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gatk-3.8
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1308 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-07-24 07:28:43 +00:00
parent 59f0c00d77
commit d044681fbe
3 changed files with 6 additions and 7 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/PrintCoverageWalker.java
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@ -12,7 +12,7 @@ import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
import org.broadinstitute.sting.gatk.walkers.By; import org.broadinstitute.sting.gatk.walkers.By;
import org.broadinstitute.sting.gatk.walkers.DataSource; import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.playground.indels.SWPairwiseAlignment; import org.broadinstitute.sting.utils.SWPairwiseAlignment;
import org.broadinstitute.sting.playground.utils.GenotypeLikelihoods; import org.broadinstitute.sting.playground.utils.GenotypeLikelihoods;
import org.broadinstitute.sting.utils.Pair; import org.broadinstitute.sting.utils.Pair;
import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.cmdLine.Argument;

3
java/src/org/broadinstitute/sting/playground/indels/IndelInspectorMain.java
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@ -14,8 +14,7 @@ import net.sf.picard.reference.ReferenceSequenceFileWalker;
import net.sf.picard.reference.ReferenceSequence; import net.sf.picard.reference.ReferenceSequence;
import net.sf.samtools.*; import net.sf.samtools.*;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.GenomeLocParser;
public class IndelInspectorMain extends CommandLineProgram { public class IndelInspectorMain extends CommandLineProgram {

6
java/src/org/broadinstitute/sting/playground/indels/PileBuilder.java
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@ -5,7 +5,7 @@ import net.sf.samtools.*;
import java.util.*; import java.util.*;
import java.io.File; import java.io.File;
import org.broadinstitute.sting.utils.PrimitivePair; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.playground.utils.CountedObject; import org.broadinstitute.sting.playground.utils.CountedObject;
import org.broadinstitute.sting.playground.utils.CountedObjectComparatorAdapter; import org.broadinstitute.sting.playground.utils.CountedObjectComparatorAdapter;
@ -167,7 +167,7 @@ public class PileBuilder implements RecordPileReceiver {
r.getCigar(), r.getAlignmentStart() - startOnRef ); r.getCigar(), r.getAlignmentStart() - startOnRef );
} }
totalMismatches += AlignmentUtils.numMismatches(r,referenceSequence); totalMismatches += AlignmentUtils.numMismatches(r,referenceSequence);
AlignmentUtils.collectAndCountIndels(r,all_indels); //AlignmentUtils.collectAndCountIndels(r,all_indels);
} }
if ( mVerbosityLevel >= ALIGNMENTS ) { if ( mVerbosityLevel >= ALIGNMENTS ) {
@ -249,7 +249,7 @@ public class PileBuilder implements RecordPileReceiver {
rtest.setReadString(r.getReadString()); rtest.setReadString(r.getReadString());
rtest.setReadUmappedFlag(r.getReadUnmappedFlag()); rtest.setReadUmappedFlag(r.getReadUnmappedFlag());
rtest.setCigar(cig); rtest.setCigar(cig);
AlignmentUtils.collectAndCountIndels(rtest,new_indels); //AlignmentUtils.collectAndCountIndels(rtest,new_indels);
new_mismatches += AlignmentUtils.numMismatches(rtest,referenceSequence); new_mismatches += AlignmentUtils.numMismatches(rtest,referenceSequence);
} }
// pileAligns.colorprint(true); // pileAligns.colorprint(true);