From faaef236ea0cbf0ad45b8b624ef51a9feeaab44c Mon Sep 17 00:00:00 2001 From: Khalid Shakir Date: Wed, 29 Jan 2014 13:25:35 -0500 Subject: [PATCH] Moved gsalib, R and other resources, Queue GATK extensions generator, Queue version java files. --- .../src/main/resources}/GATK_public.key | Bin .../gatk/phonehome/resources/GATK_AWS_access.key | Bin .../gatk/phonehome/resources/GATK_AWS_secret.key | Bin .../walkers/variantrecalibration/plot_Tranches.R | 0 .../broadinstitute/sting/utils/recalibration/BQSR.R | 0 .../extensions/gatk/ArgumentDefinitionField.java | 0 .../sting/queue/extensions/gatk/ArgumentField.java | 0 .../extensions/gatk/GATKExtensionsGenerator.java | 0 .../queue/extensions/gatk/ReadFilterField.java | 0 .../utils/R/gsalib => gsalib/src/R}/DESCRIPTION | 0 .../sting/utils/R/gsalib => gsalib/src/R}/NAMESPACE | 0 .../utils/R/gsalib => gsalib/src/R}/R/gsa.error.R | 0 .../utils/R/gsalib => gsalib/src/R}/R/gsa.getargs.R | 0 .../utils/R/gsalib => gsalib/src/R}/R/gsa.message.R | 0 .../R/gsalib => gsalib/src/R}/R/gsa.plot.venn.R | 0 .../R/gsalib => gsalib/src/R}/R/gsa.read.eval.R | 0 .../gsalib => gsalib/src/R}/R/gsa.read.gatkreport.R | 0 .../src/R}/R/gsa.read.squidmetrics.R | 0 .../R/gsalib => gsalib/src/R}/R/gsa.read.vcf.R | 0 .../gsalib => gsalib/src/R}/R/gsa.variantqc.utils.R | 0 .../utils/R/gsalib => gsalib/src/R}/R/gsa.warn.R | 0 .../R/gsalib => gsalib/src/R}/Read-and-delete-me | 0 .../R/gsalib => gsalib/src/R}/man/gsa.error.Rd | 0 .../R/gsalib => gsalib/src/R}/man/gsa.getargs.Rd | 0 .../R/gsalib => gsalib/src/R}/man/gsa.message.Rd | 0 .../R/gsalib => gsalib/src/R}/man/gsa.plot.venn.Rd | 0 .../R/gsalib => gsalib/src/R}/man/gsa.read.eval.Rd | 0 .../src/R}/man/gsa.read.gatkreport.Rd | 0 .../src/R}/man/gsa.read.squidmetrics.Rd | 0 .../R/gsalib => gsalib/src/R}/man/gsa.read.vcf.Rd | 0 .../utils/R/gsalib => gsalib/src/R}/man/gsa.warn.Rd | 0 .../R/gsalib => gsalib/src/R}/man/gsalib-package.Rd | 0 .../broadinstitute/sting/queue/QueueVersion.java | 0 .../broadinstitute/sting/queue/package-info.java | 0 .../sting/queue/util/queueJobReport.R | 0 35 files changed, 0 insertions(+), 0 deletions(-) rename public/{keys => gatk-framework/src/main/resources}/GATK_public.key (100%) rename public/{java/src => gatk-framework/src/main/resources}/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_access.key (100%) rename public/{java/src => gatk-framework/src/main/resources}/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_secret.key (100%) rename public/{R/scripts => gatk-framework/src/main/resources}/org/broadinstitute/sting/gatk/walkers/variantrecalibration/plot_Tranches.R (100%) rename public/{R/scripts => gatk-framework/src/main/resources}/org/broadinstitute/sting/utils/recalibration/BQSR.R (100%) rename public/{java/src => gatk-queue-extgen/src/main/java}/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java (100%) rename public/{java/src => gatk-queue-extgen/src/main/java}/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java (100%) rename public/{java/src => gatk-queue-extgen/src/main/java}/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java (100%) rename public/{java/src => gatk-queue-extgen/src/main/java}/org/broadinstitute/sting/queue/extensions/gatk/ReadFilterField.java (100%) rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/DESCRIPTION (100%) rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/NAMESPACE (100%) rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/R/gsa.error.R (100%) rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/R/gsa.getargs.R (100%) rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/R/gsa.message.R (100%) rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/R/gsa.plot.venn.R (100%) rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/R/gsa.read.eval.R (100%) rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/R/gsa.read.gatkreport.R (100%) rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/R/gsa.read.squidmetrics.R (100%) rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/R/gsa.read.vcf.R (100%) rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/R/gsa.variantqc.utils.R (100%) rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/R/gsa.warn.R (100%) rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/Read-and-delete-me (100%) rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/man/gsa.error.Rd (100%) rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/man/gsa.getargs.Rd (100%) rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/man/gsa.message.Rd (100%) rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/man/gsa.plot.venn.Rd (100%) rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/man/gsa.read.eval.Rd (100%) rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/man/gsa.read.gatkreport.Rd (100%) rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/man/gsa.read.squidmetrics.Rd (100%) rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/man/gsa.read.vcf.Rd (100%) rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/man/gsa.warn.Rd (100%) rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/man/gsalib-package.Rd (100%) rename public/{java/src => queue-framework/src/main/java}/org/broadinstitute/sting/queue/QueueVersion.java (100%) rename public/{java/src => queue-framework/src/main/java}/org/broadinstitute/sting/queue/package-info.java (100%) rename public/{R/scripts => queue-framework/src/main/resources}/org/broadinstitute/sting/queue/util/queueJobReport.R (100%) diff --git a/public/keys/GATK_public.key b/public/gatk-framework/src/main/resources/GATK_public.key similarity index 100% rename from public/keys/GATK_public.key rename to public/gatk-framework/src/main/resources/GATK_public.key diff --git a/public/java/src/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_access.key b/public/gatk-framework/src/main/resources/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_access.key similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_access.key rename to public/gatk-framework/src/main/resources/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_access.key diff --git a/public/java/src/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_secret.key b/public/gatk-framework/src/main/resources/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_secret.key similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_secret.key rename to public/gatk-framework/src/main/resources/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_secret.key diff --git a/public/R/scripts/org/broadinstitute/sting/gatk/walkers/variantrecalibration/plot_Tranches.R b/public/gatk-framework/src/main/resources/org/broadinstitute/sting/gatk/walkers/variantrecalibration/plot_Tranches.R similarity index 100% rename from public/R/scripts/org/broadinstitute/sting/gatk/walkers/variantrecalibration/plot_Tranches.R rename to public/gatk-framework/src/main/resources/org/broadinstitute/sting/gatk/walkers/variantrecalibration/plot_Tranches.R diff --git a/public/R/scripts/org/broadinstitute/sting/utils/recalibration/BQSR.R b/public/gatk-framework/src/main/resources/org/broadinstitute/sting/utils/recalibration/BQSR.R similarity index 100% rename from public/R/scripts/org/broadinstitute/sting/utils/recalibration/BQSR.R rename to public/gatk-framework/src/main/resources/org/broadinstitute/sting/utils/recalibration/BQSR.R diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java b/public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java rename to public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java b/public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java rename to public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java b/public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java rename to public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ReadFilterField.java b/public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ReadFilterField.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ReadFilterField.java rename to public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ReadFilterField.java diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/DESCRIPTION b/public/gsalib/src/R/DESCRIPTION similarity index 100% rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/DESCRIPTION rename to public/gsalib/src/R/DESCRIPTION diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/NAMESPACE b/public/gsalib/src/R/NAMESPACE similarity index 100% rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/NAMESPACE rename to public/gsalib/src/R/NAMESPACE diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.error.R b/public/gsalib/src/R/R/gsa.error.R similarity index 100% rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.error.R rename to public/gsalib/src/R/R/gsa.error.R diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.getargs.R b/public/gsalib/src/R/R/gsa.getargs.R similarity index 100% rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.getargs.R rename to public/gsalib/src/R/R/gsa.getargs.R diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.message.R b/public/gsalib/src/R/R/gsa.message.R similarity index 100% rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.message.R rename to public/gsalib/src/R/R/gsa.message.R diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.plot.venn.R b/public/gsalib/src/R/R/gsa.plot.venn.R similarity index 100% rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.plot.venn.R rename to public/gsalib/src/R/R/gsa.plot.venn.R diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.eval.R b/public/gsalib/src/R/R/gsa.read.eval.R similarity index 100% rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.eval.R rename to public/gsalib/src/R/R/gsa.read.eval.R diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.gatkreport.R b/public/gsalib/src/R/R/gsa.read.gatkreport.R similarity index 100% rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.gatkreport.R rename to public/gsalib/src/R/R/gsa.read.gatkreport.R diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.squidmetrics.R b/public/gsalib/src/R/R/gsa.read.squidmetrics.R similarity index 100% rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.squidmetrics.R rename to public/gsalib/src/R/R/gsa.read.squidmetrics.R diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.vcf.R b/public/gsalib/src/R/R/gsa.read.vcf.R similarity index 100% rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.vcf.R rename to public/gsalib/src/R/R/gsa.read.vcf.R diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.variantqc.utils.R b/public/gsalib/src/R/R/gsa.variantqc.utils.R similarity index 100% rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.variantqc.utils.R rename to public/gsalib/src/R/R/gsa.variantqc.utils.R diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.warn.R b/public/gsalib/src/R/R/gsa.warn.R similarity index 100% rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.warn.R rename to public/gsalib/src/R/R/gsa.warn.R diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/Read-and-delete-me b/public/gsalib/src/R/Read-and-delete-me similarity index 100% rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/Read-and-delete-me rename to public/gsalib/src/R/Read-and-delete-me diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.error.Rd b/public/gsalib/src/R/man/gsa.error.Rd similarity index 100% rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.error.Rd rename to public/gsalib/src/R/man/gsa.error.Rd diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.getargs.Rd b/public/gsalib/src/R/man/gsa.getargs.Rd similarity index 100% rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.getargs.Rd rename to public/gsalib/src/R/man/gsa.getargs.Rd diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.message.Rd b/public/gsalib/src/R/man/gsa.message.Rd similarity index 100% rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.message.Rd rename to public/gsalib/src/R/man/gsa.message.Rd diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.plot.venn.Rd b/public/gsalib/src/R/man/gsa.plot.venn.Rd similarity index 100% rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.plot.venn.Rd rename to public/gsalib/src/R/man/gsa.plot.venn.Rd diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.eval.Rd b/public/gsalib/src/R/man/gsa.read.eval.Rd similarity index 100% rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.eval.Rd rename to public/gsalib/src/R/man/gsa.read.eval.Rd diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.gatkreport.Rd b/public/gsalib/src/R/man/gsa.read.gatkreport.Rd similarity index 100% rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.gatkreport.Rd rename to public/gsalib/src/R/man/gsa.read.gatkreport.Rd diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.squidmetrics.Rd b/public/gsalib/src/R/man/gsa.read.squidmetrics.Rd similarity index 100% rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.squidmetrics.Rd rename to public/gsalib/src/R/man/gsa.read.squidmetrics.Rd diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.vcf.Rd b/public/gsalib/src/R/man/gsa.read.vcf.Rd similarity index 100% rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.vcf.Rd rename to public/gsalib/src/R/man/gsa.read.vcf.Rd diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.warn.Rd b/public/gsalib/src/R/man/gsa.warn.Rd similarity index 100% rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.warn.Rd rename to public/gsalib/src/R/man/gsa.warn.Rd diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsalib-package.Rd b/public/gsalib/src/R/man/gsalib-package.Rd similarity index 100% rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsalib-package.Rd rename to public/gsalib/src/R/man/gsalib-package.Rd diff --git a/public/java/src/org/broadinstitute/sting/queue/QueueVersion.java b/public/queue-framework/src/main/java/org/broadinstitute/sting/queue/QueueVersion.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/queue/QueueVersion.java rename to public/queue-framework/src/main/java/org/broadinstitute/sting/queue/QueueVersion.java diff --git a/public/java/src/org/broadinstitute/sting/queue/package-info.java b/public/queue-framework/src/main/java/org/broadinstitute/sting/queue/package-info.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/queue/package-info.java rename to public/queue-framework/src/main/java/org/broadinstitute/sting/queue/package-info.java diff --git a/public/R/scripts/org/broadinstitute/sting/queue/util/queueJobReport.R b/public/queue-framework/src/main/resources/org/broadinstitute/sting/queue/util/queueJobReport.R similarity index 100% rename from public/R/scripts/org/broadinstitute/sting/queue/util/queueJobReport.R rename to public/queue-framework/src/main/resources/org/broadinstitute/sting/queue/util/queueJobReport.R