : statuses)
if ( includePASS || status != CallableStatus.PASS ) // adding pass => results in a filter for genotypes
if ( isInfoField || status != CallableStatus.PASS )
output.add(status.name());
return output;
}
private IntervalStatistics createIntervalStatistic(GenomeLoc interval) {
return new IntervalStatistics(samples, interval);
private IntervalStratification createIntervalStatistic(GenomeLoc interval) {
return new IntervalStratification(samples, interval, thresholds);
}
protected static void loadAllPlugins(final ThresHolder thresholds) {
for (Class<?> stat : new PluginManager<LocusMetric>(LocusMetric.class).getPlugins()) {
try {
final LocusMetric stats = (LocusMetric) stat.newInstance();
stats.initialize(thresholds);
thresholds.locusMetricList.add(stats);
} catch (Exception e) {
throw new DynamicClassResolutionException(stat, e);
}
}
for (Class<?> stat : new PluginManager<SampleMetric>(SampleMetric.class).getPlugins()) {
try {
final SampleMetric stats = (SampleMetric) stat.newInstance();
stats.initialize(thresholds);
thresholds.sampleMetricList.add(stats);
} catch (Exception e) {
throw new DynamicClassResolutionException(stat, e);
}
}
for (Class<?> stat : new PluginManager<IntervalMetric>(IntervalMetric.class).getPlugins()) {
try {
final IntervalMetric stats = (IntervalMetric) stat.newInstance();
stats.initialize(thresholds);
thresholds.intervalMetricList.add(stats);
} catch (Exception e) {
throw new DynamicClassResolutionException(stat, e);
}
}
}
/**
* Gets the header lines for the VCF writer
*
* @return A set of VCF header lines
*/
private static Set<VCFHeaderLine> getHeaderInfo() {
Set<VCFHeaderLine> headerLines = new HashSet<VCFHeaderLine>();
// INFO fields for overall data
headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.END_KEY));
headerLines.add(new VCFInfoHeaderLine(AVG_INTERVAL_DP_KEY, 1, VCFHeaderLineType.Float, "Average depth across the interval. Sum of the depth in a loci divided by interval size."));
headerLines.add(new VCFInfoHeaderLine("Diagnose Targets", 0, VCFHeaderLineType.Flag, "DiagnoseTargets mode"));
// FORMAT fields for each genotype
headerLines.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_FILTER_KEY));
headerLines.add(new VCFFormatHeaderLine(AVG_INTERVAL_DP_KEY, 1, VCFHeaderLineType.Float, "Average sample depth across the interval. Sum of the sample specific depth in all loci divided by interval size."));
// FILTER fields
for (CallableStatus stat : CallableStatus.values())
headerLines.add(new VCFFilterHeaderLine(stat.name(), stat.description));
return headerLines;
}
}

57
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalMetric.java 100644
View File

@ -0,0 +1,57 @@
/*
* By downloading the PROGRAM you agree to the following terms of use:
*
* BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
*
* This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
*
* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
*
* 1. DEFINITIONS
* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
*
* 2. LICENSE
* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
*
* 3. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. INDEMNIFICATION
* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
*
* 5. NO REPRESENTATIONS OR WARRANTIES
* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
*
* 6. ASSIGNMENT
* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
*
* 7. MISCELLANEOUS
* 7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
* 7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
* 7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
* 7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
* 7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
/**
* Created with IntelliJ IDEA.
* User: carneiro
* Date: 4/20/13
* Time: 11:30 PM
* To change this template use File | Settings | File Templates.
*/
interface IntervalMetric extends Metric {
}

133
protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatisticsUnitTest.java → protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalStratification.java
View File

@ -44,78 +44,89 @@
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
import net.sf.samtools.SAMFileHeader;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
public class SampleStatisticsUnitTest/* extends BaseTest */ {
import java.util.*;
@DataProvider(name = "QuartileValues")
public Object[][] getQuantileValues() {
final class IntervalStratification extends AbstractStratification {
private final Map<String, AbstractStratification> samples;
private final GenomeLoc interval;
private final ThresHolder thresholds;
int[] a1 = {5};
int[] a2 = {1, 2};
int[] a5 = {10, 20, 30, 40, 50};
int[] a10 = {1, 2, 3, 4, 5, 6, 7, 8, 9, 10};
return new Object[][]{
new Object[]{a1, 0.5, 5},
new Object[]{a1, 0, 5},
new Object[]{a1, 1, 5},
new Object[]{a2, 0.5, 1.5},
new Object[]{a2, 0.25, 1},
new Object[]{a2, 0.75, 2},
new Object[]{a5, 0.5, 30},
new Object[]{a5, 0.25, 20},
new Object[]{a5, 0.75, 40},
new Object[]{a5, 0, -1},
new Object[]{a10, 0.5, 5.5},
new Object[]{a10, 0.25, 3},
new Object[]{a10, 0.75, 8}
};
public IntervalStratification(Set<String> samples, GenomeLoc interval, ThresHolder thresholds) {
this.interval = interval;
this.thresholds = thresholds;
this.samples = new HashMap<String, AbstractStratification>(samples.size());
for (String sample : samples)
this.samples.put(sample, new SampleStratification(interval, thresholds));
}
@Test(dataProvider = "QuartileValues")
public void testGetQuartile(int[] dataList, double percentage, double expected) {
Assert.assertEquals(SampleStatistics.getQuartile(dataList, percentage), expected);
public SampleStratification getSampleStatistics(String sample) {
return (SampleStratification) samples.get(sample);
}
public GenomeLoc getInterval() {
return interval;
}
public int getNSamples() {
return samples.size();
}
/**
* The function to populate data into the Statistics from the walker.
* This takes the input and manages passing the data to the SampleStatistics and Locus Statistics
*
* @param context The alignment context given from the walker
*/
public void addLocus(AlignmentContext context) {
ReadBackedPileup pileup = context.getBasePileup();
Map<String, ReadBackedPileup> samplePileups = pileup.getPileupsForSamples(samples.keySet());
for (Map.Entry<String, ReadBackedPileup> entry : samplePileups.entrySet()) {
String sample = entry.getKey();
ReadBackedPileup samplePileup = entry.getValue();
SampleStratification sampleStratification = (SampleStratification) samples.get(sample);
if (sampleStratification == null)
throw new ReviewedStingException(String.format("Trying to add locus statistics to a sample (%s) that doesn't exist in the Interval.", sample));
sampleStratification.addLocus(context.getLocation(), samplePileup);
}
}
@DataProvider(name = "ReadsAndMates")
public Object[][] getReadAndMates() {
SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
GATKSAMRecord noPair = ArtificialSAMUtils.createArtificialRead(header, "test", 0, 100, 50);
GATKSAMRecord good = ArtificialSAMUtils.createPair(header, "test", 30, 100, 150, true, false).get(0);
GATKSAMRecord bigInsertSize = ArtificialSAMUtils.createPair(header, "test", 30, 100, 151, true, false).get(0);
GATKSAMRecord inverted = ArtificialSAMUtils.createPair(header, "test", 30, 151, 150, true, false).get(0);
GATKSAMRecord sameOrientation = ArtificialSAMUtils.createPair(header, "test", 30, 100, 151, true, true).get(0);
GATKSAMRecord pairNotMapped = ArtificialSAMUtils.createPair(header, "test", 30, 100, 140, true, false).get(1);
pairNotMapped.setMateUnmappedFlag(true);
// finish test
return new Object[][]{
new Object[]{noPair, false},
new Object[]{good, true},
new Object[]{bigInsertSize, false},
new Object[]{inverted, false},
new Object[]{sameOrientation, false},
new Object[]{pairNotMapped, false}
};
/**
* {@inheritDoc}
*/
@Override
public Iterable<AbstractStratification> getElements() {
return samples.values();
}
@Test(dataProvider = "ReadsAndMates")
public void testHasValidMate(GATKSAMRecord read, boolean expected) {
//50 is out maximum insert size
Assert.assertEquals(new SampleStatistics(GenomeLoc.UNMAPPED).hasValidMate(read, ThresHolder.DEFAULTS), expected);
}
/**
* {@inheritDoc}
*/
@Override
public Iterable<CallableStatus> callableStatuses() {
final List<CallableStatus> output = new LinkedList<CallableStatus>();
// check if any of the votes pass the threshold
final int nSamples = getNSamples();
for (Map.Entry<CallableStatus, Integer> entry : getStatusTally().entrySet()) {
if ((double) entry.getValue() / nSamples > thresholds.votePercentageThreshold) {
output.add(entry.getKey());
}
}
output.addAll(queryStatus(thresholds.intervalMetricList, this));
return output;
}
}

58
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetric.java 100644
View File

@ -0,0 +1,58 @@
/*
* By downloading the PROGRAM you agree to the following terms of use:
*
* BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
*
* This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
*
* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
*
* 1. DEFINITIONS
* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
*
* 2. LICENSE
* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
*
* 3. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. INDEMNIFICATION
* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
*
* 5. NO REPRESENTATIONS OR WARRANTIES
* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
*
* 6. ASSIGNMENT
* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
*
* 7. MISCELLANEOUS
* 7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
* 7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
* 7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
* 7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
* 7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
/**
* Created with IntelliJ IDEA.
* User: carneiro
* Date: 4/20/13
* Time: 11:29 PM
* To change this template use File | Settings | File Templates.
*/
interface LocusMetric extends Metric {
public CallableStatus sampleStatus (SampleStratification sampleStratification);
}

73
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricCoverageGap.java 100644
View File

@ -0,0 +1,73 @@
/*
* By downloading the PROGRAM you agree to the following terms of use:
*
* BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
*
* This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
*
* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
*
* 1. DEFINITIONS
* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
*
* 2. LICENSE
* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
*
* 3. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. INDEMNIFICATION
* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
*
* 5. NO REPRESENTATIONS OR WARRANTIES
* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
*
* 6. ASSIGNMENT
* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
*
* 7. MISCELLANEOUS
* 7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
* 7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
* 7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
* 7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
* 7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
/**
* User: carneiro
* Date: 4/20/13
* Time: 11:44 PM
*/
final class LocusMetricCoverageGap implements LocusMetric {
private double threshold;
private static final CallableStatus CALL = CallableStatus.COVERAGE_GAPS;
@Override
public void initialize(ThresHolder thresholds) {
threshold = thresholds.coverageStatusThreshold;
}
@Override
public CallableStatus status(AbstractStratification statistics) {
final LocusStratification locusStratification = (LocusStratification) statistics;
return locusStratification.getRawCoverage() == 0 ? CALL : null;
}
@Override
public CallableStatus sampleStatus(SampleStratification sampleStratification) {
return PluginUtils.genericSampleStatus(sampleStratification, CALL, threshold);
}
}

75
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricExcessiveCoverage.java 100644
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@ -0,0 +1,75 @@
/*
* By downloading the PROGRAM you agree to the following terms of use:
*
* BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
*
* This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
*
* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
*
* 1. DEFINITIONS
* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
*
* 2. LICENSE
* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
*
* 3. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. INDEMNIFICATION
* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
*
* 5. NO REPRESENTATIONS OR WARRANTIES
* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
*
* 6. ASSIGNMENT
* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
*
* 7. MISCELLANEOUS
* 7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
* 7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
* 7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
* 7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
* 7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
/**
* User: carneiro
* Date: 4/20/13
* Time: 11:44 PM
*/
final class LocusMetricExcessiveCoverage implements LocusMetric {
private int excessiveCoverage;
private double threshold;
private static final CallableStatus CALL = CallableStatus.EXCESSIVE_COVERAGE ;
@Override
public void initialize(ThresHolder thresholds) {
this.excessiveCoverage = thresholds.maximumCoverage;
this.threshold = thresholds.coverageStatusThreshold;
}
@Override
public CallableStatus status(AbstractStratification statistics) {
final LocusStratification locusStratification = (LocusStratification) statistics;
return locusStratification.getCoverage() > excessiveCoverage ? CALL : null;
}
@Override
public CallableStatus sampleStatus(SampleStratification sampleStratification) {
return PluginUtils.genericSampleStatus(sampleStratification, CALL, threshold);
}
}

76
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricLowCoverage.java 100644
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@ -0,0 +1,76 @@
/*
* By downloading the PROGRAM you agree to the following terms of use:
*
* BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
*
* This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
*
* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
*
* 1. DEFINITIONS
* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
*
* 2. LICENSE
* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
*
* 3. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. INDEMNIFICATION
* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
*
* 5. NO REPRESENTATIONS OR WARRANTIES
* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
*
* 6. ASSIGNMENT
* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
*
* 7. MISCELLANEOUS
* 7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
* 7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
* 7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
* 7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
* 7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
/**
* User: carneiro
* Date: 4/20/13
* Time: 11:44 PM
*/
final class LocusMetricLowCoverage implements LocusMetric {
private int minCoverage;
private double threshold;
private static final CallableStatus CALL = CallableStatus.LOW_COVERAGE ;
@Override
public void initialize(ThresHolder thresholds) {
this.minCoverage = thresholds.minimumCoverage;
this.threshold = thresholds.coverageStatusThreshold;
}
@Override
public CallableStatus status(AbstractStratification statistics) {
final LocusStratification locusStratification = (LocusStratification) statistics;
final long raw = locusStratification.getRawCoverage();
return raw > 0 && raw < minCoverage ? CALL: null;
}
@Override
public CallableStatus sampleStatus(SampleStratification sampleStratification) {
return PluginUtils.genericSampleStatus(sampleStratification, CALL, threshold);
}
}

75
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricPoorQuality.java 100644
View File

@ -0,0 +1,75 @@
/*
* By downloading the PROGRAM you agree to the following terms of use:
*
* BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
*
* This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
*
* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
*
* 1. DEFINITIONS
* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
*
* 2. LICENSE
* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
*
* 3. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. INDEMNIFICATION
* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
*
* 5. NO REPRESENTATIONS OR WARRANTIES
* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
*
* 6. ASSIGNMENT
* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
*
* 7. MISCELLANEOUS
* 7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
* 7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
* 7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
* 7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
* 7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
/**
* User: carneiro
* Date: 4/20/13
* Time: 11:44 PM
*/
final class LocusMetricPoorQuality implements LocusMetric {
private int minCoverage;
private double threshold;
private static final CallableStatus CALL = CallableStatus.POOR_QUALITY ;
@Override
public void initialize(ThresHolder thresholds) {
this.minCoverage = thresholds.minimumCoverage;
this.threshold = thresholds.coverageStatusThreshold;
}
@Override
public CallableStatus status(AbstractStratification statistics) {
final LocusStratification locusStratification = (LocusStratification) statistics;
return locusStratification.getCoverage() < minCoverage && locusStratification.getRawCoverage() >= minCoverage ? CALL: null;
}
@Override
public CallableStatus sampleStatus(SampleStratification sampleStratification) {
return PluginUtils.genericSampleStatus(sampleStratification, CALL, threshold);
}
}

65
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/LocusStatistics.java → protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusStratification.java
View File

@ -44,61 +44,54 @@
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
import java.util.HashSet;
import java.util.Set;
import java.util.LinkedList;
import java.util.List;
class LocusStatistics {
private final int coverage;
private final int rawCoverage;
final class LocusStratification extends AbstractStratification {
private long coverage;
private long rawCoverage;
private final List<Metric> locusStatisticsList;
public LocusStatistics() {
this.coverage = 0;
this.rawCoverage = 0;
public LocusStratification(ThresHolder thresholds) {
this(0,0,thresholds);
}
public LocusStatistics(int coverage, int rawCoverage) {
protected LocusStratification(int coverage, int rawCoverage, ThresHolder thresholds) {
this.coverage = coverage;
this.rawCoverage = rawCoverage;
this.locusStatisticsList = thresholds.locusMetricList;
}
public int getCoverage() {
return coverage;
}
@Override
public long getCoverage() {return coverage;}
public long getRawCoverage() {return rawCoverage;}
public int getRawCoverage() {
return rawCoverage;
public void addLocus(final int coverage, final int rawCoverage) {
this.coverage = coverage;
this.rawCoverage = rawCoverage;
}
/**
* Generates all applicable statuses from the coverages in this locus
*
* @param thresholds the class contains the statistical threshold for making calls
* @return a set of all statuses that apply
*/
public Set<CallableStatus> callableStatuses(ThresHolder thresholds) {
Set<CallableStatus> output = new HashSet<CallableStatus>();
// if too much coverage
if (getCoverage() > thresholds.getMaximumCoverage())
output.add(CallableStatus.EXCESSIVE_COVERAGE);
// if not enough coverage
if (getCoverage() < thresholds.getMinimumCoverage()) {
// was there a lot of low Qual coverage?
if (getRawCoverage() >= thresholds.getMinimumCoverage())
output.add(CallableStatus.POOR_QUALITY);
// no?
else {
// is there any coverage?
if (getRawCoverage() > 0)
output.add(CallableStatus.LOW_COVERAGE);
else
output.add(CallableStatus.COVERAGE_GAPS);
public List<CallableStatus> callableStatuses() {
List<CallableStatus> output = new LinkedList<CallableStatus>();
for (Metric stats : locusStatisticsList) {
CallableStatus status = stats.status(this);
if (status != null) {
output.add(status);
}
}
return output;
}
@Override
public Iterable<AbstractStratification> getElements() {
return null;
}
}

57
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/Metric.java 100644
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/*
* By downloading the PROGRAM you agree to the following terms of use:
*
* BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
*
* This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
*
* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
*
* 1. DEFINITIONS
* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
*
* 2. LICENSE
* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
*
* 3. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. INDEMNIFICATION
* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
*
* 5. NO REPRESENTATIONS OR WARRANTIES
* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
*
* 6. ASSIGNMENT
* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
*
* 7. MISCELLANEOUS
* 7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
* 7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
* 7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
* 7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
* 7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
/**
*
* @author Mauricio Carneiro
* @since 4/23/13
*/
interface Metric {
public void initialize(ThresHolder thresholds);
public CallableStatus status (AbstractStratification statistic);
}

63
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/PluginUtils.java 100644
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/*
* By downloading the PROGRAM you agree to the following terms of use:
*
* BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
*
* This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
*
* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
*
* 1. DEFINITIONS
* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
*
* 2. LICENSE
* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
*
* 3. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. INDEMNIFICATION
* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
*
* 5. NO REPRESENTATIONS OR WARRANTIES
* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
*
* 6. ASSIGNMENT
* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
*
* 7. MISCELLANEOUS
* 7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
* 7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
* 7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
* 7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
* 7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
import java.util.Map;
/**
* User: carneiro
* Date: 4/21/13
* Time: 11:23 AM
*/
final class PluginUtils {
public static CallableStatus genericSampleStatus (final SampleStratification sampleStratification, final CallableStatus CALL, final double threshold) {
final Map<CallableStatus, Integer> totals = sampleStratification.getStatusTally();
final int size = sampleStratification.getIntervalSize();
final int statusCount = totals.containsKey(CALL) ? totals.get(CALL) : 0;
return ( (double) statusCount / size) >= threshold ? CALL: null;
}
}

57
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetric.java 100644
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@ -0,0 +1,57 @@
/*
* By downloading the PROGRAM you agree to the following terms of use:
*
* BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
*
* This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
*
* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
*
* 1. DEFINITIONS
* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
*
* 2. LICENSE
* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
*
* 3. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. INDEMNIFICATION
* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
*
* 5. NO REPRESENTATIONS OR WARRANTIES
* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
*
* 6. ASSIGNMENT
* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
*
* 7. MISCELLANEOUS
* 7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
* 7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
* 7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
* 7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
* 7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
/**
* Created with IntelliJ IDEA.
* User: carneiro
* Date: 4/20/13
* Time: 11:30 PM
* To change this template use File | Settings | File Templates.
*/
interface SampleMetric extends Metric {
}

73
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetricBadMates.java 100644
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@ -0,0 +1,73 @@
/*
* By downloading the PROGRAM you agree to the following terms of use:
*
* BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
*
* This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
*
* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
*
* 1. DEFINITIONS
* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
*
* 2. LICENSE
* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
*
* 3. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. INDEMNIFICATION
* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
*
* 5. NO REPRESENTATIONS OR WARRANTIES
* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
*
* 6. ASSIGNMENT
* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
*
* 7. MISCELLANEOUS
* 7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
* 7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
* 7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
* 7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
* 7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
/**
* User: carneiro
* Date: 4/20/13
* Time: 11:44 PM
*/
final class SampleMetricBadMates implements SampleMetric {
private static final CallableStatus CALL = CallableStatus.NO_READS ;
private double threshold;
private double votingThreshold;
@Override
public void initialize(ThresHolder thresholds) {
threshold = thresholds.badMateStatusThreshold;
votingThreshold = thresholds.votePercentageThreshold;
}
@Override
public CallableStatus status(AbstractStratification statistics) {
final SampleStratification sampleStratification = (SampleStratification) statistics;
final int nReads = sampleStratification.getnReads();
return nReads > 0 && (double) sampleStratification.getnBadMates() / nReads > threshold ? CALL : null;
}
}

66
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetricNoReads.java 100644
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@ -0,0 +1,66 @@
/*
* By downloading the PROGRAM you agree to the following terms of use:
*
* BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
*
* This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
*
* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
*
* 1. DEFINITIONS
* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
*
* 2. LICENSE
* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
*
* 3. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. INDEMNIFICATION
* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
*
* 5. NO REPRESENTATIONS OR WARRANTIES
* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
*
* 6. ASSIGNMENT
* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
*
* 7. MISCELLANEOUS
* 7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
* 7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
* 7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
* 7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
* 7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
/**
* User: carneiro
* Date: 4/20/13
* Time: 11:44 PM
*/
final class SampleMetricNoReads implements SampleMetric {
private static final CallableStatus CALL = CallableStatus.NO_READS;
@Override
public void initialize(ThresHolder thresholds) {
}
@Override
public CallableStatus status(AbstractStratification statistics) {
final SampleStratification sampleStratification = (SampleStratification) statistics;
return sampleStratification.getnReads() == 0 ? CALL : null;
}
}

162
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleStratification.java 100644
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@ -0,0 +1,162 @@
/*
* By downloading the PROGRAM you agree to the following terms of use:
*
* BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
*
* This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
*
* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
*
* 1. DEFINITIONS
* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
*
* 2. LICENSE
* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
*
* 3. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. INDEMNIFICATION
* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
*
* 5. NO REPRESENTATIONS OR WARRANTIES
* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
*
* 6. ASSIGNMENT
* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
*
* 7. MISCELLANEOUS
* 7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
* 7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
* 7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
* 7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
* 7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.util.ArrayList;
import java.util.LinkedList;
import java.util.List;
/**
* The statistics calculator for a specific sample given the interval
*/
final class SampleStratification extends AbstractStratification {
private final GenomeLoc interval;
private final ArrayList<AbstractStratification> loci;
private final ThresHolder thresholds;
private int nReads = -1;
private int nBadMates = -1;
public SampleStratification(final GenomeLoc interval, final ThresHolder thresholds) {
this.interval = interval;
this.loci = new ArrayList<AbstractStratification>(interval.size());
this.thresholds = thresholds;
nReads = 0;
nBadMates = 0;
// Initialize every loci (this way we don't have to worry about non-existent loci in the object
for (int i = 0; i < interval.size(); i++)
this.loci.add(new LocusStratification(thresholds));
}
/**
* Simple Getters
*/
public int getIntervalSize() {return interval.size();}
public int getnReads() {return nReads;}
public int getnBadMates() {return nBadMates;}
/**
* Adds a locus to the interval wide stats
*
* @param locus The locus given as a GenomeLoc
* @param pileup The pileup of that locus, this exclusively contains the sample
*/
public void addLocus(GenomeLoc locus, ReadBackedPileup pileup) {
if (!interval.containsP(locus))
throw new ReviewedStingException(String.format("Locus %s is not part of the Interval %s", locus, interval));
// a null pileup means there nothing to add
if (pileup != null) {
final int locusIndex = locus.getStart() - interval.getStart();
final int rawCoverage = pileup.depthOfCoverage();
final int coverage = pileup.getBaseAndMappingFilteredPileup(thresholds.minimumBaseQuality, thresholds.minimumMappingQuality).depthOfCoverage();
final LocusStratification locusData = (LocusStratification) loci.get(locusIndex);
locusData.addLocus(coverage, rawCoverage);
// process all the reads in this pileup (tallying number of reads and bad mates)
for (GATKSAMRecord read : pileup.getReads())
processRead(read);
}
}
@Override
public Iterable<AbstractStratification> getElements() {
return loci;
}
/**
* {@inheritDoc}
*/
@Override
public Iterable<CallableStatus> callableStatuses() {
final List<CallableStatus> output = new LinkedList<CallableStatus>();
// get the tally of all the locus callable statuses
for (Metric locusStat : thresholds.locusMetricList) {
final CallableStatus status = ((LocusMetric) locusStat).sampleStatus(this);
if (status != null) {
output.add(status);
}
}
// get the sample specific statitics statuses
for (Metric sampleStat : thresholds.sampleMetricList) {
final CallableStatus status = sampleStat.status(this);
if (status != null) {
output.add(status);
}
}
// special case, if there are no reads, then there is no sense reporting coverage gaps.
if (output.contains(CallableStatus.NO_READS) && output.contains(CallableStatus.COVERAGE_GAPS))
output.remove(CallableStatus.COVERAGE_GAPS);
return output;
}
/**
* Account for the read and check it for any statistics necessary. Reads are marked in the temporary
* attribute "seen" to make sure they're not counted twice.
*
* @param read the read
*/
private void processRead(GATKSAMRecord read) {
if (read.getTemporaryAttribute("seen") == null) {
nReads++;
if (read.getReadPairedFlag() && !read.getProperPairFlag())
nBadMates++;
read.setTemporaryAttribute("seen", true);
}
}
}

186
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/ThresHolder.java → protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java
View File

@ -44,131 +44,101 @@
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.commandline.Argument;
import java.util.HashSet;
import java.util.Set;
import java.util.LinkedList;
import java.util.List;
class ThresHolder {
public static final String AVG_INTERVAL_DP_KEY = "AVG_INTERVAL_DP";
public static final ThresHolder DEFAULTS = new ThresHolder(20, 20, 5, 700, 20, 50, 0.5, 0.2, 0.5, 0.2, 0.2, 0.5);
final class ThresHolder {
private final int minimumBaseQuality;
private final int minimumMappingQuality;
/**
* Only bases with quality greater than this will be considered in the coverage metrics.
*/
@Argument(fullName = "minimum_base_quality", shortName = "BQ", doc = "The minimum Base Quality that is considered for calls", required = false)
public int minimumBaseQuality = 20;
private final int minimumCoverage;
private final int maximumCoverage;
private final int minimumMedianDepth;
/**
* Only reads with mapping quality greater than this will be considered in the coverage metrics.
*/
@Argument(fullName = "minimum_mapping_quality", shortName = "MQ", doc = "The minimum read mapping quality considered for calls", required = false)
public int minimumMappingQuality = 20;
private final int maximumInsertSize;
/**
* If at any locus, a sample has less coverage than this, it will be reported as LOW_COVERAGE
*/
@Argument(fullName = "minimum_coverage", shortName = "min", doc = "The minimum allowable coverage, used for calling LOW_COVERAGE", required = false)
public int minimumCoverage = 5;
private final double votePercentageThreshold;
private final double lowMedianDepthThreshold;
private final double badMateStatusThreshold;
private final double coverageStatusThreshold;
private final double excessiveCoverageThreshold;
private final double qualityStatusThreshold;
/**
* If at any locus, a sample has more coverage than this, it will be reported as EXCESSIVE_COVERAGE
*/
@Argument(fullName = "maximum_coverage", shortName = "max", doc = "The maximum allowable coverage, used for calling EXCESSIVE_COVERAGE", required = false)
public int maximumCoverage = 700;
public ThresHolder(int minimumBaseQuality,
int minimumMappingQuality,
int minimumCoverage,
int maximumCoverage,
int minimumMedianDepth,
int maximumInsertSize,
double votePercentageThreshold,
double lowMedianDepthThreshold,
double badMateStatusThreshold,
double coverageStatusThreshold,
double excessiveCoverageThreshold,
double qualityStatusThreshold) {
/**
* If any sample has a paired read whose distance between alignment starts (between the pairs) is greater than this, it will be reported as BAD_MATE
*/
@Argument(fullName = "maximum_insert_size", shortName = "ins", doc = "The maximum allowed distance between a read and its mate", required = false)
public int maximumInsertSize = 500;
/**
* The proportion of samples that must have a status for it to filter the entire interval. Example: 8 out of 10 samples have low coverage status on the interval,
* with a threshold higher than 0.2, this interval will be filtered as LOW_COVERAGE.
*/
@Argument(fullName = "voting_status_threshold", shortName = "stV", doc = "The needed proportion of samples containing a call for the interval to adopt the call ", required = false)
public double votePercentageThreshold = 0.50;
/**
* The proportion of reads in the loci that must have bad mates for the sample to be reported as BAD_MATE
*/
@Argument(fullName = "bad_mate_status_threshold", shortName = "stBM", doc = "The proportion of the loci needed for calling BAD_MATE", required = false)
public double badMateStatusThreshold = 0.50;
/**
* The proportion of loci in a sample that must fall under the LOW_COVERAGE or COVERAGE_GAPS category for the sample to be reported as either (or both)
*/
@Argument(fullName = "coverage_status_threshold", shortName = "stC", doc = "The proportion of the loci needed for calling LOW_COVERAGE and COVERAGE_GAPS", required = false)
public double coverageStatusThreshold = 0.20;
/**
* The proportion of loci in a sample that must fall under the EXCESSIVE_COVERAGE category for the sample to be reported as EXCESSIVE_COVERAGE
*/
@Argument(fullName = "excessive_coverage_status_threshold", shortName = "stXC", doc = "The proportion of the loci needed for calling EXCESSIVE_COVERAGE", required = false)
public double excessiveCoverageThreshold = 0.20;
/**
* The proportion of loci in a sample that must fall under the LOW_QUALITY category for the sample to be reported as LOW_QUALITY
*/
@Argument(fullName = "quality_status_threshold", shortName = "stQ", doc = "The proportion of the loci needed for calling POOR_QUALITY", required = false)
public double qualityStatusThreshold = 0.50;
public final List<Metric> locusMetricList = new LinkedList<Metric>();
public final List<Metric> sampleMetricList = new LinkedList<Metric>();
public final List<Metric> intervalMetricList = new LinkedList<Metric>();
public ThresHolder() {}
public ThresHolder(final int minimumBaseQuality,
final int minimumMappingQuality,
final int minimumCoverage,
final int maximumCoverage,
final int maximumInsertSize,
final double votePercentageThreshold,
final double badMateStatusThreshold,
final double coverageStatusThreshold,
final double excessiveCoverageThreshold,
final double qualityStatusThreshold) {
this.minimumBaseQuality = minimumBaseQuality;
this.minimumMappingQuality = minimumMappingQuality;
this.minimumCoverage = minimumCoverage;
this.maximumCoverage = maximumCoverage;
this.minimumMedianDepth = minimumMedianDepth;
this.maximumInsertSize = maximumInsertSize;
this.votePercentageThreshold = votePercentageThreshold;
this.lowMedianDepthThreshold = lowMedianDepthThreshold;
this.badMateStatusThreshold = badMateStatusThreshold;
this.coverageStatusThreshold = coverageStatusThreshold;
this.excessiveCoverageThreshold = excessiveCoverageThreshold;
this.qualityStatusThreshold = qualityStatusThreshold;
}
public int getMinimumCoverage() {
return minimumCoverage;
}
public int getMaximumCoverage() {
return maximumCoverage;
}
public int getMinimumMedianDepth() {
return minimumMedianDepth;
}
public int getMaximumInsertSize() {
return maximumInsertSize;
}
public double getVotePercentageThreshold() {
return votePercentageThreshold;
}
public double getLowMedianDepthThreshold() {
return lowMedianDepthThreshold;
}
public double getBadMateStatusThreshold() {
return badMateStatusThreshold;
}
public double getCoverageStatusThreshold() {
return coverageStatusThreshold;
}
public double getExcessiveCoverageThreshold() {
return excessiveCoverageThreshold;
}
public double getQualityStatusThreshold() {
return qualityStatusThreshold;
}
public int getFilteredCoverage(ReadBackedPileup pileup) {
return pileup.getBaseAndMappingFilteredPileup(minimumBaseQuality, minimumMappingQuality).depthOfCoverage();
}
/**
* Gets the header lines for the VCF writer
*
* @return A set of VCF header lines
*/
public static Set<VCFHeaderLine> getHeaderInfo() {
Set<VCFHeaderLine> headerLines = new HashSet<VCFHeaderLine>();
// INFO fields for overall data
headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.END_KEY));
headerLines.add(new VCFInfoHeaderLine(AVG_INTERVAL_DP_KEY, 1, VCFHeaderLineType.Float, "Average depth across the interval. Sum of the depth in a loci divided by interval size."));
headerLines.add(new VCFInfoHeaderLine("Diagnose Targets", 0, VCFHeaderLineType.Flag, "DiagnoseTargets mode"));
// FORMAT fields for each genotype
// todo -- find the appropriate VCF constants
headerLines.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_FILTER_KEY));
headerLines.add(new VCFFormatHeaderLine(AVG_INTERVAL_DP_KEY, 1, VCFHeaderLineType.Float, "Average depth across the interval. Sum of the depth in a loci divided by interval size."));
headerLines.add(new VCFFormatHeaderLine("Q1", 1, VCFHeaderLineType.Float, "Lower Quartile of depth distribution."));
headerLines.add(new VCFFormatHeaderLine("MED", 1, VCFHeaderLineType.Float, "Median of depth distribution."));
headerLines.add(new VCFFormatHeaderLine("Q3", 1, VCFHeaderLineType.Float, "Upper Quartile of depth Distribution."));
// FILTER fields
for (CallableStatus stat : CallableStatus.values())
headerLines.add(new VCFFilterHeaderLine(stat.name(), stat.description));
return headerLines;
}
}

172
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@ -1,172 +0,0 @@
/*
* By downloading the PROGRAM you agree to the following terms of use:
*
* BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
*
* This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
*
* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
*
* 1. DEFINITIONS
* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
*
* 2. LICENSE
* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
*
* 3. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. INDEMNIFICATION
* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
*
* 5. NO REPRESENTATIONS OR WARRANTIES
* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
*
* 6. ASSIGNMENT
* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
*
* 7. MISCELLANEOUS
* 7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
* 7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
* 7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
* 7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
* 7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
class IntervalStatistics {
private final Map<String, SampleStatistics> samples;
private final GenomeLoc interval;
private boolean hasNref = false;
private int preComputedTotalCoverage = -1; // avoids re-calculating the total sum (-1 means we haven't pre-computed it yet)
/*
private double minMedianDepth = 20.0;
private double badMedianDepthPercentage = 0.20;
private double votePercentage = 0.50;
*/
public IntervalStatistics(Set<String> samples, GenomeLoc interval/*, int minimumCoverageThreshold, int maximumCoverageThreshold, int minimumMappingQuality, int minimumBaseQuality*/) {
this.interval = interval;
this.samples = new HashMap<String, SampleStatistics>(samples.size());
for (String sample : samples)
this.samples.put(sample, new SampleStatistics(interval /*, minimumCoverageThreshold, maximumCoverageThreshold, minimumMappingQuality, minimumBaseQuality*/));
}
public SampleStatistics getSample(String sample) {
return samples.get(sample);
}
public GenomeLoc getInterval() {
return interval;
}
/**
* The function to populate data into the Statistics from the walker.
* This takes the input and manages passing the data to the SampleStatistics and Locus Statistics
*
* @param context The alignment context given from the walker
* @param ref the reference context given from the walker
* @param thresholds the class contains the statistical threshold for making calls
*/
public void addLocus(AlignmentContext context, ReferenceContext ref, ThresHolder thresholds) {
ReadBackedPileup pileup = context.getBasePileup();
//System.out.println(ref.getLocus().toString());
Map<String, ReadBackedPileup> samplePileups = pileup.getPileupsForSamples(samples.keySet());
for (Map.Entry<String, ReadBackedPileup> entry : samplePileups.entrySet()) {
String sample = entry.getKey();
ReadBackedPileup samplePileup = entry.getValue();
SampleStatistics sampleStatistics = samples.get(sample);
if (sampleStatistics == null)
throw new ReviewedStingException(String.format("Trying to add locus statistics to a sample (%s) that doesn't exist in the Interval.", sample));
sampleStatistics.addLocus(context.getLocation(), samplePileup, thresholds);
}
if (!hasNref && ref.getBase() == 'N')
hasNref = true;
}
public double averageCoverage() {
if (preComputedTotalCoverage < 0)
calculateTotalCoverage();
return (double) preComputedTotalCoverage / interval.size();
}
private void calculateTotalCoverage() {
preComputedTotalCoverage = 0;
for (SampleStatistics sample : samples.values())
preComputedTotalCoverage += sample.totalCoverage();
}
/**
* Return the Callable statuses for the interval as a whole
* todo -- add missingness filter
*
* @param thresholds the class contains the statistical threshold for making calls
* @return the callable status(es) for the whole interval
*/
public Set<CallableStatus> callableStatuses(ThresHolder thresholds) {
Set<CallableStatus> output = new HashSet<CallableStatus>();
// Initialize the Map
Map<CallableStatus, Integer> votes = new HashMap<CallableStatus, Integer>();
for (CallableStatus status : CallableStatus.values())
votes.put(status, 0);
// tally up the votes
for (SampleStatistics sample : samples.values())
for (CallableStatus status : sample.getCallableStatuses(thresholds))
votes.put(status, votes.get(status) + 1);
// output tall values above the threshold
for (CallableStatus status : votes.keySet()) {
if (votes.get(status) > (samples.size() * thresholds.getVotePercentageThreshold()) && !(status.equals(CallableStatus.PASS)))
output.add(status);
}
if (hasNref)
output.add(CallableStatus.REF_N);
// get median DP of each sample
int nLowMedianDepth = 0;
for (SampleStatistics sample : samples.values()) {
if (sample.getQuantileDepth(0.5) < thresholds.getMinimumMedianDepth())
nLowMedianDepth++;
}
if (nLowMedianDepth > (samples.size() * thresholds.getLowMedianDepthThreshold()))
output.add(CallableStatus.LOW_MEDIAN_DEPTH);
return output;
}
}

320
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@ -1,320 +0,0 @@
/*
* By downloading the PROGRAM you agree to the following terms of use:
*
* BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
*
* This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
*
* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
*
* 1. DEFINITIONS
* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
*
* 2. LICENSE
* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
*
* 3. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. INDEMNIFICATION
* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
*
* 5. NO REPRESENTATIONS OR WARRANTIES
* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
*
* 6. ASSIGNMENT
* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
*
* 7. MISCELLANEOUS
* 7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
* 7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
* 7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
* 7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
* 7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.util.*;
/**
* The statistics calculator for a specific sample given the interval
*/
class SampleStatistics {
private final GenomeLoc interval;
private final ArrayList<LocusStatistics> loci;
private int[] preSortedDepths = null;
private int preComputedTotalCoverage = -1; // avoids re-calculating the total sum (-1 means we haven't pre-computed it yet)
private int nReads = -1;
private int nBadMates = -1;
private SampleStatistics(GenomeLoc interval, ArrayList<LocusStatistics> loci) {
this.interval = interval;
this.loci = loci;
nReads = 0;
nBadMates = 0;
}
public SampleStatistics(GenomeLoc interval) {
this(interval, new ArrayList<LocusStatistics>(interval.size()));
// Initialize every loci (this way we don't have to worry about non-existent loci in the object
for (int i = 0; i < interval.size(); i++)
this.loci.add(new LocusStatistics());
}
public long totalCoverage() {
if (preComputedTotalCoverage < 0)
calculateTotalCoverage();
return preComputedTotalCoverage;
}
public double averageCoverage() {
if (preComputedTotalCoverage < 0)
calculateTotalCoverage();
return (double) preComputedTotalCoverage / loci.size();
}
/**
* Calculates the callable statuses of the entire sample
*
* @param thresholds the class contains the statistical threshold for making calls
* @return the callable statuses of the entire sample
*/
public Set<CallableStatus> getCallableStatuses(ThresHolder thresholds) {
// We check if reads are present ot prevent div / 0 exceptions
if (nReads == 0) {
return Collections.singleton(CallableStatus.NO_READS);
}
Set<CallableStatus> output = new HashSet<CallableStatus>();
Map<CallableStatus, Double> totals = new HashMap<CallableStatus, Double>(CallableStatus.values().length);
// initialize map
for (CallableStatus status : CallableStatus.values())
totals.put(status, 0.0);
// sum up all the callable statuses for each locus
for (int i = 0; i < interval.size(); i++) {
for (CallableStatus status : callableStatus(i, thresholds)) {
double count = totals.get(status);
totals.put(status, count + 1);
}
}
double intervalSize = interval.size();
if (((double) nBadMates / nReads) >= thresholds.getBadMateStatusThreshold())
output.add(CallableStatus.BAD_MATE);
if ((totals.get(CallableStatus.COVERAGE_GAPS) / intervalSize) >= thresholds.getCoverageStatusThreshold())
output.add(CallableStatus.COVERAGE_GAPS);
if ((totals.get(CallableStatus.LOW_COVERAGE) / intervalSize) >= thresholds.getCoverageStatusThreshold())
output.add(CallableStatus.LOW_COVERAGE);
if ((totals.get(CallableStatus.EXCESSIVE_COVERAGE) / intervalSize) >= thresholds.getExcessiveCoverageThreshold())
output.add(CallableStatus.EXCESSIVE_COVERAGE);
if ((totals.get(CallableStatus.POOR_QUALITY) / intervalSize) >= thresholds.getQualityStatusThreshold())
output.add(CallableStatus.POOR_QUALITY);
if (totals.get(CallableStatus.REF_N) > 0)
output.add(CallableStatus.REF_N);
if (output.isEmpty()) {
output.add(CallableStatus.PASS);
}
return output;
}
/**
* Adds a locus to the interval wide stats
*
* @param locus The locus given as a GenomeLoc
* @param pileup The pileup of that locus, this exclusively contains the sample
* @param thresholds the class contains the statistical threshold for making calls
*/
public void addLocus(GenomeLoc locus, ReadBackedPileup pileup, ThresHolder thresholds) {
if (!interval.containsP(locus))
throw new ReviewedStingException(String.format("Locus %s is not part of the Interval %s", locus, interval));
// a null pileup means there nothing ot add
if (pileup != null) {
int locusIndex = locus.getStart() - interval.getStart();
int rawCoverage = pileup.depthOfCoverage();
int coverage = thresholds.getFilteredCoverage(pileup);
LocusStatistics locusData = new LocusStatistics(coverage, rawCoverage);
loci.set(locusIndex, locusData);
for (GATKSAMRecord read : pileup.getReads())
processRead(read, thresholds);
}
}
private void processRead(GATKSAMRecord read, ThresHolder thresholds) {
// Was this read already processed?
if (read.getTemporaryAttribute("checkedBadMate") == null) {
nReads++;
if (!hasValidMate(read, thresholds))
nBadMates++;
read.setTemporaryAttribute("checkedBadMate", true);
}
}
/**
* returns the callable status of a given locus without taking the reference base into account.
*
* @param locusIndex location in the genome to inquire (only one locus)
* @param thresholds the class contains the statistical threshold for making calls
* @return the callable status of a locus
*/
private Set<CallableStatus> callableStatus(int locusIndex, ThresHolder thresholds) {
LocusStatistics locus = loci.get(locusIndex);
return locus.callableStatuses(thresholds);
}
private void calculateTotalCoverage() {
preComputedTotalCoverage = 0;
for (LocusStatistics locus : loci)
preComputedTotalCoverage += locus.getCoverage();
}
public double getQuantileDepth(double percentage) {
if (preSortedDepths == null)
getDepthsAsSortedArray();
return getQuartile(preSortedDepths, percentage);
}
static double getQuartile(int[] data, double percentage) {
int size = data.length;
if (size == 1)
return (double) data[0];
if (percentage == 0.5) {
return getMedian(data);
}
double position = (size - 1.0) / 2;
if (percentage == 0.25) {
// if the position is a whole number
return getMedian(Arrays.copyOfRange(data, 0, (int) position + 1));
}
if (percentage == 0.75) {
if (position % 1 == 0) {
return getMedian(Arrays.copyOfRange(data, (int) position, size));
} else {
return getMedian(Arrays.copyOfRange(data, (int) position + 1, size));
}
}
return -1;
}
// Assumes data is sorted
private static double getMedian(int[] data) {
double size = (double) data.length;
if (size == 1)
return (double) data[0];
double position = (size - 1.0) / 2;
if (position % 1 == 0)
return (double) data[(int) position];
else {
double high = (double) data[(int) Math.ceil(position)];
double low = (double) data[(int) Math.floor(position)];
return (high + low) / 2;
}
}
private void getDepthsAsSortedArray() {
preSortedDepths = new int[loci.size()];
for (int i = 0; i < loci.size(); i++)
preSortedDepths[i] = loci.get(i).getCoverage();
Arrays.sort(preSortedDepths);
}
boolean hasValidMate(GATKSAMRecord read, ThresHolder thresholds) {
/** Check the following
* Does it have a pair?
* reasonable insert size?
* inverted?
* same orientation?
* same contig?
* is pair mapped?
* todo - is forced mate?
*
*/
// has NO pair
if (!read.getReadPairedFlag())
return false;
// different contigs
if (!read.getMateReferenceIndex().equals(read.getReferenceIndex()))
return false;
// unmapped
if (read.getMateUnmappedFlag() || read.getReadUnmappedFlag())
return false;
// same orientation
if (read.getReadNegativeStrandFlag() == read.getMateNegativeStrandFlag())
return false;
// inverted
if (read.getReadNegativeStrandFlag() ==
read.getAlignmentStart() < read.getMateAlignmentStart())
return false;
// TODO note: IGV uses a different algorithm for insert size, there should be a common util class that does this for you
// mates are too far apart
if (Math.abs(read.getAlignmentStart() - read.getMateAlignmentStart()) > thresholds.getMaximumInsertSize())
return false;
return true;
}
public int getnReads() {
return nReads;
}
public int getnBadMates() {
return nBadMates;
}
}

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/BaseCoverageDistributionIntegrationTest.java → protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/BaseCoverageDistributionIntegrationTest.java
View File

@ -44,7 +44,7 @@
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
package org.broadinstitute.sting.gatk.walkers.diagnostics;
import org.broadinstitute.sting.WalkerTest;
import org.testng.annotations.DataProvider;

16
protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargetsIntegrationTest.java → protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java
View File

@ -44,33 +44,33 @@
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.WalkerTest;
import org.testng.annotations.Test;
import java.util.Arrays;
public class DiagnoseTargetsIntegrationTest extends WalkerTest {
final static String REF = b37KGReference;
final String singleSample = validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.bam";
final String multiSample = validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam";
final String L = validationDataLocation + "DT-itest.interval_list";
final static String REF = BaseTest.b37KGReference;
final String singleSample = BaseTest.validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.bam";
final String multiSample = BaseTest.validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam";
final String L = BaseTest.validationDataLocation + "DT-itest.interval_list";
private void DTTest(String testName, String args, String md5) {
String base = String.format("-T DiagnoseTargets --no_cmdline_in_header -R %s -L %s", REF, L) + " -o %s ";
WalkerTestSpec spec = new WalkerTestSpec(base + args, Arrays.asList(md5));
//spec.disableShadowBCF();
executeTest(testName, spec);
}
@Test(enabled = true)
public void testSingleSample() {
DTTest("testSingleSample ", "-I " + singleSample + " -max 75", "9954b21163d3e66db232938ec509067f");
DTTest("testSingleSample ", "-I " + singleSample + " -max 75", "850304909477afa8c2a8f128d6eedde9");
}
@Test(enabled = true)
public void testMultiSample() {
DTTest("testMultiSample ", "-I " + multiSample, "7c5277261e8e9dd74666f04843ffb09c");
DTTest("testMultiSample ", "-I " + multiSample, "bedd19bcf21d1a779f6706c0351c9d26");
}
}

42
protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/LocusStatisticsUnitTest.java → protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusStatisticsUnitTest.java
View File

@ -44,40 +44,46 @@
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.util.Set;
import java.util.List;
public class LocusStatisticsUnitTest /*extends BaseTest*/ {
public class LocusStatisticsUnitTest {
ThresHolder thresholds = new ThresHolder();
@BeforeClass
public void init() {
DiagnoseTargets.loadAllPlugins(thresholds);
}
@Test(dataProvider = "StatusTestValues")
public void testCallableStatuses(int coverage, int rawCoverage, CallableStatus status) {
// The min Coverage threshold is 10, the max is 100
ThresHolder thresholds = new ThresHolder(20, 20, 10, 100, 20, 50, 0.5, 0.2, 0.5, 0.2, 0.2, 0.5);
Set<CallableStatus> statuses = new LocusStatistics(coverage, rawCoverage).callableStatuses(thresholds);
// Check to make sure the status provides matches the actual
List<CallableStatus> statuses = new LocusStratification(coverage, rawCoverage, thresholds).callableStatuses();
Assert.assertTrue((status == null) ? statuses.isEmpty() : (statuses.contains(status) && statuses.size() == 1));
}
@DataProvider(name = "StatusTestValues")
public Object[][] getStatusTestValues() {
final int max = thresholds.maximumCoverage;
final int min = thresholds.minimumCoverage;
return new Object[][]{
new Object[]{100, 100, null},
new Object[]{100, 101, null},
new Object[]{101, 101, CallableStatus.EXCESSIVE_COVERAGE},
new Object[]{10, 101, null},
new Object[]{9, 101, CallableStatus.POOR_QUALITY},
new Object[]{9, 10, CallableStatus.POOR_QUALITY},
new Object[]{9, 9, CallableStatus.LOW_COVERAGE},
new Object[]{max, max, null},
new Object[]{max, max+1, null},
new Object[]{max+1, max+1, CallableStatus.EXCESSIVE_COVERAGE},
new Object[]{min, max+1, null},
new Object[]{min-1, max+1, CallableStatus.POOR_QUALITY},
new Object[]{min-1, min, CallableStatus.POOR_QUALITY},
new Object[]{min-1, min-1, CallableStatus.LOW_COVERAGE},
new Object[]{0, 0, CallableStatus.COVERAGE_GAPS},
new Object[]{0, 9, CallableStatus.LOW_COVERAGE},
new Object[]{0, 101, CallableStatus.POOR_QUALITY},
new Object[]{10, Integer.MAX_VALUE, null},
new Object[]{0, min-1, CallableStatus.LOW_COVERAGE},
new Object[]{0, max+1, CallableStatus.POOR_QUALITY},
new Object[]{min, Integer.MAX_VALUE, null},
new Object[]{Integer.MAX_VALUE, Integer.MAX_VALUE, CallableStatus.EXCESSIVE_COVERAGE},
};
}