zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Updating the recalibrator to use non-depricated getPileup() method. Adding documentation to AnalyzeAnnotations so that the walker isn't marked as unclean at compile time. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2688 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-01-26 14:15:09 +00:00
parent c231547204
commit 0345d9f6a5
2 changed files with 13 additions and 8 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
View File

@ -47,7 +47,7 @@ import net.sf.samtools.SAMRecord;
/**
* This walker is designed to work as the first pass in a two-pass processing step.
* It does a by-locus traversal operating only at sites that are not in dbSNP.
* We assume that all reference mismatches we see are therefore errors and indicitive of poor base quality.
* We assume that all reference mismatches we see are therefore errors and indicative of poor base quality.
* This walker generates tables based on various user-specified covariates (such as read group, reported quality score, cycle, and dinucleotide)
* Since there is a large amount of data one can then calculate an empirical probability of error
* given the particular covariates seen at this site, where p(error) = num mismatches / num observations
@ -238,7 +238,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
}
// Only use data from non-dbsnp sites
// Assume every mismatch at a non-dbsnp site is indicitive of poor quality
// Assume every mismatch at a non-dbsnp site is indicative of poor quality
if( !isSNP && ( ++numUnprocessed >= PROCESS_EVERY_NTH_LOCUS ) ) {
numUnprocessed = 0; // Reset the counter because we are processing this very locus
@ -248,7 +248,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
byte[] bases;
// For each read at this locus
for( PileupElement p : context.getPileup() ) {
for( PileupElement p : context.getBasePileup() ) {
read = p.getRead();
offset = p.getOffset();
@ -305,7 +305,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
* @param ref The reference base
*/
private static void updateMismatchCounts(final Pair<Long, Long> counts, final AlignmentContext context, final char ref) {
for( PileupElement p : context.getPileup() ) {
for( PileupElement p : context.getBasePileup() ) {
final char readChar = (char)(p.getBase());
final int readCharBaseIndex = BaseUtils.simpleBaseToBaseIndex(readChar);
final int refCharBaseIndex = BaseUtils.simpleBaseToBaseIndex(ref);

13
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java
View File

@ -36,9 +36,11 @@ import java.io.IOException;
*/
/**
* Created by IntelliJ IDEA.
* User: rpoplin
* Date: Jan 15, 2010
* Takes variant calls as .vcf files and creates plots of truth metrics as a function of the various annotations found in the INFO field.
*
* @author rpoplin
* @since Jan 15, 2010
* @help.summary Takes variant calls as .vcf files and creates plots of truth metrics as a function of the various annotations found in the INFO field.
*/
public class AnalyzeAnnotationsWalker extends RodWalker<Integer, Integer> {
@ -56,7 +58,7 @@ public class AnalyzeAnnotationsWalker extends RodWalker<Integer, Integer> {
private int MIN_VARIANTS_PER_BIN = 1000;
@Argument(fullName = "max_variants_per_bin", shortName = "maxBinSize", doc = "The maximum number of variants in a bin.", required = false)
private int MAX_VARIANTS_PER_BIN = 20000;
@Argument(fullName = "sampleName", shortName = "sampleName", doc = "Only process variants for this sample.", required = false)
@Argument(fullName = "sampleName", shortName = "sampleName", doc = "If supplied, only process variants found in this sample.", required = false)
private String SAMPLE_NAME = null;
@ -71,6 +73,9 @@ public class AnalyzeAnnotationsWalker extends RodWalker<Integer, Integer> {
//
//---------------------------------------------------------------------------------------------------------------
/**
* Create the output directory and setup the path variables
*/
public void initialize() {
// create the output directory where all the data tables and plots will go