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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/ebanks/Sting_rodrefactor into rodrewrite

This commit is contained in:
Mark DePristo 2011-09-07 10:50:00 -04:00
parent d471617c65 9559115ad5
commit a02636a1ac
8 changed files with 62 additions and 21 deletions
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23
public/R/queueJobReport.R
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@ -12,7 +12,9 @@ if ( onCMDLine ) {
inputFileName = args[1]
outputPDF = args[2]
} else {
inputFileName = "~/Desktop/broadLocal/GATK/unstable/report.txt"
#inputFileName = "~/Desktop/broadLocal/GATK/unstable/report.txt"
inputFileName = "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/Q-25718@node1149.jobreport.txt"
#inputFileName = "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/rodPerformanceGoals/history/report.082711.txt"
outputPDF = NA
}
@ -113,11 +115,22 @@ plotGroup <- function(groupTable) {
textplot(as.data.frame(sum), show.rownames=F)
title(paste("Job summary for", name, "itemizing each iteration"), cex=3)
# histogram of job times by groupAnnotations
if ( length(groupAnnotations) == 1 && dim(sub)[1] > 1 ) {
# todo -- how do we group by annotations?
p <- ggplot(data=sub, aes(x=runtime)) + geom_histogram()
p <- p + xlab("runtime in seconds") + ylab("No. of jobs")
p <- p + opts(title=paste("Job runtime histogram for", name))
print(p)
}
# as above, but averaging over all iterations
groupAnnotationsNoIteration = setdiff(groupAnnotations, "iteration")
sum = cast(melt(sub, id.vars=groupAnnotationsNoIteration, measure.vars=c("runtime")), ... ~ ., fun.aggregate=c(mean, sd))
textplot(as.data.frame(sum), show.rownames=F)
title(paste("Job summary for", name, "averaging over all iterations"), cex=3)
if ( dim(sub)[1] > 1 ) {
sum = cast(melt(sub, id.vars=groupAnnotationsNoIteration, measure.vars=c("runtime")), ... ~ ., fun.aggregate=c(mean, sd))
textplot(as.data.frame(sum), show.rownames=F)
title(paste("Job summary for", name, "averaging over all iterations"), cex=3)
}
}
# print out some useful basic information
@ -146,7 +159,7 @@ plotJobsGantt(gatkReportData, T)
plotJobsGantt(gatkReportData, F)
plotProgressByTime(gatkReportData)
for ( group in gatkReportData ) {
plotGroup(group)
plotGroup(group)
}
if ( ! is.na(outputPDF) ) {

5
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -52,6 +52,11 @@ public class UnifiedArgumentCollection {
@Argument(fullName = "heterozygosity", shortName = "hets", doc = "Heterozygosity value used to compute prior likelihoods for any locus", required = false)
public Double heterozygosity = DiploidSNPGenotypePriors.HUMAN_HETEROZYGOSITY;
/**
* The PCR error rate is independent of the sequencing error rate, which is necessary because we cannot necessarily
* distinguish between PCR errors vs. sequencing errors. The practical implication for this value is that it
* effectively acts as a cap on the base qualities.
*/
@Argument(fullName = "pcr_error_rate", shortName = "pcr_error", doc = "The PCR error rate to be used for computing fragment-based likelihoods", required = false)
public Double PCR_error = DiploidSNPGenotypeLikelihoods.DEFAULT_PCR_ERROR_RATE;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
View File

@ -214,7 +214,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
@Argument(fullName="sample_expressions", shortName="se", doc="Regular expression to select many samples from the ROD tracks provided. Can be specified multiple times", required=false)
public Set<String> sampleExpressions ;
@Argument(fullName="sample_file", shortName="sf", doc="File containing a list of samples (one per line) to include. Can be specified multiple times", required=false)
@Input(fullName="sample_file", shortName="sf", doc="File containing a list of samples (one per line) to include. Can be specified multiple times", required=false)
public Set<File> sampleFiles;
/**
@ -226,7 +226,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
/**
* Note that sample exclusion takes precedence over inclusion, so that if a sample is in both lists it will be excluded.
*/
@Argument(fullName="exclude_sample_file", shortName="xl_sf", doc="File containing a list of samples (one per line) to exclude. Can be specified multiple times", required=false)
@Input(fullName="exclude_sample_file", shortName="xl_sf", doc="File containing a list of samples (one per line) to exclude. Can be specified multiple times", required=false)
public Set<File> XLsampleFiles = new HashSet<File>(0);
/**

3
public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java
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@ -252,7 +252,8 @@ public class ClippingOp {
if (start == 0 && stop == read.getReadLength() -1)
return new SAMRecord(read.getHeader());
CigarShift cigarShift = hardClipCigar(read.getCigar(), start, stop);
// If the read is unmapped there is no Cigar string and neither should we create a new cigar string
CigarShift cigarShift = (read.getReadUnmappedFlag()) ? new CigarShift(new Cigar(), 0, 0) : hardClipCigar(read.getCigar(), start, stop);
// the cigar may force a shift left or right (or both) in case we are left with insertions
// starting or ending the read after applying the hard clip on start/stop.

2
public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
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@ -82,7 +82,7 @@ public class PileupElement {
// --------------------------------------------------------------------------
private Integer getReducedReadQualityTagValue() {
return (Integer)getRead().getAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG);
return getRead().getIntegerAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG);
}
public boolean isReducedRead() {

16
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
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@ -41,6 +41,10 @@ public class GATKSAMRecord extends SAMRecord {
// because some values can be null, we don't want to duplicate effort
private boolean retrievedReadGroup = false;
/** A private cache for the reduced read quality. Null indicates the value hasn't be fetched yet or isn't available */
private boolean lookedUpReducedReadQuality = false;
private Integer reducedReadQuality;
// These temporary attributes were added here to make life easier for
// certain algorithms by providing a way to label or attach arbitrary data to
// individual GATKSAMRecords.
@ -338,7 +342,17 @@ public class GATKSAMRecord extends SAMRecord {
public Object getAttribute(final String tag) { return mRecord.getAttribute(tag); }
public Integer getIntegerAttribute(final String tag) { return mRecord.getIntegerAttribute(tag); }
public Integer getIntegerAttribute(final String tag) {
if ( tag == ReadUtils.REDUCED_READ_QUALITY_TAG ) {
if ( ! lookedUpReducedReadQuality ) {
lookedUpReducedReadQuality = true;
reducedReadQuality = mRecord.getIntegerAttribute(tag);
}
return reducedReadQuality;
} else {
return mRecord.getIntegerAttribute(tag);
}
}
public Short getShortAttribute(final String tag) { return mRecord.getShortAttribute(tag); }

18
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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@ -11,7 +11,7 @@ import net.sf.samtools.SAMFileReader
import net.sf.samtools.SAMFileHeader.SortOrder
import org.broadinstitute.sting.queue.util.QScriptUtils
import org.broadinstitute.sting.queue.function.{CommandLineFunction, ListWriterFunction}
import org.broadinstitute.sting.queue.function.ListWriterFunction
class DataProcessingPipeline extends QScript {
qscript =>
@ -31,7 +31,7 @@ class DataProcessingPipeline extends QScript {
var reference: File = _
@Input(doc="dbsnp ROD to use (must be in VCF format)", fullName="dbsnp", shortName="D", required=true)
var dbSNP: File = _
var dbSNP: List[File] = List()
/****************************************************************************
* Optional Parameters
@ -43,7 +43,7 @@ class DataProcessingPipeline extends QScript {
//
@Input(doc="extra VCF files to use as reference indels for Indel Realignment", fullName="extra_indels", shortName="indels", required=false)
var indels: File = _
var indels: List[File] = List()
@Input(doc="The path to the binary of bwa (usually BAM files have already been mapped - but if you want to remap this is the option)", fullName="path_to_bwa", shortName="bwa", required=false)
var bwaPath: File = _
@ -159,7 +159,7 @@ class DataProcessingPipeline extends QScript {
for (rg <- readGroups) {
val intermediateInBam: File = if (index == readGroups.length) { inBam } else { swapExt(outBam, ".bam", index+1 + "-rg.bam") }
val intermediateOutBam: File = if (index > 1) {swapExt(outBam, ".bam", index + "-rg.bam") } else { outBam}
val readGroup = new ReadGroup(rg.getReadGroupId, rg.getPlatform, rg.getLibrary, rg.getPlatformUnit, rg.getSample, rg.getSequencingCenter, rg.getDescription)
val readGroup = new ReadGroup(rg.getReadGroupId, rg.getLibrary, rg.getPlatform, rg.getPlatformUnit, rg.getSample, rg.getSequencingCenter, rg.getDescription)
add(addReadGroup(intermediateInBam, intermediateOutBam, readGroup))
index = index - 1
}
@ -321,9 +321,9 @@ class DataProcessingPipeline extends QScript {
this.input_file = inBams
this.out = outIntervals
this.mismatchFraction = 0.0
this.known :+= qscript.dbSNP
this.known ++= qscript.dbSNP
if (indels != null)
this.known :+= qscript.indels
this.known ++= qscript.indels
this.scatterCount = nContigs
this.analysisName = queueLogDir + outIntervals + ".target"
this.jobName = queueLogDir + outIntervals + ".target"
@ -333,9 +333,9 @@ class DataProcessingPipeline extends QScript {
this.input_file = inBams
this.targetIntervals = tIntervals
this.out = outBam
this.known :+= qscript.dbSNP
this.known ++= qscript.dbSNP
if (qscript.indels != null)
this.known :+= qscript.indels
this.known ++= qscript.indels
this.consensusDeterminationModel = cleanModelEnum
this.compress = 0
this.scatterCount = nContigs
@ -344,7 +344,7 @@ class DataProcessingPipeline extends QScript {
}
case class cov (inBam: File, outRecalFile: File) extends CountCovariates with CommandLineGATKArgs {
this.knownSites :+= qscript.dbSNP
this.knownSites ++= qscript.dbSNP
this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
this.input_file :+= inBam
this.recal_file = outRecalFile

12
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
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@ -1,6 +1,5 @@
package org.broadinstitute.sting.queue.qscripts
import org.broadinstitute.sting.commandline.Hidden
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport
@ -70,7 +69,8 @@ class MethodsDevelopmentCallingPipeline extends QScript {
val goldStandardClusterFile = new File(goldStandardName + ".clusters")
}
val hg19 = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
val b37_decoy = new File("/humgen/1kg/reference/human_g1k_v37_decoy.fasta")
val hg19 = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
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")
@ -124,6 +124,14 @@ class MethodsDevelopmentCallingPipeline extends QScript {
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.bwa.cleaned.recal.bam"),
new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, 99.0, !lowPass, !exome, 3),
"WExTrioDecoy" -> new Target("CEUTrio.HiSeq.WEx.b37_decoy", b37_decoy, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.b37_decoy.list"),
new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
"/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 3.3, 98.0, !lowPass, exome, 3),
"WGSTrioDecoy" -> new Target("CEUTrio.HiSeq.WGS.b37_decoy", b37_decoy, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.b37_decoy.list"),
new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, 99.0, !lowPass, !exome, 3),
"FIN" -> new Target("FIN", b37, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/1kg/processing/pipeline_test_bams/FIN.79sample.Nov2010.chr20.bam"),
new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **