zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge branch 'sgintervals'

This commit is contained in:
Mark DePristo 2011-09-19 12:02:41 -04:00
parent 3e93f246f7 4ad330008d
commit cfde0e674b
8 changed files with 222 additions and 139 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

26
public/R/queueJobReport.R
View File

@ -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)

9
public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
View File

@ -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();
}
}
}

2
public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
View File

@ -306,7 +306,7 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Serializable, HasGenome
@Override
public int hashCode() {
return (int)( start << 16 + stop << 4 + contigIndex );
return start << 16 | stop << 4 | contigIndex;
}

57
public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
View File

@ -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<GenomeLoc> locs, List<Integer> splits, List<File> 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<List<GenomeLoc>> splitIntervalsToSubLists(List<GenomeLoc> locs, List<Integer> splits) {
int locIndex = 1;
int start = 0;
List<List<GenomeLoc>> sublists = new ArrayList<List<GenomeLoc>>(splits.size());
for (Integer stop: splits) {
IntervalList intervalList = new IntervalList(fileHeader);
List<GenomeLoc> curList = new ArrayList<GenomeLoc>();
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<List<GenomeLoc>> splits, List<File> 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<GenomeLoc> 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<Integer> splitFixedIntervals(List<GenomeLoc> locs, int numParts) {
public static List<List<GenomeLoc>> splitFixedIntervals(List<GenomeLoc> 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<Integer> splitPoints = new ArrayList<Integer>();
final long locsSize = intervalSize(locs);
final List<Integer> splitPoints = new ArrayList<Integer>();
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<Integer> splitPoints, List<GenomeLoc> 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<GenomeLoc> locs) {
long size = 0;
for ( final GenomeLoc loc : locs )
size += loc.size();
return size;
}
}

123
public/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java
View File

@ -30,6 +30,20 @@ public class IntervalUtilsUnitTest extends BaseTest {
private SAMFileHeader hg19Header;
private GenomeLocParser hg19GenomeLocParser;
private List<GenomeLoc> hg19ReferenceLocs;
private List<GenomeLoc> hg19exomeIntervals;
private List<GenomeLoc> getLocs(String... intervals) {
return getLocs(Arrays.asList(intervals));
}
private List<GenomeLoc> getLocs(List<String> intervals) {
if (intervals.size() == 0)
return hg18ReferenceLocs;
List<GenomeLoc> locs = new ArrayList<GenomeLoc>();
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<List<GenomeLoc>> 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<GenomeLoc> 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<GenomeLoc> getLocs(String... intervals) {
return getLocs(Arrays.asList(intervals));
}
private List<GenomeLoc> getLocs(List<String> intervals) {
if (intervals.size() == 0)
return hg18ReferenceLocs;
List<GenomeLoc> locs = new ArrayList<GenomeLoc>();
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<File> files = testFiles("basic.", 3, ".intervals");
List<GenomeLoc> locs = getLocs("chr1", "chr2", "chr3");
List<Integer> splits = IntervalUtils.splitFixedIntervals(locs, files.size());
IntervalUtils.scatterFixedIntervals(hg18Header, locs, splits, files);
List<List<GenomeLoc>> splits = IntervalUtils.splitFixedIntervals(locs, files.size());
IntervalUtils.scatterFixedIntervals(hg18Header, splits, files);
List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()), false);
List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()), false);
@ -200,8 +258,8 @@ public class IntervalUtilsUnitTest extends BaseTest {
List<File> files = testFiles("less.", 3, ".intervals");
List<GenomeLoc> locs = getLocs("chr1", "chr2", "chr3", "chr4");
List<Integer> splits = IntervalUtils.splitFixedIntervals(locs, files.size());
IntervalUtils.scatterFixedIntervals(hg18Header, locs, splits, files);
List<List<GenomeLoc>> splits = IntervalUtils.splitFixedIntervals(locs, files.size());
IntervalUtils.scatterFixedIntervals(hg18Header, splits, files);
List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()), false);
List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()), false);
@ -228,8 +286,8 @@ public class IntervalUtilsUnitTest extends BaseTest {
public void testScatterFixedIntervalsMoreFiles() {
List<File> files = testFiles("more.", 3, ".intervals");
List<GenomeLoc> locs = getLocs("chr1", "chr2");
List<Integer> splits = IntervalUtils.splitFixedIntervals(locs, locs.size()); // locs.size() instead of files.size()
IntervalUtils.scatterFixedIntervals(hg18Header, locs, splits, files);
List<List<GenomeLoc>> 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<File> files = testFiles("split.", 3, ".intervals");
List<GenomeLoc> locs = getLocs(intervals);
List<Integer> splits = IntervalUtils.splitFixedIntervals(locs, files.size());
IntervalUtils.scatterFixedIntervals(hg18Header, locs, splits, files);
List<List<GenomeLoc>> splits = IntervalUtils.splitFixedIntervals(locs, files.size());
IntervalUtils.scatterFixedIntervals(hg18Header, splits, files);
List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()), false);
List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()), false);
@ -270,8 +328,8 @@ public class IntervalUtilsUnitTest extends BaseTest {
List<File> files = testFiles("split.", 3, ".intervals");
List<GenomeLoc> locs = getLocs(intervals);
List<Integer> splits = IntervalUtils.splitFixedIntervals(locs, files.size());
IntervalUtils.scatterFixedIntervals(hg18Header, locs, splits, files);
List<List<GenomeLoc>> splits = IntervalUtils.splitFixedIntervals(locs, files.size());
IntervalUtils.scatterFixedIntervals(hg18Header, splits, files);
List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()), false);
List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()), false);
@ -298,8 +356,8 @@ public class IntervalUtilsUnitTest extends BaseTest {
List<File> files = testFiles("split.", 3, ".intervals");
List<GenomeLoc> locs = getLocs(intervals);
List<Integer> splits = IntervalUtils.splitFixedIntervals(locs, files.size());
IntervalUtils.scatterFixedIntervals(hg18Header, locs, splits, files);
List<List<GenomeLoc>> splits = IntervalUtils.splitFixedIntervals(locs, files.size());
IntervalUtils.scatterFixedIntervals(hg18Header, splits, files);
List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()), false);
List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()), false);
@ -319,7 +377,7 @@ public class IntervalUtilsUnitTest extends BaseTest {
public void testScatterFixedIntervalsFile() {
List<File> files = testFiles("sg.", 20, ".intervals");
List<GenomeLoc> locs = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(BaseTest.GATKDataLocation + "whole_exome_agilent_designed_120.targets.hg18.chr20.interval_list"), false);
List<Integer> splits = IntervalUtils.splitFixedIntervals(locs, files.size());
List<List<GenomeLoc>> 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<File> files = testFiles("sg.", 85, ".intervals");
List<Integer> splits = IntervalUtils.splitFixedIntervals(hg19ReferenceLocs, files.size());
IntervalUtils.scatterFixedIntervals(hg19Header, hg19ReferenceLocs, splits, files);
List<List<GenomeLoc>> 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();

130
public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala
View File

@ -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
// })
// }
}

4
public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala
View File

@ -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)
}
}

10
public/scala/test/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala
View File

@ -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