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CountCovariates uses new optimized ReadBackedPileup. It also smarter about re-doing calculations for the dnsnp variation rate sanity check. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2188 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2009-11-30 20:35:40 +00:00
parent add2fa7ab4
commit 4969cb1957
2 changed files with 17 additions and 16 deletions
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29
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
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@ -11,6 +11,7 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrde
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.cmdLine.ArgumentCollection;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.genotype.Variation;
import java.io.PrintStream;
@ -100,7 +101,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
private long countedBases = 0; // Number of bases used in the calculations, used for reporting in the output file
private long skippedSites = 0; // Number of loci skipped because it was a dbSNP site, used for reporting in the output file
private int numUnprocessed = 0; // Number of consecutive loci skipped because we are only processing every Nth site
private static final String versionString = "v2.0.9"; // Major version, minor version, and build number
private static final String versionString = "v2.0.10"; // Major version, minor version, and build number
private Pair<Long, Long> dbSNP_counts = new Pair<Long, Long>(0L, 0L); // mismatch/base counts for dbSNP loci
private Pair<Long, Long> novel_counts = new Pair<Long, Long>(0L, 0L); // mismatch/base counts for non-dbSNP loci
private static final double DBSNP_VS_NOVEL_MISMATCH_RATE = 2.0; // rate at which dbSNP sites (on an individual level) mismatch relative to novel sites (determined by looking at NA12878)
@ -122,6 +123,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
logger.info( "CovariateCounterWalker version: " + versionString );
if( RAC.FORCE_READ_GROUP != null ) { RAC.DEFAULT_READ_GROUP = RAC.FORCE_READ_GROUP; }
if( RAC.FORCE_PLATFORM != null ) { RAC.DEFAULT_PLATFORM = RAC.FORCE_PLATFORM; }
DBSNP_VALIDATION_CHECK_FREQUENCY *= PROCESS_EVERY_NTH_LOCUS;
// Get a list of all available covariates
final List<Class<? extends Covariate>> classes = PackageUtils.getClassesImplementingInterface( Covariate.class );
@ -262,20 +264,16 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
if( !isSNP && ( ++numUnprocessed >= PROCESS_EVERY_NTH_LOCUS ) ) {
numUnprocessed = 0; // Reset the counter because we are processing this very locus
// Long list of variables that are preallocated for use in for loop below
final List<SAMRecord> reads = context.getReads();
final List<Integer> offsets = context.getOffsets();
SAMRecord read;
int offset;
byte refBase;
byte prevBase;
byte[] colorSpaceQuals;
final int numReads = reads.size();
// For each read at this locus
for( int iii = 0; iii < numReads; iii++ ) {
read = reads.get(iii);
offset = offsets.get(iii); // offset is zero based so quals[offset] and bases[offset] is correct
for ( PileupElement p : context.getPileup() ) {
read = p.getRead();
offset = p.getOffset();
RecalDataManager.parseSAMRecord(read, RAC);
@ -317,11 +315,9 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
}
}
countedSites++;
updateMismatchCounts(novel_counts, context, ref.getBase()); // For sanity check to ensure novel mismatch rate vs dnsnp mismatch rate is reasonable
} else { // We skipped over the dbSNP site, and we are only processing every Nth locus
skippedSites++;
if( isSNP) {
if( isSNP ) {
updateMismatchCounts(dbSNP_counts, context, ref.getBase());// For sanity check to ensure novel mismatch rate vs dnsnp mismatch rate is reasonable
}
}
@ -343,10 +339,8 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
* @param ref The reference base
*/
private static void updateMismatchCounts(Pair<Long, Long> counts, AlignmentContext context, char ref) {
List<SAMRecord> reads = context.getReads();
List<Integer> offsets = context.getOffsets();
for(int iii = 0; iii < reads.size(); iii++ ) {
char readChar = (char)(reads.get(iii).getReadBases()[offsets.get(iii)]);
for( PileupElement p : context.getPileup() ) {
char readChar = (char)(p.getBase());
int readCharBaseIndex = BaseUtils.simpleBaseToBaseIndex(readChar);
int refCharBaseIndex = BaseUtils.simpleBaseToBaseIndex(ref);
@ -410,10 +404,13 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
// Need the bases to determine whether or not we have a mismatch
byte base = read.getReadBases()[offset];
long curMismatches = datum.getNumMismatches();
// Add one to the number of observations and potentially one to the number of mismatches
datum.increment( (char)base, (char)refBase ); // Dangerous: If you don't cast to char than the bytes default to the (long, long) version of the increment method which is really bad
countedBases++;
novel_counts.second++;
novel_counts.first += datum.getNumMismatches() - curMismatches; // For sanity check to ensure novel mismatch rate vs dnsnp mismatch rate is reasonable
}

4
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDatum.java
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@ -129,6 +129,10 @@ public class RecalDatum {
public final Long getNumObservations() {
return numObservations;
}
public final Long getNumMismatches() {
return numMismatches;
}
public String toString() {
return String.format( "RecalDatum: %d,%d,%d", numObservations, numMismatches, (int)empiricalQualByte() );