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Moved gsalib, R and other resources, Queue GATK extensions generator, Queue version java files.

This commit is contained in:
Khalid Shakir 2014-01-29 13:25:35 -05:00 committed by David Roazen
parent eb52dc6a9b
commit faaef236ea
35 changed files with 0 additions and 0 deletions
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public/keys/GATK_public.key → public/gatk-framework/src/main/resources/GATK_public.key
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public/java/src/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_access.key → public/gatk-framework/src/main/resources/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_access.key
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public/java/src/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_secret.key → public/gatk-framework/src/main/resources/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_secret.key
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public/R/scripts/org/broadinstitute/sting/gatk/walkers/variantrecalibration/plot_Tranches.R → public/gatk-framework/src/main/resources/org/broadinstitute/sting/gatk/walkers/variantrecalibration/plot_Tranches.R
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public/R/scripts/org/broadinstitute/sting/utils/recalibration/BQSR.R → public/gatk-framework/src/main/resources/org/broadinstitute/sting/utils/recalibration/BQSR.R
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public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java → public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
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public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java → public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java
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public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java → public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
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public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ReadFilterField.java → public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ReadFilterField.java
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public/R/src/org/broadinstitute/sting/utils/R/gsalib/DESCRIPTION → public/gsalib/src/R/DESCRIPTION
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public/R/src/org/broadinstitute/sting/utils/R/gsalib/NAMESPACE → public/gsalib/src/R/NAMESPACE
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public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.error.R → public/gsalib/src/R/R/gsa.error.R
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public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.getargs.R → public/gsalib/src/R/R/gsa.getargs.R
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public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.message.R → public/gsalib/src/R/R/gsa.message.R
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public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.plot.venn.R → public/gsalib/src/R/R/gsa.plot.venn.R
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public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.eval.R → public/gsalib/src/R/R/gsa.read.eval.R
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public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.gatkreport.R → public/gsalib/src/R/R/gsa.read.gatkreport.R
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public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.squidmetrics.R → public/gsalib/src/R/R/gsa.read.squidmetrics.R
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public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.vcf.R → public/gsalib/src/R/R/gsa.read.vcf.R
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public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.variantqc.utils.R → public/gsalib/src/R/R/gsa.variantqc.utils.R
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public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.warn.R → public/gsalib/src/R/R/gsa.warn.R
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public/R/src/org/broadinstitute/sting/utils/R/gsalib/Read-and-delete-me → public/gsalib/src/R/Read-and-delete-me
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public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.error.Rd → public/gsalib/src/R/man/gsa.error.Rd
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public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.getargs.Rd → public/gsalib/src/R/man/gsa.getargs.Rd
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public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.message.Rd → public/gsalib/src/R/man/gsa.message.Rd
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public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.plot.venn.Rd → public/gsalib/src/R/man/gsa.plot.venn.Rd
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public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.eval.Rd → public/gsalib/src/R/man/gsa.read.eval.Rd
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public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.gatkreport.Rd → public/gsalib/src/R/man/gsa.read.gatkreport.Rd
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public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.squidmetrics.Rd → public/gsalib/src/R/man/gsa.read.squidmetrics.Rd
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public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.vcf.Rd → public/gsalib/src/R/man/gsa.read.vcf.Rd
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public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.warn.Rd → public/gsalib/src/R/man/gsa.warn.Rd
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public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsalib-package.Rd → public/gsalib/src/R/man/gsalib-package.Rd
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public/java/src/org/broadinstitute/sting/queue/QueueVersion.java → public/queue-framework/src/main/java/org/broadinstitute/sting/queue/QueueVersion.java
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public/java/src/org/broadinstitute/sting/queue/package-info.java → public/queue-framework/src/main/java/org/broadinstitute/sting/queue/package-info.java
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public/R/scripts/org/broadinstitute/sting/queue/util/queueJobReport.R → public/queue-framework/src/main/resources/org/broadinstitute/sting/queue/util/queueJobReport.R
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