Implemented NQS covariate. Extended Cycle covariate to handle 454 and SOLID reads. Added a Primer Round covariate for SOLID reads.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2039 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin
parent
bf451873ff
commit
394c839974
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@ -41,5 +41,5 @@ public interface Covariate {
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public Comparable getValue(SAMRecord read, int offset, String readGroup, byte[] quals, char[] bases, char refBase); //used to pick out the value from attributes of the read
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public Comparable getValue(String str); // used to get value from input file
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public int estimatedNumberOfBins(); // used to estimate the amount space required in the HashMap
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public int estimatedNumberOfBins(); // used to estimate the amount space required for the HashMap
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}
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@ -6,10 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import org.broadinstitute.sting.utils.PackageUtils;
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import org.broadinstitute.sting.utils.StingException;
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import org.broadinstitute.sting.utils.BaseUtils;
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import org.broadinstitute.sting.utils.Pair;
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import org.broadinstitute.sting.utils.*;
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import java.io.PrintStream;
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import java.io.FileNotFoundException;
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@ -70,9 +67,11 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
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@Argument(fullName="min_mapping_quality", shortName="minmap", required=false, doc="Only use reads with at least this mapping quality score")
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private int MIN_MAPPING_QUALITY = 1;
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@Argument(fullName = "use_original_quals", shortName="OQ", doc="If provided, we will use use the quals from the original qualities OQ attribute field instead of the quals in the regular QUALS field", required=false)
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private boolean USE_ORIGINAL_QUALS = false; // BUGBUG need to pass this value to the proper covariates
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private boolean USE_ORIGINAL_QUALS = false;
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@Argument(fullName = "platform", shortName="pl", doc="Which sequencing technology was used? This is important for the cycle covariate. Options are SLX, 454, and SOLID.", required=false)
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private String PLATFORM = "SLX";
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@Argument(fullName = "windowSizeNQS", shortName="nqs", doc="How big of a window should the MinimumNQSCovariate use for its calculation", required=false)
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private int WINDOW_SIZE = 1;
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@Argument(fullName="recal_file", shortName="rf", required=false, doc="Filename for the outputted covariates table recalibration file")
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private String RECAL_FILE = "output.recal_data.csv";
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@Argument(fullName="noPrintHeader", shortName="noHeader", required=false, doc="Don't print the usual header on the table recalibration file")
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@ -83,7 +82,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
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private RecalDataManager dataManager; // Holds the data HashMap, mostly used by TableRecalibrationWalker to create collapsed data hashmaps
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private ArrayList<Covariate> requestedCovariates; // A list to hold the covariate objects that were requested
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//private HashMap<SAMRecord, String> readGroupHashMap; // A hash map that hashes the read object itself into the read group name
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// This is done for optimization purposes because pulling the read group out of the SAMRecord is expensive
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// This is done for optimization purposes because pulling the read group out of the SAMRecord is expensive
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private long countedSites = 0; // Number of loci used in the calculations, used for reporting in the output file
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private long countedBases = 0; // Number of bases used in the calculations, used for reporting in the output file
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private long skippedSites = 0; // Number of loci skipped because it was a dbSNP site, used for reporting in the output file
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@ -119,7 +118,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
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requestedCovariates = new ArrayList<Covariate>();
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if( validateOldRecalibrator ) {
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requestedCovariates.add( new ReadGroupCovariate() );
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requestedCovariates.add( new CycleCovariate() ); // unfortunately the ordering here is different to match the output of the old recalibrator
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requestedCovariates.add( new CycleCovariate( PLATFORM ) ); // unfortunately the ordering here is different to match the output of the old recalibrator
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requestedCovariates.add( new QualityScoreCovariate() );
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requestedCovariates.add( new DinucCovariate() );
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//estimatedCapacity = 300 * 200 * 40 * 16;
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@ -139,6 +138,10 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
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try {
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// Now that we've found a matching class, try to instantiate it
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Covariate covariate = (Covariate)covClass.newInstance();
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// some covariates need parameters (user supplied command line arguments) passed to them
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if( covariate instanceof CycleCovariate ) { covariate = new CycleCovariate( PLATFORM ); }
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else if( covariate instanceof PrimerRoundCovariate ) { covariate = new PrimerRoundCovariate( PLATFORM ); }
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else if( covariate instanceof MinimumNQSCovariate ) { covariate = new MinimumNQSCovariate( WINDOW_SIZE ); }
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requestedCovariates.add( covariate );
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//estimatedCapacity *= covariate.estimatedNumberOfBins(); // update the estimated initial capacity
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} catch ( InstantiationException e ) {
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@ -157,7 +160,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
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logger.info( "Note: Using default set of covariates because none were specified." );
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requestedCovariates.add( new ReadGroupCovariate() );
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requestedCovariates.add( new QualityScoreCovariate() );
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requestedCovariates.add( new CycleCovariate() );
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requestedCovariates.add( new CycleCovariate( PLATFORM ) );
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requestedCovariates.add( new DinucCovariate() );
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//estimatedCapacity = 300 * 40 * 200 * 16;
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}
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@ -222,6 +225,16 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
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if( offset > 0 && offset < read.getReadLength() - 1) {
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quals = read.getBaseQualities();
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// Check if we need to use the original quality scores instead
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if ( USE_ORIGINAL_QUALS && read.getAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG) != null ) {
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Object obj = read.getAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG);
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if ( obj instanceof String )
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quals = QualityUtils.fastqToPhred((String)obj);
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else {
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throw new RuntimeException(String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG, read.getReadName()));
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}
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}
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// skip if base quality is zero
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if( quals[offset] > 0 ) {
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bases = read.getReadString().toCharArray();
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@ -36,11 +36,10 @@ import net.sf.samtools.SAMRecord;
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*
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* The Cycle covariate.
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* For Solexa the cycle is simply the position in the read (counting backwards if it is a negative strand read)
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* Yet to be implemented:
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* - For 454 the cycle is the number of discontinuous nucleotides seen during the length of the read
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* For 454 the cycle is the number of discontinuous nucleotides seen during the length of the read
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* For example, for the read: AAACCCCGAAATTTTTTT
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* the cycle would be 111222234445555555
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* - For SOLiD the cycle is a more complicated mixture of ligation cycle and primer round
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* For SOLiD the cycle is a more complicated mixture of ligation cycle and primer round
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*/
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public class CycleCovariate implements Covariate {
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@ -64,9 +63,18 @@ public class CycleCovariate implements Covariate {
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}
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return cycle;
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} else if( platform.equalsIgnoreCase( "454" ) ) {
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return 0; //BUGBUG: not yet implemented
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int cycle = 1;
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char prevBase = bases[0];
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for( int iii = 1; iii <= offset; iii++ ) {
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if(bases[iii] != prevBase) { // this base doesn't match the previous one so it is a new cycle
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cycle++;
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prevBase = bases[iii];
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}
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}
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return cycle;
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} else if( platform.equalsIgnoreCase( "SOLID" ) ) {
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return 0; //BUGBUG: not yet implemented
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// the ligation cycle according to http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_057511.pdf
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return (offset / 5) + 1; // integer division
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} else {
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throw new StingException( "Requested platform (" + platform + ") not supported in CycleCovariate." );
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}
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@ -74,7 +82,7 @@ public class CycleCovariate implements Covariate {
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}
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public final Comparable getValue(final String str) {
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return (int)Integer.parseInt( str );
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return (int)Integer.parseInt( str ); // cast to primitive int (as opposed to Integer Object) is required so that the return value from the two getValue methods hash to same thing
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}
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public final int estimatedNumberOfBins() {
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@ -43,11 +43,11 @@ public class MappingQualityCovariate implements Covariate {
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public final Comparable getValue(final SAMRecord read, final int offset, final String readGroup,
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final byte[] quals, final char[] bases, final char refBase) {
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return (Integer)(read.getMappingQuality()); // cast to Object Integer is required so that return values from the two getValue methods hash to the same code
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return read.getMappingQuality();
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}
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public final Comparable getValue(final String str) {
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return Integer.parseInt( str );
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return (int)Integer.parseInt( str ); // cast to primitive int (as opposed to Integer Object) is required so that the return value from the two getValue methods hash to same thing
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}
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public final int estimatedNumberOfBins() {
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@ -34,48 +34,38 @@ import org.broadinstitute.sting.utils.QualityUtils;
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* Date: Nov 4, 2009
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*
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* The Minimum Neighborhood Quality Score covariate, originally described by Chris Hartl.
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* This covariate is the minimum base quality score along the length of the read.
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* BUGBUG: I don't think this is what was intended by Chris. Covariate interface must change to implement the real covariate.
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* This covariate is the minimum base quality score in the read in a small window around the current base.
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*/
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public class MinimumNQSCovariate implements Covariate {
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public final static String ORIGINAL_QUAL_ATTRIBUTE_TAG = "OQ";
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private boolean USE_ORIGINAL_QUALS;
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private int windowReach; // how far in each direction from the current base to look
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public MinimumNQSCovariate() { // empty constructor is required to instantiate covariate in CovariateCounterWalker and TableRecalibrationWalker
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USE_ORIGINAL_QUALS = false;
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windowReach = 1; // window size = 3 was the best covariate according to Chris's analysis
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}
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public MinimumNQSCovariate(final boolean originalQuals) {
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USE_ORIGINAL_QUALS = originalQuals;
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public MinimumNQSCovariate(final int windowSize) {
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windowReach = windowSize / 2; // integer division
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}
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public final Comparable getValue(final SAMRecord read, final int offset, final String readGroup,
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final byte[] quals, final char[] bases, final char refBase) {
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//BUGBUG: Original qualities
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//if ( USE_ORIGINAL_QUALS && read.getAttribute(ORIGINAL_QUAL_ATTRIBUTE_TAG) != null ) {
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// Object obj = read.getAttribute(ORIGINAL_QUAL_ATTRIBUTE_TAG);
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// if ( obj instanceof String )
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// quals = QualityUtils.fastqToPhred((String)obj);
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// else {
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// throw new RuntimeException(String.format("Value encoded by %s in %s isn't a string!", ORIGINAL_QUAL_ATTRIBUTE_TAG, read.getReadName()));
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// }
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//}
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// Loop over the list of qualities and find the minimum
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Integer minQual = (int)(quals[0]);
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for ( int qual : quals ) {
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if( qual < minQual ) {
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minQual = qual;
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// Loop over the list of base quality scores in the window and find the minimum
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int minQual = quals[offset];
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int minIndex = Math.max(offset - windowReach, 0);
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int maxIndex = Math.min(offset + windowReach, quals.length - 1);
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for ( int iii = minIndex; iii < maxIndex; iii++ ) {
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if( quals[iii] < minQual ) {
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minQual = quals[iii];
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}
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}
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return minQual;
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}
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public final Comparable getValue(final String str) {
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return Integer.parseInt( str );
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return (int)Integer.parseInt( str ); // cast to primitive int (as opposed to Integer Object) is required so that the return value from the two getValue methods hash to same thing
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}
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public final int estimatedNumberOfBins() {
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@ -0,0 +1,79 @@
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package org.broadinstitute.sting.playground.gatk.walkers.Recalibration;
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import org.broadinstitute.sting.utils.StingException;
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import net.sf.samtools.SAMRecord;
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/*
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* Copyright (c) 2009 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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/**
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* Created by IntelliJ IDEA.
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* User: rpoplin
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* Date: Nov 13, 2009
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*
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* The Primer Round covariate.
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* For Solexa and 454 this is the same value of the length of the read.
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* For SOLiD this is different for each position according to http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_057511.pdf
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*/
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public class PrimerRoundCovariate implements Covariate {
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private String platform;
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public PrimerRoundCovariate() { // empty constructor is required to instantiate covariate in CovariateCounterWalker and TableRecalibrationWalker
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platform = "SLX";
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}
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public PrimerRoundCovariate(final String _platform) {
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platform = _platform;
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}
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public final Comparable getValue(final SAMRecord read, final int offset, final String readGroup,
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final byte[] quals, final char[] bases, final char refBase) {
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if( platform.equalsIgnoreCase( "SLX" ) ) {
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return 1; // nothing to do here because it is always the same
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} else if( platform.equalsIgnoreCase( "454" ) ) {
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return 1; // nothing to do here because it is always the same
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} else if( platform.equalsIgnoreCase( "SOLID" ) ) {
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return offset % 5; // the primer round according to http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_057511.pdf
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} else {
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throw new StingException( "Requested platform (" + platform + ") not supported in PrimerRoundCovariate." );
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}
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}
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public final Comparable getValue(final String str) {
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return (int)Integer.parseInt( str ); // cast to primitive int (as opposed to Integer Object) is required so that the return value from the two getValue methods hash to same thing
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}
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public final int estimatedNumberOfBins() {
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return 5;
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}
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public String toString() {
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return "Primer Round";
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}
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}
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@ -38,36 +38,17 @@ import org.broadinstitute.sting.utils.QualityUtils;
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public class QualityScoreCovariate implements Covariate {
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public final static String ORIGINAL_QUAL_ATTRIBUTE_TAG = "OQ";
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protected boolean USE_ORIGINAL_QUALS;
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public QualityScoreCovariate() { // empty constructor is required to instantiate covariate in CovariateCounterWalker and TableRecalibrationWalker
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USE_ORIGINAL_QUALS = false;
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}
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public QualityScoreCovariate(final boolean originalQuals) {
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USE_ORIGINAL_QUALS = originalQuals;
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}
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public final Comparable getValue(final SAMRecord read, final int offset, final String readGroup,
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public final Comparable getValue(final SAMRecord read, final int offset, final String readGroup,
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final byte[] quals, final char[] bases, final char refBase) {
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//BUGBUG: original qualities
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//if ( USE_ORIGINAL_QUALS && read.getAttribute(ORIGINAL_QUAL_ATTRIBUTE_TAG) != null ) {
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// Object obj = read.getAttribute(ORIGINAL_QUAL_ATTRIBUTE_TAG);
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// if ( obj instanceof String )
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// quals = QualityUtils.fastqToPhred((String)obj);
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// else {
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// throw new RuntimeException(String.format("Value encoded by %s in %s isn't a string!", ORIGINAL_QUAL_ATTRIBUTE_TAG, read.getReadName()));
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// }
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//}
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//Integer returnQual = (int)quals[offset];
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return (int)quals[offset]; // returning an Integer Object (as opposed to primitive int) is required so that return values from the two getValue methods hash to the same code
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return (int)quals[offset];
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}
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public final Comparable getValue(final String str) {
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return (int)Integer.parseInt( str );
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return (int)Integer.parseInt( str ); // cast to primitive int (as opposed to Integer Object) is required so that the return value from the two getValue methods hash to same thing
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}
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public final int estimatedNumberOfBins() {
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@ -44,6 +44,8 @@ public class RecalDataManager {
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private boolean collapsedTablesCreated;
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public NHashMap<Double> dataSumExpectedErrors;
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public final static String ORIGINAL_QUAL_ATTRIBUTE_TAG = "OQ";
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RecalDataManager() {
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data = new NHashMap<RecalDatum>();
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collapsedTablesCreated = false;
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@ -63,7 +63,11 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
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@Argument(fullName="preserve_qscores_less_than", shortName="pQ", doc="If provided, bases with quality scores less than this threshold won't be recalibrated. In general its unsafe to change qualities scores below < 5, since base callers use these values to indicate random or bad bases", required=false)
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public int PRESERVE_QSCORES_LESS_THAN = 5;
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@Argument(fullName = "use_original_quals", shortName="OQ", doc="If provided, we will use use the quals from the original qualities OQ attribute field instead of the quals in the regular QUALS field", required=false)
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public boolean USE_ORIGINAL_QUALS = false;
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private boolean USE_ORIGINAL_QUALS = false;
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@Argument(fullName = "platform", shortName="pl", doc="Which sequencing technology was used? This is important for the cycle covariate. Options are SLX, 454, and SOLID.", required=false)
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private String PLATFORM = "SLX";
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@Argument(fullName = "windowSizeNQS", shortName="nqs", doc="How big of a window should the MinimumNQSCovariate use for its calculation", required=false)
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private int WINDOW_SIZE = 1;
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@Argument(fullName="smoothing", shortName="sm", required = false, doc="Number of imaginary counts to add to each bin in order to smooth out bins with few data points")
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public int SMOOTHING = 1;
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@ -82,8 +86,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
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private static Pattern COMMENT_PATTERN = Pattern.compile("^#.*");
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private static Pattern COVARIATE_PATTERN = Pattern.compile("^@!.*");
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public final static String ORIGINAL_QUAL_ATTRIBUTE_TAG = "OQ";
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//---------------------------------------------------------------------------------------------------------------
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||||
//
|
||||
// initialize
|
||||
|
|
@ -102,7 +105,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
|
|||
|
||||
int lineNumber = 0;
|
||||
boolean foundAllCovariates = false;
|
||||
int estimatedCapacity = 1;
|
||||
//int estimatedCapacity = 1;
|
||||
|
||||
// Read in the covariates that were used from the input file
|
||||
requestedCovariates = new ArrayList<Covariate>();
|
||||
|
|
@ -128,8 +131,12 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
|
|||
foundClass = true;
|
||||
try {
|
||||
Covariate covariate = (Covariate)covClass.newInstance();
|
||||
// some covariates need parameters (user supplied command line arguments) passed to them
|
||||
if( covariate instanceof CycleCovariate ) { covariate = new CycleCovariate( PLATFORM ); }
|
||||
else if( covariate instanceof PrimerRoundCovariate ) { covariate = new PrimerRoundCovariate( PLATFORM ); }
|
||||
else if( covariate instanceof MinimumNQSCovariate ) { covariate = new MinimumNQSCovariate( WINDOW_SIZE ); }
|
||||
requestedCovariates.add( covariate );
|
||||
estimatedCapacity *= covariate.estimatedNumberOfBins();
|
||||
//estimatedCapacity *= covariate.estimatedNumberOfBins();
|
||||
|
||||
} catch ( InstantiationException e ) {
|
||||
throw new StingException( String.format("Can not instantiate covariate class '%s': must be concrete class.", covClass.getSimpleName()) );
|
||||
|
|
@ -150,7 +157,8 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
|
|||
foundAllCovariates = true;
|
||||
logger.info( "The covariates being used here: " );
|
||||
logger.info( requestedCovariates );
|
||||
dataManager = new RecalDataManager( estimatedCapacity );
|
||||
//dataManager = new RecalDataManager( estimatedCapacity );
|
||||
dataManager = new RecalDataManager();
|
||||
|
||||
}
|
||||
addCSVData(line); // parse the line and add the data to the HashMap
|
||||
|
|
@ -209,12 +217,12 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
|
|||
|
||||
byte[] originalQuals = read.getBaseQualities();
|
||||
// Check if we need to use the original quality scores instead
|
||||
if ( USE_ORIGINAL_QUALS && read.getAttribute(ORIGINAL_QUAL_ATTRIBUTE_TAG) != null ) {
|
||||
Object obj = read.getAttribute(ORIGINAL_QUAL_ATTRIBUTE_TAG);
|
||||
if ( USE_ORIGINAL_QUALS && read.getAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG) != null ) {
|
||||
Object obj = read.getAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG);
|
||||
if ( obj instanceof String )
|
||||
originalQuals = QualityUtils.fastqToPhred((String)obj);
|
||||
else {
|
||||
throw new RuntimeException(String.format("Value encoded by %s in %s isn't a string!", ORIGINAL_QUAL_ATTRIBUTE_TAG, read.getReadName()));
|
||||
throw new RuntimeException(String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG, read.getReadName()));
|
||||
}
|
||||
}
|
||||
byte[] recalQuals = originalQuals.clone();
|
||||
|
|
@ -255,8 +263,8 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
|
|||
|
||||
preserveQScores( originalQuals, recalQuals ); // overwrite the work done if original quality score is too low
|
||||
read.setBaseQualities(recalQuals); // overwrite old qualities with new recalibrated qualities
|
||||
if ( read.getAttribute(ORIGINAL_QUAL_ATTRIBUTE_TAG) == null ) { // save the old qualities if the tag isn't already taken in the read
|
||||
read.setAttribute(ORIGINAL_QUAL_ATTRIBUTE_TAG, QualityUtils.phredToFastq(originalQuals));
|
||||
if ( read.getAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG) == null ) { // save the old qualities if the tag isn't already taken in the read
|
||||
read.setAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG, QualityUtils.phredToFastq(originalQuals));
|
||||
}
|
||||
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue