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misc code cleanup 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2190 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2009-11-30 21:16:00 +00:00
parent e793e62fc9
commit b89b9adb2c
5 changed files with 19 additions and 23 deletions
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11
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
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@ -101,7 +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 = "v2.0.10"; // Major version, minor version, and build number
private static final String versionString = "v2.0.11"; // 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)
@ -269,6 +269,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
byte refBase;
byte prevBase;
byte[] colorSpaceQuals;
byte[] bases;
// For each read at this locus
for ( PileupElement p : context.getPileup() ) {
@ -284,16 +285,18 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
// Skip if base quality is zero
if( read.getBaseQualities()[offset] > 0 ) {
bases = read.getReadBases();
refBase = (byte)ref.getBase();
prevBase = read.getReadBases()[offset - 1];
prevBase = bases[offset - 1];
// DinucCovariate is responsible for getting the complement bases if needed
if( read.getReadNegativeStrandFlag() ) {
prevBase = read.getReadBases()[offset + 1];
prevBase = bases[offset + 1];
}
// Skip if this base or the previous one was an 'N' or etc.
if( BaseUtils.isRegularBase( (char)prevBase ) && BaseUtils.isRegularBase( (char)(read.getReadBases()[offset]) ) ) {
// BUGBUG: For DinucCovariate we should use previous reference base, not the previous base in this read.
if( BaseUtils.isRegularBase( (char)prevBase ) && BaseUtils.isRegularBase( (char)(bases[offset]) ) ) {
// SOLID bams insert the reference base into the read if the color space quality is zero, so skip over them
colorSpaceQuals = null;

7
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
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@ -114,12 +114,9 @@ public class CycleCovariate implements Covariate {
}
warnedUserBadPlatform = true;
}
//ReadHashDatum correctedReadDatum = new ReadHashDatum( readDatum );
//correctedReadDatum.platform = defaultPlatform;
return 0; // BUGBUG: broken at the moment
//return getValue( correctedReadDatum, offset ); // a recursive call
read.getReadGroup().setPlatform( defaultPlatform );
return getValue( read, offset ); // a recursive call
}
}
// Used to get the covariate's value from input csv file in TableRecalibrationWalker

13
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java
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@ -60,23 +60,20 @@ public class DinucCovariate implements Covariate {
byte base;
byte prevBase;
byte[] bases = read.getReadBases();
// If this is a negative strand read then we need to reverse the direction for our previous base
if( read.getReadNegativeStrandFlag() ) {
base = (byte)BaseUtils.simpleComplement( (char)(read.getReadBases()[offset]) );
prevBase = (byte)BaseUtils.simpleComplement( (char)(read.getReadBases()[offset + 1]) );
base = (byte)BaseUtils.simpleComplement( (char)(bases[offset]) );
prevBase = (byte)BaseUtils.simpleComplement( (char)(bases[offset + 1]) );
} else {
base = read.getReadBases()[offset];
prevBase = read.getReadBases()[offset - 1];
base = bases[offset];
prevBase = bases[offset - 1];
}
//char[] charArray = {(char)prevBase, (char)base};
//return new String( charArray ); // This is an expensive call
return dinucHashMap.get( Dinuc.hashBytes( prevBase, base ) );
//return String.format("%c%c", prevBase, base); // This return statement is too slow
}
// Used to get the covariate's value from input csv file in TableRecalibrationWalker
public final Comparable getValue( final String str ) {
//return str;
return dinucHashMap.get( Dinuc.hashBytes( (byte)str.charAt(0), (byte)str.charAt(1) ) );
}

6
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
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@ -252,15 +252,15 @@ public class RecalDataManager {
((GATKSAMRecord)read).setReadGroup( readGroup );
}
if( RAC.FORCE_READ_GROUP != null && !read.getReadGroup().getReadGroupId().equals(RAC.FORCE_READ_GROUP) ) { // Collapse all the read groups into a single common String provided by the user
if( RAC.FORCE_READ_GROUP != null && !readGroup.getReadGroupId().equals(RAC.FORCE_READ_GROUP) ) { // Collapse all the read groups into a single common String provided by the user
String oldPlatform = readGroup.getPlatform();
readGroup = new SAMReadGroupRecord( RAC.FORCE_READ_GROUP );
readGroup.setPlatform( oldPlatform );
((GATKSAMRecord)read).setReadGroup( readGroup );
}
if( RAC.FORCE_PLATFORM != null && !read.getReadGroup().getPlatform().equals(RAC.FORCE_PLATFORM)) {
read.getReadGroup().setPlatform( RAC.FORCE_PLATFORM );
if( RAC.FORCE_PLATFORM != null && !readGroup.getPlatform().equals(RAC.FORCE_PLATFORM)) {
readGroup.setPlatform( RAC.FORCE_PLATFORM );
}
}
}

5
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
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@ -93,7 +93,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
private static final Pattern COMMENT_PATTERN = Pattern.compile("^#.*");
private static final Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*");
private static final Pattern COVARIATE_PATTERN = Pattern.compile("^ReadGroup,QualityScore,.*");
private static final String versionString = "v2.0.7"; // Major version, minor version, and build number
private static final String versionString = "v2.0.8"; // Major version, minor version, and build number
private SAMFileWriter OUTPUT_BAM = null;// The File Writer that will write out the recalibrated bam
//---------------------------------------------------------------------------------------------------------------
@ -257,7 +257,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
// Check if the data line is malformed, for example if the read group string contains a comma then it won't be parsed correctly
if( vals.length != requestedCovariates.size() + 3 ) { // +3 because of nObservations, nMismatch, and Qempirical
throw new StingException("Malformed input recalibration file. Found data line with too many fields: " + line +
" --Perhaps the read group string contains a comma and isn't parsed correctly.");
" --Perhaps the read group string contains a comma and isn't being parsed correctly.");
}
ArrayList<Comparable> key = new ArrayList<Comparable>();
@ -483,6 +483,5 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
if ( output != null ) {
output.close();
}
super.onTraversalDone(output);
}
}