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Change in Methods development pipeline: dbsnp130 can't be used for anything, changed it to dbsnp129. Optimization for HaplotypeScore and the to-be-committed ReadRosRankSumTest in AlignmentUtils 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5301 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2011-02-24 16:09:03 +00:00
parent 97e1a5262e
commit 255cc246a2
3 changed files with 39 additions and 26 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
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@ -63,7 +63,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
*
* @author rpoplin
* @since Nov 3, 2009
* @help.summary Second pass of the recalibration. Uses the table generated by CountCovariates to update the base quality scores of the input bam file using a sequential table calculation making the base quality scores more accurately reflect the actual quality of the bases as mesaured by reference mismatch rate.
* @help.summary Second pass of the recalibration. Uses the table generated by CountCovariates to update the base quality scores of the input bam file using a sequential table calculation making the base quality scores more accurately reflect the actual quality of the bases as measured by reference mismatch rate.
*/
@BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_OUTPUT)

58
java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
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@ -31,6 +31,7 @@ import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement;
import net.sf.samtools.util.StringUtil;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.*;
import org.broadinstitute.sting.utils.Utils;
@ -368,6 +369,18 @@ public class AlignmentUtils {
return n;
}
public static int getNumAlignedBases(final SAMRecord r) {
int n = 0;
final Cigar cigar = r.getCigar();
if (cigar == null) return 0;
for (final CigarElement e : cigar.getCigarElements()) {
if (e.getOperator() == CigarOperator.M ) { n += e.getLength(); }
}
return n;
}
@Deprecated
public static char[] alignmentToCharArray( final Cigar cigar, final char[] read, final char[] ref ) {
@ -468,37 +481,30 @@ public class AlignmentUtils {
switch( ce.getOperator() ) {
case I:
case S:
for ( int jjj = 0; jjj < elementLength; jjj++ ) {
if( pos == pileupOffset ) {
return alignmentPos;
}
pos++;
pos += elementLength;
if( pos >= pileupOffset ) {
return alignmentPos;
}
break;
case D:
case N:
if(!atDeletion) {
for ( int jjj = 0; jjj < elementLength; jjj++ ) {
alignmentPos++;
}
alignmentPos += elementLength;
} else {
for ( int jjj = 0; jjj < elementLength; jjj++ ) {
if( pos == pileupOffset ) {
return alignmentPos;
}
pos++;
alignmentPos++;
if( pos + elementLength >= pileupOffset ) {
return alignmentPos + (pileupOffset - pos);
} else {
pos += elementLength;
alignmentPos += elementLength;
}
}
break;
case M:
for ( int jjj = 0; jjj < elementLength; jjj++ ) {
if( pos == pileupOffset ) {
return alignmentPos;
}
pos++;
alignmentPos++;
if( pos + elementLength >= pileupOffset ) {
return alignmentPos + (pileupOffset - pos);
} else {
pos += elementLength;
alignmentPos += elementLength;
}
break;
case H:
@ -547,7 +553,15 @@ public class AlignmentUtils {
final int elementLength = ce.getLength();
switch( ce.getOperator() ) {
case I:
case I:
/*
if( alignPos > 0 ) {
if( alignment[alignPos-1] == BaseUtils.A ) { alignment[alignPos-1] = PileupElement.A_FOLLOWED_BY_INSERTION_BASE; }
else if( alignment[alignPos-1] == BaseUtils.C ) { alignment[alignPos-1] = PileupElement.C_FOLLOWED_BY_INSERTION_BASE; }
else if( alignment[alignPos-1] == BaseUtils.T ) { alignment[alignPos-1] = PileupElement.T_FOLLOWED_BY_INSERTION_BASE; }
else if( alignment[alignPos-1] == BaseUtils.G ) { alignment[alignPos-1] = PileupElement.G_FOLLOWED_BY_INSERTION_BASE; }
}
*/
case S:
for ( int jjj = 0; jjj < elementLength; jjj++ ) {
readPos++;

5
scala/qscript/core/MethodsDevelopmentCallingPipeline.scala
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@ -73,9 +73,8 @@ class MethodsDevelopmentCallingPipeline extends QScript {
val hg18 = new File("/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta")
val b36 = new File("/humgen/1kg/reference/human_b36_both.fasta")
val b37 = new File("/humgen/1kg/reference/human_g1k_v37.fasta")
val dbSNP_hg18 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_130_hg18.rod" // Special case for NA12878 collections that can't use 132 because they are part of it.
val dbSNP_hg18_129 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_129_hg18.rod"
val dbSNP_b36 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_130_b36.rod"
val dbSNP_hg18_129 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_129_hg18.rod" // Special case for NA12878 collections that can't use 132 because they are part of it.
val dbSNP_b36 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_129_b36.rod"
val dbSNP_b37 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_132_b37.leftAligned.vcf"
val dbSNP_b37_129 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_129_b37.rod" // Special case for NA12878 collections that can't use 132 because they are part of it.
val hapmap_hg18 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/sites_r27_nr.hg18_fwd.vcf"