diff --git a/public/R/queueJobReport.R b/public/R/queueJobReport.R
index 31916361e..de6aa045e 100644
--- a/public/R/queueJobReport.R
+++ b/public/R/queueJobReport.R
@@ -12,14 +12,14 @@ if ( onCMDLine ) {
inputFileName = args[1]
outputPDF = args[2]
} else {
- #inputFileName = "~/Desktop/broadLocal/GATK/unstable/report.txt"
- inputFileName = "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/Q-25718@node1149.jobreport.txt"
+ inputFileName = "~/Desktop/Q-30033@gsa1.jobreport.txt"
+ #inputFileName = "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/Q-25718@node1149.jobreport.txt"
#inputFileName = "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/rodPerformanceGoals/history/report.082711.txt"
outputPDF = NA
}
-RUNTIME_UNITS = "(sec)"
-ORIGINAL_UNITS_TO_SECONDS = 1/1000
+RUNTIME_UNITS = "(hours)"
+ORIGINAL_UNITS_TO_SECONDS = 1/1000/60/60
#
# Helper function to aggregate all of the jobs in the report across all tables
@@ -33,7 +33,7 @@ allJobsFromReport <- function(report) {
#
# Creates segmentation plots of time (x) vs. job (y) with segments for the duration of the job
#
-plotJobsGantt <- function(gatkReport, sortOverall) {
+plotJobsGantt <- function(gatkReport, sortOverall, includeText) {
allJobs = allJobsFromReport(gatkReport)
if ( sortOverall ) {
title = "All jobs, by analysis, by start time"
@@ -44,16 +44,18 @@ plotJobsGantt <- function(gatkReport, sortOverall) {
}
allJobs$index = 1:nrow(allJobs)
minTime = min(allJobs$startTime)
- allJobs$relStartTime = allJobs$startTime - minTime
- allJobs$relDoneTime = allJobs$doneTime - minTime
+ allJobs$relStartTime = (allJobs$startTime - minTime) * ORIGINAL_UNITS_TO_SECONDS
+ allJobs$relDoneTime = (allJobs$doneTime - minTime) * ORIGINAL_UNITS_TO_SECONDS
allJobs$ganttName = paste(allJobs$jobName, "@", allJobs$exechosts)
maxRelTime = max(allJobs$relDoneTime)
p <- ggplot(data=allJobs, aes(x=relStartTime, y=index, color=analysisName))
- p <- p + geom_segment(aes(xend=relDoneTime, yend=index), size=2, arrow=arrow(length = unit(0.1, "cm")))
- p <- p + geom_text(aes(x=relDoneTime, label=ganttName, hjust=-0.2), size=2)
+ p <- p + theme_bw()
+ p <- p + geom_segment(aes(xend=relDoneTime, yend=index), size=1, arrow=arrow(length = unit(0.1, "cm")))
+ if ( includeText )
+ p <- p + geom_text(aes(x=relDoneTime, label=ganttName, hjust=-0.2), size=2)
p <- p + xlim(0, maxRelTime * 1.1)
p <- p + xlab(paste("Start time (relative to first job)", RUNTIME_UNITS))
- p <- p + ylab("Job")
+ p <- p + ylab("Job number")
p <- p + opts(title=title)
print(p)
}
@@ -157,8 +159,8 @@ if ( ! is.na(outputPDF) ) {
pdf(outputPDF, height=8.5, width=11)
}
-plotJobsGantt(gatkReportData, T)
-plotJobsGantt(gatkReportData, F)
+plotJobsGantt(gatkReportData, T, F)
+plotJobsGantt(gatkReportData, F, F)
plotProgressByTime(gatkReportData)
for ( group in gatkReportData ) {
plotGroup(group)
diff --git a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
index 4d94130a8..5a7658031 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
@@ -293,15 +293,16 @@ public class GATKRunReport {
* That is, postReport() is guarenteed not to fail for any reason.
*/
private File postReportToLocalDisk(File rootDir) {
+ String filename = getID() + ".report.xml.gz";
+ File file = new File(rootDir, filename);
try {
- String filename = getID() + ".report.xml.gz";
- File file = new File(rootDir, filename);
postReportToFile(file);
logger.debug("Wrote report to " + file);
return file;
} catch ( Exception e ) {
// we catch everything, and no matter what eat the error
exceptDuringRunReport("Couldn't read report file", e);
+ file.delete();
return null;
}
}
@@ -312,6 +313,7 @@ public class GATKRunReport {
File localFile = postReportToLocalDisk(new File("./"));
logger.debug("Generating GATK report to AWS S3 based on local file " + localFile);
if ( localFile != null ) { // we succeeded in creating the local file
+ localFile.deleteOnExit();
try {
// stop us from printing the annoying, and meaningless, mime types warning
Logger mimeTypeLogger = Logger.getLogger(org.jets3t.service.utils.Mimetypes.class);
@@ -336,14 +338,13 @@ public class GATKRunReport {
//logger.info("Uploading " + localFile + " to AWS bucket");
S3Object s3Object = s3Service.putObject(REPORT_BUCKET_NAME, fileObject);
logger.debug("Uploaded to AWS: " + s3Object);
+ logger.info("Uploaded run statistics report to AWS S3");
} catch ( S3ServiceException e ) {
exceptDuringRunReport("S3 exception occurred", e);
} catch ( NoSuchAlgorithmException e ) {
exceptDuringRunReport("Couldn't calculate MD5", e);
} catch ( IOException e ) {
exceptDuringRunReport("Couldn't read report file", e);
- } finally {
- localFile.delete();
}
}
}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
index 664c319ab..86f97a36c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
@@ -63,12 +63,9 @@ import java.util.*;
* Input
*
* One or more bam files (with proper headers) to be analyzed for coverage statistics
+ * (Optional) A REFSEQ Rod to aggregate coverage to the gene level
*
- *
- *(Optional) A REFSEQ Rod to aggregate coverage to the gene level
- *
- * (for information about creating the REFSEQ Rod, please consult the RefSeqCodec documentation)
- *
+ *
* Output
*
* Tables pertaining to different coverage summaries. Suffix on the table files declares the contents:
@@ -96,7 +93,7 @@ import java.util.*;
*
* java -Xmx2g -jar GenomeAnalysisTK.jar \
* -R ref.fasta \
- * -T DepthOfCoverage \
+ * -T VariantEval \
* -o file_name_base \
* -I input_bams.list
* [-geneList refSeq.sorted.txt] \
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
index 2a877fb09..bf9ff35de 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
@@ -309,6 +309,7 @@ public class VariantsToTable extends RodWalker {
getters.put("HOM-REF", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHomRefCount()); } });
getters.put("HOM-VAR", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHomVarCount()); } });
getters.put("NO-CALL", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getNoCallCount()); } });
+ getters.put("TYPE", new Getter() { public String get(VariantContext vc) { return vc.getType().toString(); } });
getters.put("VAR", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHetCount() + vc.getHomVarCount()); } });
getters.put("NSAMPLES", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getNSamples()); } });
getters.put("NCALLED", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getNSamples() - vc.getNoCallCount()); } });
diff --git a/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
index b96923589..b66198713 100644
--- a/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
+++ b/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
@@ -306,7 +306,7 @@ public class GenomeLoc implements Comparable, Serializable, HasGenome
@Override
public int hashCode() {
- return (int)( start << 16 + stop << 4 + contigIndex );
+ return start << 16 | stop << 4 | contigIndex;
}
diff --git a/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java b/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
index f9997bfd8..1b4703e4a 100755
--- a/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
@@ -190,11 +190,21 @@ public class SampleUtils {
}
- public static List getSamplesFromCommandLineInput(Collection sampleArgs) {
+ /**
+ * Returns a new set of samples, containing a final list of samples expanded from sampleArgs
+ *
+ * Each element E of sampleArgs can either be a literal sample name or a file. For each E,
+ * we try to read a file named E from disk, and if possible all lines from that file are expanded
+ * into unique sample names.
+ *
+ * @param sampleArgs
+ * @return
+ */
+ public static Set getSamplesFromCommandLineInput(Collection sampleArgs) {
if (sampleArgs != null) {
// Let's first go through the list and see if we were given any files. We'll add every entry in the file to our
// sample list set, and treat the entries as if they had been specified on the command line.
- List samplesFromFiles = new ArrayList();
+ Set samplesFromFiles = new HashSet();
for (String SAMPLE_EXPRESSION : sampleArgs) {
File sampleFile = new File(SAMPLE_EXPRESSION);
@@ -203,7 +213,7 @@ public class SampleUtils {
List lines = reader.readLines();
for (String line : lines) {
- samplesFromFiles.add(line);
+ samplesFromFiles.add(line.trim());
}
} catch (FileNotFoundException e) {
samplesFromFiles.add(SAMPLE_EXPRESSION); // not a file, so must be a sample
@@ -212,7 +222,8 @@ public class SampleUtils {
return samplesFromFiles;
}
- return new ArrayList();
+
+ return new HashSet();
}
public static Set getSamplesFromCommandLineInput(Collection vcfSamples, Collection sampleExpressions) {
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java
index f142fa5aa..d94d9ff84 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java
@@ -12,35 +12,19 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
import java.util.ArrayList;
/**
- * Allows for reading in RefSeq information
+ * TODO FOR CHRIS HARTL
*
*
- * Parses a sorted UCSC RefSeq file (see below) into relevant features: the gene name, the unique gene name (if multiple transcrips get separate entries), exons, gene start/stop, coding start/stop,
- * strandedness of transcription.
+ * Codec Description
*
*
*
- * Instructions for generating a RefSeq file for use with the RefSeq codec can be found on the Wiki here
- * http://www.broadinstitute.org/gsa/wiki/index.php/RefSeq
+ * See also: link to file specification
*
- * Usage
- * The RefSeq Rod can be bound as any other rod, and is specified by REFSEQ, for example
- *
- * -refSeqBinding:REFSEQ /path/to/refSeq.txt
- *
- *
- * You will need to consult individual walkers for the binding name ("refSeqBinding", above)
*
* File format example
- * If you want to define your own file for use, the format is (tab delimited):
- * bin, name, chrom, strand, transcription start, transcription end, coding start, coding end, num exons, exon starts, exon ends, id, alt. name, coding start status (complete/incomplete), coding end status (complete,incomplete)
- * and exon frames, for example:
- *
- * 76 NM_001011874 1 - 3204562 3661579 3206102 3661429 3 3204562,3411782,3660632, 3207049,3411982,3661579, 0 Xkr4 cmpl cmpl 1,2,0,
- *
- * for more information see here
*
- *
+ * A BAM file containing exactly one sample.
*
*
* @author Mark DePristo
diff --git a/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java b/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
index f551e1368..41cbbe59f 100644
--- a/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
@@ -334,24 +334,44 @@ public class IntervalUtils {
}
/**
- * Splits an interval list into multiple files.
- * @param fileHeader The sam file header.
+ * Splits an interval list into multiple sublists.
* @param locs The genome locs to split.
* @param splits The stop points for the genome locs returned by splitFixedIntervals.
- * @param scatterParts The output interval lists to write to.
+ * @return A list of lists of genome locs, split according to splits
*/
- public static void scatterFixedIntervals(SAMFileHeader fileHeader, List locs, List splits, List scatterParts) {
- if (splits.size() != scatterParts.size())
- throw new UserException.BadArgumentValue("splits", String.format("Split points %d does not equal the number of scatter parts %d.", splits.size(), scatterParts.size()));
- int fileIndex = 0;
+ public static List> splitIntervalsToSubLists(List locs, List splits) {
int locIndex = 1;
int start = 0;
+ List> sublists = new ArrayList>(splits.size());
for (Integer stop: splits) {
- IntervalList intervalList = new IntervalList(fileHeader);
+ List curList = new ArrayList();
for (int i = start; i < stop; i++)
- intervalList.add(toInterval(locs.get(i), locIndex++));
- intervalList.write(scatterParts.get(fileIndex++));
+ curList.add(locs.get(i));
start = stop;
+ sublists.add(curList);
+ }
+
+ return sublists;
+ }
+
+
+ /**
+ * Splits an interval list into multiple files.
+ * @param fileHeader The sam file header.
+ * @param splits Pre-divided genome locs returned by splitFixedIntervals.
+ * @param scatterParts The output interval lists to write to.
+ */
+ public static void scatterFixedIntervals(SAMFileHeader fileHeader, List> splits, List scatterParts) {
+ if (splits.size() != scatterParts.size())
+ throw new UserException.BadArgumentValue("splits", String.format("Split points %d does not equal the number of scatter parts %d.", splits.size(), scatterParts.size()));
+
+ int fileIndex = 0;
+ int locIndex = 1;
+ for (final List split : splits) {
+ IntervalList intervalList = new IntervalList(fileHeader);
+ for (final GenomeLoc loc : split)
+ intervalList.add(toInterval(loc, locIndex++));
+ intervalList.write(scatterParts.get(fileIndex++));
}
}
@@ -361,17 +381,15 @@ public class IntervalUtils {
* @param numParts Number of parts to split the locs into.
* @return The stop points to split the genome locs.
*/
- public static List splitFixedIntervals(List locs, int numParts) {
+ public static List> splitFixedIntervals(List locs, int numParts) {
if (locs.size() < numParts)
throw new UserException.BadArgumentValue("scatterParts", String.format("Cannot scatter %d locs into %d parts.", locs.size(), numParts));
- long locsSize = 0;
- for (GenomeLoc loc: locs)
- locsSize += loc.size();
- List splitPoints = new ArrayList();
+ final long locsSize = intervalSize(locs);
+ final List splitPoints = new ArrayList();
addFixedSplit(splitPoints, locs, locsSize, 0, locs.size(), numParts);
Collections.sort(splitPoints);
splitPoints.add(locs.size());
- return splitPoints;
+ return splitIntervalsToSubLists(locs, splitPoints);
}
private static void addFixedSplit(List splitPoints, List locs, long locsSize, int startIndex, int stopIndex, int numParts) {
@@ -441,4 +459,11 @@ public class IntervalUtils {
return merged;
}
}
+
+ public static final long intervalSize(final List locs) {
+ long size = 0;
+ for ( final GenomeLoc loc : locs )
+ size += loc.size();
+ return size;
+ }
}
diff --git a/public/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java
index bb892eec8..98b878d23 100644
--- a/public/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java
@@ -30,6 +30,20 @@ public class IntervalUtilsUnitTest extends BaseTest {
private SAMFileHeader hg19Header;
private GenomeLocParser hg19GenomeLocParser;
private List hg19ReferenceLocs;
+ private List hg19exomeIntervals;
+
+ private List getLocs(String... intervals) {
+ return getLocs(Arrays.asList(intervals));
+ }
+
+ private List getLocs(List intervals) {
+ if (intervals.size() == 0)
+ return hg18ReferenceLocs;
+ List locs = new ArrayList();
+ for (String interval: intervals)
+ locs.add(hg18GenomeLocParser.parseGenomeLoc(interval));
+ return locs;
+ }
@BeforeClass
public void init() {
@@ -54,12 +68,69 @@ public class IntervalUtilsUnitTest extends BaseTest {
ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(hg19Ref);
hg19GenomeLocParser = new GenomeLocParser(seq);
hg19ReferenceLocs = Collections.unmodifiableList(GenomeLocSortedSet.createSetFromSequenceDictionary(referenceDataSource.getReference().getSequenceDictionary()).toList()) ;
+
+ hg19exomeIntervals = Collections.unmodifiableList(IntervalUtils.parseIntervalArguments(hg19GenomeLocParser, Arrays.asList(hg19Intervals), false));
}
catch(FileNotFoundException ex) {
throw new UserException.CouldNotReadInputFile(hg19Ref,ex);
}
}
+ // -------------------------------------------------------------------------------------
+ //
+ // tests to ensure the quality of the interval cuts of the interval cutting functions
+ //
+ // -------------------------------------------------------------------------------------
+
+ private class IntervalSlicingTest extends TestDataProvider {
+ public int parts;
+ public double maxAllowableVariance;
+
+ private IntervalSlicingTest(final int parts, final double maxAllowableVariance) {
+ super(IntervalSlicingTest.class);
+ this.parts = parts;
+ this.maxAllowableVariance = maxAllowableVariance;
+ }
+
+ public String toString() {
+ return String.format("IntervalSlicingTest parts=%d maxVar=%.2f", parts, maxAllowableVariance);
+ }
+ }
+
+ @DataProvider(name = "intervalslicingdata")
+ public Object[][] createTrees() {
+ new IntervalSlicingTest(1, 0);
+ new IntervalSlicingTest(2, 1);
+ new IntervalSlicingTest(5, 1);
+ new IntervalSlicingTest(10, 1);
+ new IntervalSlicingTest(67, 1);
+ new IntervalSlicingTest(100, 1);
+ new IntervalSlicingTest(500, 1);
+ new IntervalSlicingTest(1000, 1);
+ return IntervalSlicingTest.getTests(IntervalSlicingTest.class);
+ }
+
+ @Test(enabled = true, dataProvider = "intervalslicingdata")
+ public void testFixedScatterIntervalsAlgorithm(IntervalSlicingTest test) {
+ List> splits = IntervalUtils.splitFixedIntervals(hg19exomeIntervals, test.parts);
+
+ long totalSize = IntervalUtils.intervalSize(hg19exomeIntervals);
+ long idealSplitSize = totalSize / test.parts;
+
+ long sumOfSplitSizes = 0;
+ int counter = 0;
+ for ( final List split : splits ) {
+ long splitSize = IntervalUtils.intervalSize(split);
+ double sigma = (splitSize - idealSplitSize) / (1.0 * idealSplitSize);
+ //logger.warn(String.format("Split %d size %d ideal %d sigma %.2f", counter, splitSize, idealSplitSize, sigma));
+ counter++;
+ sumOfSplitSizes += splitSize;
+ Assert.assertTrue(Math.abs(sigma) <= test.maxAllowableVariance, String.format("Interval %d (size %d ideal %d) has a variance %.2f outside of the tolerated range %.2f", counter, splitSize, idealSplitSize, sigma, test.maxAllowableVariance));
+ }
+
+ Assert.assertEquals(totalSize, sumOfSplitSizes, "Split intervals don't contain the exact number of bases in the origianl intervals");
+ }
+
@Test(expectedExceptions=UserException.class)
public void testMergeListsBySetOperatorNoOverlap() {
// a couple of lists we'll use for the testing
@@ -129,19 +200,6 @@ public class IntervalUtilsUnitTest extends BaseTest {
Assert.assertEquals((long)lengths.get("chrX"), 154913754);
}
- private List getLocs(String... intervals) {
- return getLocs(Arrays.asList(intervals));
- }
-
- private List getLocs(List intervals) {
- if (intervals.size() == 0)
- return hg18ReferenceLocs;
- List locs = new ArrayList();
- for (String interval: intervals)
- locs.add(hg18GenomeLocParser.parseGenomeLoc(interval));
- return locs;
- }
-
@Test
public void testParseIntervalArguments() {
Assert.assertEquals(getLocs().size(), 45);
@@ -174,8 +232,8 @@ public class IntervalUtilsUnitTest extends BaseTest {
List files = testFiles("basic.", 3, ".intervals");
List locs = getLocs("chr1", "chr2", "chr3");
- List splits = IntervalUtils.splitFixedIntervals(locs, files.size());
- IntervalUtils.scatterFixedIntervals(hg18Header, locs, splits, files);
+ List> splits = IntervalUtils.splitFixedIntervals(locs, files.size());
+ IntervalUtils.scatterFixedIntervals(hg18Header, splits, files);
List locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()), false);
List locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()), false);
@@ -200,8 +258,8 @@ public class IntervalUtilsUnitTest extends BaseTest {
List files = testFiles("less.", 3, ".intervals");
List locs = getLocs("chr1", "chr2", "chr3", "chr4");
- List splits = IntervalUtils.splitFixedIntervals(locs, files.size());
- IntervalUtils.scatterFixedIntervals(hg18Header, locs, splits, files);
+ List> splits = IntervalUtils.splitFixedIntervals(locs, files.size());
+ IntervalUtils.scatterFixedIntervals(hg18Header, splits, files);
List locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()), false);
List locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()), false);
@@ -228,8 +286,8 @@ public class IntervalUtilsUnitTest extends BaseTest {
public void testScatterFixedIntervalsMoreFiles() {
List files = testFiles("more.", 3, ".intervals");
List locs = getLocs("chr1", "chr2");
- List splits = IntervalUtils.splitFixedIntervals(locs, locs.size()); // locs.size() instead of files.size()
- IntervalUtils.scatterFixedIntervals(hg18Header, locs, splits, files);
+ List> splits = IntervalUtils.splitFixedIntervals(locs, locs.size()); // locs.size() instead of files.size()
+ IntervalUtils.scatterFixedIntervals(hg18Header, splits, files);
}
@Test
public void testScatterFixedIntervalsStart() {
@@ -242,8 +300,8 @@ public class IntervalUtilsUnitTest extends BaseTest {
List files = testFiles("split.", 3, ".intervals");
List locs = getLocs(intervals);
- List splits = IntervalUtils.splitFixedIntervals(locs, files.size());
- IntervalUtils.scatterFixedIntervals(hg18Header, locs, splits, files);
+ List> splits = IntervalUtils.splitFixedIntervals(locs, files.size());
+ IntervalUtils.scatterFixedIntervals(hg18Header, splits, files);
List locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()), false);
List locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()), false);
@@ -270,8 +328,8 @@ public class IntervalUtilsUnitTest extends BaseTest {
List files = testFiles("split.", 3, ".intervals");
List locs = getLocs(intervals);
- List splits = IntervalUtils.splitFixedIntervals(locs, files.size());
- IntervalUtils.scatterFixedIntervals(hg18Header, locs, splits, files);
+ List> splits = IntervalUtils.splitFixedIntervals(locs, files.size());
+ IntervalUtils.scatterFixedIntervals(hg18Header, splits, files);
List locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()), false);
List locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()), false);
@@ -298,8 +356,8 @@ public class IntervalUtilsUnitTest extends BaseTest {
List files = testFiles("split.", 3, ".intervals");
List locs = getLocs(intervals);
- List splits = IntervalUtils.splitFixedIntervals(locs, files.size());
- IntervalUtils.scatterFixedIntervals(hg18Header, locs, splits, files);
+ List> splits = IntervalUtils.splitFixedIntervals(locs, files.size());
+ IntervalUtils.scatterFixedIntervals(hg18Header, splits, files);
List locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()), false);
List locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()), false);
@@ -319,7 +377,7 @@ public class IntervalUtilsUnitTest extends BaseTest {
public void testScatterFixedIntervalsFile() {
List files = testFiles("sg.", 20, ".intervals");
List locs = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(BaseTest.GATKDataLocation + "whole_exome_agilent_designed_120.targets.hg18.chr20.interval_list"), false);
- List splits = IntervalUtils.splitFixedIntervals(locs, files.size());
+ List> splits = IntervalUtils.splitFixedIntervals(locs, files.size());
int[] counts = {
125, 138, 287, 291, 312, 105, 155, 324,
@@ -332,16 +390,13 @@ public class IntervalUtilsUnitTest extends BaseTest {
};
//String splitCounts = "";
- for (int lastIndex = 0, i = 0; i < splits.size(); i++) {
- int splitIndex = splits.get(i);
- int splitCount = (splitIndex - lastIndex);
- //splitCounts += ", " + splitCount;
- lastIndex = splitIndex;
+ for (int i = 0; i < splits.size(); i++) {
+ int splitCount = splits.get(i).size();
Assert.assertEquals(splitCount, counts[i], "Num intervals in split " + i);
}
//System.out.println(splitCounts.substring(2));
- IntervalUtils.scatterFixedIntervals(hg18Header, locs, splits, files);
+ IntervalUtils.scatterFixedIntervals(hg18Header, splits, files);
int locIndex = 0;
for (int i = 0; i < files.size(); i++) {
@@ -357,8 +412,8 @@ public class IntervalUtilsUnitTest extends BaseTest {
@Test
public void testScatterFixedIntervalsMax() {
List files = testFiles("sg.", 85, ".intervals");
- List splits = IntervalUtils.splitFixedIntervals(hg19ReferenceLocs, files.size());
- IntervalUtils.scatterFixedIntervals(hg19Header, hg19ReferenceLocs, splits, files);
+ List> splits = IntervalUtils.splitFixedIntervals(hg19ReferenceLocs, files.size());
+ IntervalUtils.scatterFixedIntervals(hg19Header, splits, files);
for (int i = 0; i < files.size(); i++) {
String file = files.get(i).toString();
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala
index aae5e438c..0fb997f43 100755
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala
@@ -1,65 +1,65 @@
-/*
- * Copyright (c) 2011, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.queue.extensions.gatk
-
-import java.io.File
-import collection.JavaConversions._
-import org.broadinstitute.sting.utils.interval.IntervalUtils
-import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource
-import net.sf.samtools.SAMFileHeader
-import java.util.Collections
-import org.broadinstitute.sting.utils.{GenomeLoc, GenomeLocSortedSet, GenomeLocParser}
-
-case class GATKIntervals(reference: File, intervals: List[String]) {
- private lazy val referenceDataSource = new ReferenceDataSource(reference)
- private var splitsBySize = Map.empty[Int, java.util.List[java.lang.Integer]]
-
- lazy val samFileHeader = {
- val header = new SAMFileHeader
- header.setSequenceDictionary(referenceDataSource.getReference.getSequenceDictionary)
- header
- }
-
- lazy val locs: java.util.List[GenomeLoc] = {
- val parser = new GenomeLocParser(referenceDataSource.getReference)
- val parsedLocs =
- if (intervals.isEmpty)
- GenomeLocSortedSet.createSetFromSequenceDictionary(samFileHeader.getSequenceDictionary).toList
- else
- IntervalUtils.parseIntervalArguments(parser, intervals, false)
- Collections.sort(parsedLocs)
- Collections.unmodifiableList(parsedLocs)
- }
-
- lazy val contigs = locs.map(_.getContig).distinct.toList
-
- def getSplits(size: Int) = {
- splitsBySize.getOrElse(size, {
- val splits: java.util.List[java.lang.Integer] = IntervalUtils.splitFixedIntervals(locs, size)
- splitsBySize += size -> splits
- splits
- })
- }
-}
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.queue.extensions.gatk
+
+import java.io.File
+import collection.JavaConversions._
+import org.broadinstitute.sting.utils.interval.IntervalUtils
+import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource
+import net.sf.samtools.SAMFileHeader
+import java.util.Collections
+import org.broadinstitute.sting.utils.{GenomeLoc, GenomeLocSortedSet, GenomeLocParser}
+
+case class GATKIntervals(reference: File, intervals: List[String]) {
+ private lazy val referenceDataSource = new ReferenceDataSource(reference)
+// private var splitsBySize = Map.empty[Int, java.util.List[java.lang.Integer]]
+
+ lazy val samFileHeader = {
+ val header = new SAMFileHeader
+ header.setSequenceDictionary(referenceDataSource.getReference.getSequenceDictionary)
+ header
+ }
+
+ lazy val locs: java.util.List[GenomeLoc] = {
+ val parser = new GenomeLocParser(referenceDataSource.getReference)
+ val parsedLocs =
+ if (intervals.isEmpty)
+ GenomeLocSortedSet.createSetFromSequenceDictionary(samFileHeader.getSequenceDictionary).toList
+ else
+ IntervalUtils.parseIntervalArguments(parser, intervals, false)
+ Collections.sort(parsedLocs)
+ Collections.unmodifiableList(parsedLocs)
+ }
+
+ lazy val contigs = locs.map(_.getContig).distinct.toList
+
+// def getSplits(size: Int) = {
+// splitsBySize.getOrElse(size, {
+// val splits: java.util.List[java.lang.Integer] = IntervalUtils.splitFixedIntervals(locs, size)
+// splitsBySize += size -> splits
+// splits
+// })
+// }
+}
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala
index d88d272b9..f65d5ab29 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala
@@ -37,7 +37,7 @@ class IntervalScatterFunction extends GATKScatterFunction with InProcessFunction
def run() {
val gi = GATKScatterFunction.getGATKIntervals(this.referenceSequence, this.intervals)
- IntervalUtils.scatterFixedIntervals(gi.samFileHeader, gi.locs,
- gi.getSplits(this.scatterOutputFiles.size), this.scatterOutputFiles)
+ val splits = IntervalUtils.splitFixedIntervals(gi.locs, this.scatterOutputFiles.size)
+ IntervalUtils.scatterFixedIntervals(gi.samFileHeader, splits, this.scatterOutputFiles)
}
}
diff --git a/public/scala/test/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala b/public/scala/test/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala
index b3a2d23ae..38abe24ef 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala
@@ -53,8 +53,8 @@ class GATKIntervalsUnitTest {
val gi = new GATKIntervals(hg18Reference, List("chr1:1-1", "chr2:2-3", "chr3:3-5"))
Assert.assertEquals(gi.locs.toList, List(chr1, chr2, chr3))
Assert.assertEquals(gi.contigs, List("chr1", "chr2", "chr3"))
- Assert.assertEquals(gi.getSplits(2).toList, List(2, 3))
- Assert.assertEquals(gi.getSplits(3).toList, List(1, 2, 3))
+// Assert.assertEquals(gi.getSplits(2).toList, List(2, 3))
+// Assert.assertEquals(gi.getSplits(3).toList, List(1, 2, 3))
}
@Test(timeOut = 30000)
@@ -65,7 +65,7 @@ class GATKIntervalsUnitTest {
// for(Item item: javaConvertedScalaList)
// This for loop is actually an O(N^2) operation as the iterator calls the
// O(N) javaConvertedScalaList.size() for each iteration of the loop.
- Assert.assertEquals(gi.getSplits(gi.locs.size).size, 189894)
+ //Assert.assertEquals(gi.getSplits(gi.locs.size).size, 189894)
Assert.assertEquals(gi.contigs.size, 24)
}
@@ -74,8 +74,8 @@ class GATKIntervalsUnitTest {
val gi = new GATKIntervals(hg18Reference, Nil)
Assert.assertEquals(gi.locs, hg18ReferenceLocs)
Assert.assertEquals(gi.contigs.size, hg18ReferenceLocs.size)
- Assert.assertEquals(gi.getSplits(2).toList, List(10, 45))
- Assert.assertEquals(gi.getSplits(4).toList, List(5, 10, 16, 45))
+// Assert.assertEquals(gi.getSplits(2).toList, List(10, 45))
+// Assert.assertEquals(gi.getSplits(4).toList, List(5, 10, 16, 45))
}
@Test