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Incorporating Guillermo's patch to eliminate compile-time dependency of (core) UG indel model 

on oneoffs.  Thanks Guillermo!  We'll polish the patch when you free up a bit.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5888 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-05-27 02:22:19 +00:00
parent fd21c5d100
commit a77ca2d36a
1 changed files with 14 additions and 11 deletions
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25
java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
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@ -31,11 +31,11 @@ import net.sf.samtools.CigarOperator;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broad.tribble.util.variantcontext.Allele; import org.broad.tribble.util.variantcontext.Allele;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.Covariate; /*import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.Covariate;
import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalDataManager; import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalDataManager;
import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalDatum; import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalDatum;
import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalibrationArgumentCollection; import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalibrationArgumentCollection;
import org.broadinstitute.sting.utils.MathUtils; */import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.collections.NestedHashMap; import org.broadinstitute.sting.utils.collections.NestedHashMap;
@ -124,7 +124,7 @@ public class PairHMMIndelErrorModel {
// Private Member Variables // Private Member Variables
///////////////////////////// /////////////////////////////
//copy+ //copy+
private RecalDataManager dataManager; // Holds the data HashMap, mostly used by TableRecalibrationWalker to create collapsed data hashmaps /* private RecalDataManager dataManager; // Holds the data HashMap, mostly used by TableRecalibrationWalker to create collapsed data hashmaps
private final ArrayList<Covariate> requestedCovariates = new ArrayList<Covariate>(); // List of covariates to be used in this calculation private final ArrayList<Covariate> requestedCovariates = new ArrayList<Covariate>(); // List of covariates to be used in this calculation
private static final Pattern COMMENT_PATTERN = Pattern.compile("^#.*"); private static final Pattern COMMENT_PATTERN = Pattern.compile("^#.*");
private static final Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*"); private static final Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*");
@ -133,7 +133,7 @@ public class PairHMMIndelErrorModel {
private long numReadsWithMalformedColorSpace = 0; private long numReadsWithMalformedColorSpace = 0;
private RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection(); private RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();
private NestedHashMap qualityScoreByFullCovariateKey = new NestedHashMap(); // Caches the result of performSequentialQualityCalculation(..) for all sets of covariate values. private NestedHashMap qualityScoreByFullCovariateKey = new NestedHashMap(); // Caches the result of performSequentialQualityCalculation(..) for all sets of covariate values.
*/
//copy- //copy-
static { static {
LOG_ONE_HALF= -Math.log10(2.0); LOG_ONE_HALF= -Math.log10(2.0);
@ -157,7 +157,7 @@ public class PairHMMIndelErrorModel {
// read data from recal file // read data from recal file
// gdebug - start copy from TableRecalibrationWalker // gdebug - start copy from TableRecalibrationWalker
if (gpf) { /* if (gpf) {
boolean sawEOF = false; boolean sawEOF = false;
boolean REQUIRE_EOF = false; boolean REQUIRE_EOF = false;
@ -244,12 +244,12 @@ public class PairHMMIndelErrorModel {
dataManager.generateEmpiricalQualities( SMOOTHING, MAX_QUALITY_SCORE ); dataManager.generateEmpiricalQualities( SMOOTHING, MAX_QUALITY_SCORE );
} }
// debug end copy // debug end copy
*/
} }
/** /**
* For each covariate read in a value and parse it. Associate those values with the data itself (num observation and num mismatches) * For each covariate read in a value and parse it. Associate those values with the data itself (num observation and num mismatches)
* @param line A line of CSV data read from the recalibration table data file
*/ */
/*
private void addCSVData(final File file, final String line) { private void addCSVData(final File file, final String line) {
final String[] vals = line.split(","); final String[] vals = line.split(",");
@ -273,7 +273,7 @@ public class PairHMMIndelErrorModel {
dataManager.addToAllTables( key, datum, PRESERVE_QSCORES_LESS_THAN ); dataManager.addToAllTables( key, datum, PRESERVE_QSCORES_LESS_THAN );
} }
*/
public PairHMMIndelErrorModel(double indelGOP, double indelGCP, boolean deb, boolean doCDP, boolean dovit) { public PairHMMIndelErrorModel(double indelGOP, double indelGCP, boolean deb, boolean doCDP, boolean dovit) {
this(indelGOP, indelGCP, deb, doCDP); this(indelGOP, indelGCP, deb, doCDP);
this.doViterbi = dovit; this.doViterbi = dovit;
@ -766,6 +766,7 @@ public class PairHMMIndelErrorModel {
} }
} }
else { else {
//System.out.format("%d %s\n",p.getRead().getAlignmentStart(), p.getRead().getClass().getName());
GATKSAMRecord read = ReadUtils.hardClipAdaptorSequence(p.getRead()); GATKSAMRecord read = ReadUtils.hardClipAdaptorSequence(p.getRead());
if (read == null) if (read == null)
continue; continue;
@ -776,7 +777,7 @@ public class PairHMMIndelErrorModel {
double[] recalQuals = null; double[] recalQuals = null;
/*
if (getGapPenaltiesFromFile) { if (getGapPenaltiesFromFile) {
RecalDataManager.parseSAMRecord( read, RAC ); RecalDataManager.parseSAMRecord( read, RAC );
@ -820,7 +821,7 @@ public class PairHMMIndelErrorModel {
} }
System.out.println(); System.out.println();
} }
} } */
// get bases of candidate haplotypes that overlap with reads // get bases of candidate haplotypes that overlap with reads
final int trailingBases = 3; final int trailingBases = 3;
@ -1078,6 +1079,7 @@ public class PairHMMIndelErrorModel {
* @param key The list of Comparables that were calculated from the covariates * @param key The list of Comparables that were calculated from the covariates
* @return A recalibrated quality score as a byte * @return A recalibrated quality score as a byte
*/ */
/*
private byte performSequentialQualityCalculation( final Object... key ) { private byte performSequentialQualityCalculation( final Object... key ) {
final byte qualFromRead = (byte)Integer.parseInt(key[1].toString()); final byte qualFromRead = (byte)Integer.parseInt(key[1].toString());
@ -1133,6 +1135,7 @@ public class PairHMMIndelErrorModel {
//} //}
//return newQualityByte; //return newQualityByte;
}
}
*/
} }