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A new argument: --targetIntervalsSorted (boolean flag). If specified, the interval file is assumed to be sorted (duh!) and it is NOT slurped into the memory but instead traversed directly on disk as needed. If the file turns out to be unsorted, an exception will be thrown at the point where inconsistency occurs (can be late into the processing!). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3547 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-06-14 16:00:22 +00:00
parent 671ac00748
commit 4ab1f440c3
1 changed files with 16 additions and 6 deletions
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22
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -32,11 +32,11 @@ import org.broadinstitute.sting.utils.interval.IntervalUtils;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator;
import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.ReadUtils;
@ -57,6 +57,10 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
@Argument(fullName="targetIntervals", shortName="targetIntervals", doc="intervals file output from RealignerTargetCreator", required=true)
protected String intervalsFile = null;
@Argument(fullName="targetIntervalsSorted", shortName="targetSorted",doc="If specified, the tool assumes that target interval list is sorted"+
" (can save considerable chunk of memory); if the list turns out to be unsorted, the computation will abort")
protected boolean TARGET_SORTED = false;
@Argument(fullName="LODThresholdForCleaning", shortName="LOD", doc="LOD threshold above which the cleaner will clean", required=false)
protected double LOD_THRESHOLD = 5.0;
@ -157,12 +161,17 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
if ( MISMATCH_THRESHOLD <= 0.0 || MISMATCH_THRESHOLD > 1.0 )
throw new RuntimeException("Entropy threshold must be a fraction between 0 and 1");
// read in the intervals for cleaning
GenomeLocSortedSet locs = IntervalUtils.sortAndMergeIntervals(IntervalUtils.parseIntervalArguments(Arrays.asList(intervalsFile)),
if ( TARGET_SORTED && IntervalUtils.isIntervalFile(intervalsFile)) {
// prepare to read intervals one-by-one, as needed (assuming they are sorted).
intervals = new IntervalFileMergingIterator( new java.io.File(intervalsFile), IntervalMergingRule.OVERLAPPING_ONLY );
} else {
// read in the whole list of intervals for cleaning
GenomeLocSortedSet locs = IntervalUtils.sortAndMergeIntervals(IntervalUtils.parseIntervalArguments(Arrays.asList(intervalsFile)),
IntervalMergingRule.OVERLAPPING_ONLY);
intervals = locs.iterator();
intervals = locs.iterator();
}
currentInterval = intervals.hasNext() ? intervals.next() : null;
System.out.println("Interval: "+currentInterval);
// set up the output writer(s)
if ( baseWriterFilename != null ) {
writers = new HashMap<String, SAMFileWriter>();
@ -353,6 +362,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
do {
currentInterval = intervals.hasNext() ? intervals.next() : null;
System.out.println("Interval: "+currentInterval);
} while ( currentInterval != null && (readLoc == null || currentInterval.isBefore(readLoc)) );
// call back into map now that the state has been updated