diff --git a/build.xml b/build.xml
index d3377a763..7389503bb 100644
--- a/build.xml
+++ b/build.xml
@@ -679,20 +679,6 @@
-
-
-
-
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-
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@@ -750,12 +736,6 @@
-
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-
diff --git a/public/R/scripts/org/broadinstitute/sting/analyzecovariates/plot_residualError_OtherCovariate.R b/public/R/scripts/org/broadinstitute/sting/analyzecovariates/plot_residualError_OtherCovariate.R
deleted file mode 100644
index 15c6fc8f0..000000000
--- a/public/R/scripts/org/broadinstitute/sting/analyzecovariates/plot_residualError_OtherCovariate.R
+++ /dev/null
@@ -1,121 +0,0 @@
-#!/bin/env Rscript
-
-library(tools)
-
-args <- commandArgs(TRUE)
-verbose = TRUE
-
-input = args[1]
-covariateName = args[2]
-
-outfile = paste(input, ".qual_diff_v_", covariateName, ".pdf", sep="")
-pdf(outfile, height=7, width=7)
-par(cex=1.1)
-c <- read.table(input, header=T)
-c <- c[sort.list(c[,1]),]
-
-#
-# Plot residual error as a function of the covariate
-#
-
-d.good <- c[c$nBases >= 1000,]
-d.1000 <- c[c$nBases < 1000,]
-rmseGood = sqrt( sum(as.numeric((d.good$Qempirical-d.good$Qreported)^2 * d.good$nBases)) / sum(as.numeric(d.good$nBases)) ) # prevent integer overflow with as.numeric, ugh
-rmseAll = sqrt( sum(as.numeric((c$Qempirical-c$Qreported)^2 * c$nBases)) / sum(as.numeric(c$nBases)) )
-theTitle = paste("RMSE_good =", round(rmseGood,digits=3), ", RMSE_all =", round(rmseAll,digits=3))
-if( length(d.good$nBases) == length(c$nBases) ) {
- theTitle = paste("RMSE =", round(rmseAll,digits=3))
-}
-# Don't let residual error go off the edge of the plot
-d.good$residualError = d.good$Qempirical-d.good$Qreported
-d.good$residualError[which(d.good$residualError > 10)] = 10
-d.good$residualError[which(d.good$residualError < -10)] = -10
-d.1000$residualError = d.1000$Qempirical-d.1000$Qreported
-d.1000$residualError[which(d.1000$residualError > 10)] = 10
-d.1000$residualError[which(d.1000$residualError < -10)] = -10
-c$residualError = c$Qempirical-c$Qreported
-c$residualError[which(c$residualError > 10)] = 10
-c$residualError[which(c$residualError < -10)] = -10
-pointType = "p"
-if( length(c$Covariate) <= 20 ) {
- pointType = "o"
-}
-if( is.numeric(c$Covariate) ) {
- plot(d.good$Covariate, d.good$residualError, type=pointType, main=theTitle, ylab="Empirical - Reported Quality", xlab=covariateName, col="blue", pch=20, ylim=c(-10, 10), xlim=c(min(c$Covariate),max(c$Covariate)))
- points(d.1000$Covariate, d.1000$residualError, type=pointType, col="cornflowerblue", pch=20)
-} else { # Dinuc (and other non-numeric covariates) are different to make their plots look nice
- plot(c$Covariate, c$residualError, type="l", main=theTitle, ylab="Empirical - Reported Quality", xlab=covariateName, col="blue", ylim=c(-10, 10))
- points(d.1000$Covariate, d.1000$residualError, type="l", col="cornflowerblue")
-}
-dev.off()
-
-if (exists('compactPDF')) {
- compactPDF(outfile)
-}
-
-#
-# Plot mean quality versus the covariate
-#
-
-outfile = paste(input, ".reported_qual_v_", covariateName, ".pdf", sep="")
-pdf(outfile, height=7, width=7)
-par(cex=1.1)
-pointType = "p"
-if( length(c$Covariate) <= 20 ) {
- pointType = "o"
-}
-theTitle = paste("Quality By", covariateName);
-if( is.numeric(c$Covariate) ) {
- plot(d.good$Covariate, d.good$Qreported, type=pointType, main=theTitle, ylab="Mean Reported Quality", xlab=covariateName, col="blue", pch=20, ylim=c(0, 40), xlim=c(min(c$Covariate),max(c$Covariate)))
- points(d.1000$Covariate, d.1000$Qreported, type=pointType, col="cornflowerblue", pch=20)
-} else { # Dinuc (and other non-numeric covariates) are different to make their plots look nice
- plot(c$Covariate, c$Qreported, type="l", main=theTitle, ylab="Mean Reported Quality", xlab=covariateName, col="blue", ylim=c(0, 40))
- points(d.1000$Covariate, d.1000$Qreported, type="l", col="cornflowerblue")
-}
-dev.off()
-
-if (exists('compactPDF')) {
- compactPDF(outfile)
-}
-
-#
-# Plot histogram of the covariate
-#
-
-e = d.good
-f = d.1000
-outfile = paste(input, ".", covariateName,"_hist.pdf", sep="")
-pdf(outfile, height=7, width=7)
-hst=subset(data.frame(e$Covariate, e$nBases), e.nBases != 0)
-hst2=subset(data.frame(f$Covariate, f$nBases), f.nBases != 0)
-
-lwdSize=2
-if( length(c$Covariate) <= 20 ) {
- lwdSize=7
-} else if( length(c$Covariate) <= 70 ) {
- lwdSize=4
-}
-
-if( is.numeric(c$Covariate) ) {
- if( length(hst$e.Covariate) == 0 ) {
- plot(hst2$f.Covariate, hst2$f.nBases, type="h", lwd=lwdSize, col="cornflowerblue", main=paste(covariateName,"histogram"), ylim=c(0, max(hst2$f.nBases)), xlab=covariateName, ylab="Count",yaxt="n",xlim=c(min(c$Covariate),max(c$Covariate)))
- } else {
- plot(hst$e.Covariate, hst$e.nBases, type="h", lwd=lwdSize, main=paste(covariateName,"histogram"), xlab=covariateName, ylim=c(0, max(hst$e.nBases)),ylab="Number of Bases",yaxt="n",xlim=c(min(c$Covariate),max(c$Covariate)))
- points(hst2$f.Covariate, hst2$f.nBases, type="h", lwd=lwdSize, col="cornflowerblue")
- }
- axis(2,axTicks(2), format(axTicks(2), scientific=F))
-} else { # Dinuc (and other non-numeric covariates) are different to make their plots look nice
- hst=subset(data.frame(c$Covariate, c$nBases), c.nBases != 0)
- plot(1:length(hst$c.Covariate), hst$c.nBases, type="h", lwd=lwdSize, main=paste(covariateName,"histogram"), ylim=c(0, max(hst$c.nBases)),xlab=covariateName, ylab="Number of Bases",yaxt="n",xaxt="n")
- if( length(hst$c.Covariate) > 9 ) {
- axis(1, at=seq(1,length(hst$c.Covariate),2), labels = hst$c.Covariate[seq(1,length(hst$c.Covariate),2)])
- } else {
- axis(1, at=seq(1,length(hst$c.Covariate),1), labels = hst$c.Covariate)
- }
- axis(2,axTicks(2), format(axTicks(2), scientific=F))
-}
-dev.off()
-
-if (exists('compactPDF')) {
- compactPDF(outfile)
-}
diff --git a/public/R/scripts/org/broadinstitute/sting/analyzecovariates/plot_residualError_QualityScoreCovariate.R b/public/R/scripts/org/broadinstitute/sting/analyzecovariates/plot_residualError_QualityScoreCovariate.R
deleted file mode 100644
index 33eeb1f16..000000000
--- a/public/R/scripts/org/broadinstitute/sting/analyzecovariates/plot_residualError_QualityScoreCovariate.R
+++ /dev/null
@@ -1,84 +0,0 @@
-#!/bin/env Rscript
-
-library(tools)
-
-args <- commandArgs(TRUE)
-
-input = args[1]
-Qcutoff = as.numeric(args[2])
-maxQ = as.numeric(args[3])
-maxHist = as.numeric(args[4])
-
-t=read.table(input, header=T)
-
-#
-# Plot of reported quality versus empirical quality
-#
-
-outfile = paste(input, ".quality_emp_v_stated.pdf", sep="")
-pdf(outfile, height=7, width=7)
-d.good <- t[t$nBases >= 10000 & t$Qreported >= Qcutoff,]
-d.1000 <- t[t$nBases < 1000 & t$Qreported >= Qcutoff,]
-d.10000 <- t[t$nBases < 10000 & t$nBases >= 1000 & t$Qreported >= Qcutoff,]
-f <- t[t$Qreported < Qcutoff,]
-e <- rbind(d.good, d.1000, d.10000)
-rmseGood = sqrt( sum(as.numeric((d.good$Qempirical-d.good$Qreported)^2 * d.good$nBases)) / sum(as.numeric(d.good$nBases)) ) # prevent integer overflow with as.numeric, ugh
-rmseAll = sqrt( sum(as.numeric((e$Qempirical-e$Qreported)^2 * e$nBases)) / sum(as.numeric(e$nBases)) )
-theTitle = paste("RMSE_good =", round(rmseGood,digits=3), ", RMSE_all =", round(rmseAll,digits=3))
-if( length(t$nBases) - length(f$nBases) == length(d.good$nBases) ) {
- theTitle = paste("RMSE =", round(rmseAll,digits=3));
-}
-plot(d.good$Qreported, d.good$Qempirical, type="p", col="blue", main=theTitle, xlim=c(0,maxQ), ylim=c(0,maxQ), pch=16, xlab="Reported quality score", ylab="Empirical quality score")
-points(d.1000$Qreported, d.1000$Qempirical, type="p", col="lightblue", pch=16)
-points(d.10000$Qreported, d.10000$Qempirical, type="p", col="cornflowerblue", pch=16)
-points(f$Qreported, f$Qempirical, type="p", col="maroon1", pch=16)
-abline(0,1, lty=2)
-dev.off()
-
-if (exists('compactPDF')) {
- compactPDF(outfile)
-}
-
-#
-# Plot Q empirical histogram
-#
-
-outfile = paste(input, ".quality_emp_hist.pdf", sep="")
-pdf(outfile, height=7, width=7)
-hst=subset(data.frame(e$Qempirical, e$nBases), e.nBases != 0)
-hst2=subset(data.frame(f$Qempirical, f$nBases), f.nBases != 0)
-percentBases=hst$e.nBases / sum(as.numeric(hst$e.nBases))
-entropy = -sum(log2(percentBases)*percentBases)
-yMax = max(hst$e.nBases)
-if(maxHist != 0) {
-yMax = maxHist
-}
-plot(hst$e.Qempirical, hst$e.nBases, type="h", lwd=4, xlim=c(0,maxQ), ylim=c(0,yMax), main=paste("Empirical quality score histogram, entropy = ",round(entropy,digits=3)), xlab="Empirical quality score", ylab="Number of Bases",yaxt="n")
-points(hst2$f.Qempirical, hst2$f.nBases, type="h", lwd=4, col="maroon1")
-axis(2,axTicks(2), format(axTicks(2), scientific=F))
-dev.off()
-
-if (exists('compactPDF')) {
- compactPDF(outfile)
-}
-
-#
-# Plot Q reported histogram
-#
-
-outfile = paste(input, ".quality_rep_hist.pdf", sep="")
-pdf(outfile, height=7, width=7)
-hst=subset(data.frame(e$Qreported, e$nBases), e.nBases != 0)
-hst2=subset(data.frame(f$Qreported, f$nBases), f.nBases != 0)
-yMax = max(hst$e.nBases)
-if(maxHist != 0) {
-yMax = maxHist
-}
-plot(hst$e.Qreported, hst$e.nBases, type="h", lwd=4, xlim=c(0,maxQ), ylim=c(0,yMax), main=paste("Reported quality score histogram, entropy = ",round(entropy,digits=3)), xlab="Reported quality score", ylab="Number of Bases",yaxt="n")
-points(hst2$f.Qreported, hst2$f.nBases, type="h", lwd=4, col="maroon1")
-axis(2,axTicks(2), format(axTicks(2), scientific=F))
-dev.off()
-
-if (exists('compactPDF')) {
- compactPDF(outfile)
-}
diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
index dcdef5aab..883436582 100644
--- a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
+++ b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
@@ -195,7 +195,6 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
private static final List gatkPackages = Arrays.asList(
"org.broadinstitute.sting.gatk",
"org.broadinstitute.sting.pipeline",
- "org.broadinstitute.sting.analyzecovariates",
"org.broadinstitute.sting.gatk.datasources.reads.utilities");
/**
@@ -252,7 +251,7 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
*/
private void writeFilter(String className, List argumentFields, Set> dependents) throws IOException {
String content = getContent(TRAIT_TEMPLATE, "org.broadinstitute.sting.queue.function.CommandLineFunction",
- className, "", false, String.format(" + \" --read_filter %s\"", className), argumentFields, dependents);
+ className, "", false, String.format(" + required(\"--read_filter\", \"%s\")", className), argumentFields, dependents);
writeFile(GATK_EXTENSIONS_PACKAGE_NAME + "." + className, content);
}
diff --git a/public/packages/AnalyzeCovariates.xml b/public/packages/AnalyzeCovariates.xml
deleted file mode 100644
index 27a72eabd..000000000
--- a/public/packages/AnalyzeCovariates.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/public/packages/GATK-Picard.xml b/public/packages/GATK-Picard.xml
deleted file mode 100644
index 251f584f7..000000000
--- a/public/packages/GATK-Picard.xml
+++ /dev/null
@@ -1,51 +0,0 @@
-
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diff --git a/public/packages/GATKEngine.xml b/public/packages/GATKEngine.xml
index 78f3f0cea..2de0273f3 100644
--- a/public/packages/GATKEngine.xml
+++ b/public/packages/GATKEngine.xml
@@ -48,11 +48,11 @@
-
-
-
-
-
-
+
+
+
+
+
+
diff --git a/public/packages/GenomeAnalysisTK.xml b/public/packages/GenomeAnalysisTK.xml
index b6c83274c..e95c992b6 100644
--- a/public/packages/GenomeAnalysisTK.xml
+++ b/public/packages/GenomeAnalysisTK.xml
@@ -33,10 +33,8 @@
-
-
-
-
+
+
diff --git a/public/packages/GenomeAnalysisTKLite.xml b/public/packages/GenomeAnalysisTKLite.xml
index fed85271d..b2f73434c 100644
--- a/public/packages/GenomeAnalysisTKLite.xml
+++ b/public/packages/GenomeAnalysisTKLite.xml
@@ -33,9 +33,6 @@
-
-
-
diff --git a/public/packages/Queue.xml b/public/packages/Queue.xml
index b57a5c1c2..621a549d5 100644
--- a/public/packages/Queue.xml
+++ b/public/packages/Queue.xml
@@ -32,7 +32,6 @@
-
diff --git a/public/packages/QueueLite.xml b/public/packages/QueueLite.xml
index 73fd1884a..0ead68fb0 100644
--- a/public/packages/QueueLite.xml
+++ b/public/packages/QueueLite.xml
@@ -32,7 +32,6 @@
-