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Now iterate over a large set of tiny intervals efficiently. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@130 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-03-22 12:04:11 +00:00
parent df2a7039cb
commit 149ac3d96c
2 changed files with 68 additions and 14 deletions
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17
core/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
View File

@ -1,17 +1,21 @@
package org.broadinstitute.sting.gatk; package org.broadinstitute.sting.gatk;
import net.sf.samtools.SAMFileReader.ValidationStringency; import net.sf.samtools.SAMFileReader.ValidationStringency;
import net.sf.samtools.SAMSequenceRecord;
import edu.mit.broad.picard.cmdline.CommandLineProgram; import edu.mit.broad.picard.cmdline.CommandLineProgram;
import edu.mit.broad.picard.cmdline.Usage; import edu.mit.broad.picard.cmdline.Usage;
import edu.mit.broad.picard.cmdline.Option; import edu.mit.broad.picard.cmdline.Option;
import edu.mit.broad.picard.reference.ReferenceSequenceFileFactory;
import edu.mit.broad.picard.reference.ReferenceSequenceFile;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.refdata.rodDbSNP; import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
import org.broadinstitute.sting.gatk.refdata.rodGFF; import org.broadinstitute.sting.gatk.refdata.rodGFF;
import java.io.*; import java.io.*;
import java.util.HashMap; import java.util.*;
public class GenomeAnalysisTK extends CommandLineProgram { public class GenomeAnalysisTK extends CommandLineProgram {
// Usage and parameters // Usage and parameters
@ -70,6 +74,17 @@ public class GenomeAnalysisTK extends CommandLineProgram {
this.engine = new TraversalEngine(INPUT_FILE, REF_FILE_ARG, rods); this.engine = new TraversalEngine(INPUT_FILE, REF_FILE_ARG, rods);
// Prepare the sort ordering w.r.t. the sequence dictionary
final ReferenceSequenceFile refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(REF_FILE_ARG);
List<SAMSequenceRecord> refContigs = refFile.getSequenceDictionary().getSequences();
HashMap<String, Integer> refContigOrdering = new HashMap<String, Integer>();
int i = 0;
for ( SAMSequenceRecord contig : refContigs ) {
refContigOrdering.put(contig.getSequenceName(), i);
i++;
}
GenomeLoc.setContigOrdering(refContigOrdering);
ValidationStringency strictness; ValidationStringency strictness;
if ( STRICTNESS_ARG == null ) { if ( STRICTNESS_ARG == null ) {
strictness = ValidationStringency.STRICT; strictness = ValidationStringency.STRICT;

65
core/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java
View File

@ -203,10 +203,7 @@ public class TraversalEngine {
GenomeLoc[] locs = (GenomeLoc[])result.toArray(new GenomeLoc[0]); GenomeLoc[] locs = (GenomeLoc[])result.toArray(new GenomeLoc[0]);
Arrays.sort(locs); Arrays.sort(locs);
for ( GenomeLoc l : locs ) System.out.printf(" Locations are: %s%n", Utils.join("\n", Functions.map( Operators.toString, Arrays.asList(locs) ) ) );
System.out.printf(" -> %s%n", l);
System.out.printf(" Locations are: %s%n", Utils.join(" ", Functions.map( Operators.toString, Arrays.asList(locs) ) ) );
return locs; return locs;
} }
@ -220,9 +217,13 @@ public class TraversalEngine {
*/ */
public boolean inLocations( GenomeLoc curr ) { public boolean inLocations( GenomeLoc curr ) {
if ( this.locs == null ) if ( this.locs == null )
{
return true; return true;
else { }
for ( GenomeLoc loc : this.locs ) { else
{
for ( GenomeLoc loc : this.locs )
{
//System.out.printf(" Overlap %s vs. %s => %b%n", loc, curr, loc.overlapsP(curr)); //System.out.printf(" Overlap %s vs. %s => %b%n", loc, curr, loc.overlapsP(curr));
if ( loc.overlapsP(curr) ) if ( loc.overlapsP(curr) )
return true; return true;
@ -537,21 +538,59 @@ public class TraversalEngine {
boolean done = false; boolean done = false;
GenomeLoc prevLoc = null; GenomeLoc prevLoc = null;
while ( iter.hasNext() && ! done ) { int current_interval_index = -1;
int current_interval_offset = -1;
while ( iter.hasNext() && ! done )
{
this.nRecords++; this.nRecords++;
// actually get the read and hand it to the walker // actually get the read and hand it to the walker
final LocusContext locus = iter.next(); LocusContext locus = iter.next();
// Poor man's version of index LOL // Poor man's version of index LOL
// HALP! I HAZ 10K INTERVALS 2 INDX // HALP! I HAZ 10K INTERVALS 2 INDX
GenomeLoc curLoc = locus.getLocation(); if ( ((this.locs != null) && (this.locs.length != 0)) && ((current_interval_index == -1) || (!locus.getLocation().overlapsP(this.locs[current_interval_index]))))
if ( inLocations(curLoc) ) { {
if ( prevLoc != null && curLoc.compareContigs(prevLoc) != 0 ) // Advance to the next locus.
System.out.printf("Traversing to next chromosome...%n"); current_interval_index += 1;
current_interval_offset = 0;
if (this.locs.length <= current_interval_index) { done = true; break; }
//System.out.format("DEBUG Seeking from %s to %s\n", locus.getLocation().toString(), this.locs[current_interval_index].toString());
while ((!locus.getLocation().overlapsP(this.locs[current_interval_index])) && (iter.hasNext()))
{
switch (locus.getLocation().compareTo(this.locs[current_interval_index]))
{
case -1 :
locus = iter.next();
//System.out.format("DEBUG at %s\n", locus.getLocation().toString());
break;
case 0 :
break;
case 1 :
current_interval_index += 1;
current_interval_offset = 0;
//System.out.format("DEBUG Giving up on old locus, Seeking from %s to %s\n", locus.getLocation().toString(), this.locs[current_interval_index].toString());
break;
}
}
//System.out.format("DEBUG Got there.\n");
}
else
{
current_interval_offset += 1;
}
{
//System.out.format("Working at %s\n", locus.getLocation().toString());
// Jump forward in the reference to this locus location // Jump forward in the reference to this locus location
final ReferenceIterator refSite = refIter.seekForward(locus.getLocation()); final ReferenceIterator refSite;
refSite = refIter.seekForward(locus.getLocation());
final char refBase = refSite.getBaseAsChar(); final char refBase = refSite.getBaseAsChar();
locus.setReferenceContig(refSite.getCurrentContig()); locus.setReferenceContig(refSite.getCurrentContig());