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status.txt
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# On branch master
# Changes to be committed:
# (use "git reset HEAD <file>..." to unstage)
#
# new file: modules/compute/demo/asobara/parameters.csv
# new file: modules/compute/demo/asobara/protocols/Abyss.ftl
# new file: modules/compute/demo/asobara/protocols/Fastqc.ftl
# new file: modules/compute/demo/asobara/protocols/Submit.sh.ftl
# new file: modules/compute/demo/asobara/templates/Helpers.ftl
# new file: modules/compute/demo/asobara/templates/Macros.ftl
# new file: modules/compute/demo/asobara/workflow.csv
# new file: modules/compute/demo/asobara/worksheet.csv
# new file: modules/compute/demo/burnDown/output/dataTransfer.sh
# new file: modules/compute/demo/burnDown/output/parameters.csv
# new file: modules/compute/demo/burnDown/output/runlocal.sh
# new file: modules/compute/demo/burnDown/output/s00_CreateChartPDF_64.sh
# new file: modules/compute/demo/burnDown/output/submit.sh
# new file: modules/compute/demo/burnDown/output/workflow.csv
# new file: modules/compute/demo/burnDown/output/worksheet.csv
# new file: modules/compute/demo/burnDown/parameters.csv
# new file: modules/compute/demo/burnDown/protocols/CreateChartPDF.ftl
# new file: modules/compute/demo/burnDown/protocols/DataTransfer.sh.ftl
# new file: modules/compute/demo/burnDown/protocols/Submit.sh.ftl
# new file: modules/compute/demo/burnDown/templates/Footer.ftl
# new file: modules/compute/demo/burnDown/templates/Header.ftl
# new file: modules/compute/demo/burnDown/workflow.csv
# new file: modules/compute/demo/burnDown/worksheet.csv
# new file: modules/compute/demo/debug/protocols/Submit.sh.ftl
# new file: modules/compute/demo/debugCompute4/assembly.zip
# new file: modules/compute/demo/debugCompute4/assembly/Asobara_worksheet_run0486.csv
# new file: modules/compute/demo/debugCompute4/assembly/Asobara_worksheet_run0486_noInternalSampleID.csv
# new file: modules/compute/demo/debugCompute4/assembly/example_cmd.sh
# new file: modules/compute/demo/debugCompute4/assembly/parameters.csv
# new file: modules/compute/demo/debugCompute4/assembly/protocols/Abyss.ftl
# new file: modules/compute/demo/debugCompute4/assembly/protocols/Fastqc.ftl
# new file: modules/compute/demo/debugCompute4/assembly/protocols/Footer.ftl
# new file: modules/compute/demo/debugCompute4/assembly/protocols/Header.ftl
# new file: modules/compute/demo/debugCompute4/assembly/protocols/Helpers.ftl
# new file: modules/compute/demo/debugCompute4/assembly/protocols/Macros.ftl
# new file: modules/compute/demo/debugCompute4/assembly/protocols/NGSHeader.ftl
# new file: modules/compute/demo/debugCompute4/assembly/protocols/PBSHeader.ftl
# new file: modules/compute/demo/debugCompute4/assembly/protocols/Submit.sh.ftl
# new file: modules/compute/demo/debugCompute4/assembly/scripts/Asobara_worksheet_run0486_noInternalSampleID.csv
# new file: modules/compute/demo/debugCompute4/assembly/scripts/dataTransfer.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/parameters.csv
# new file: modules/compute/demo/debugCompute4/assembly/scripts/runlocal.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_1.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_10.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_11.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_12.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_13.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_14.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_15.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_16.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_17.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_18.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_19.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_2.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_20.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_21.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_22.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_23.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_24.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_25.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_26.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_27.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_28.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_29.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_3.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_30.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_31.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_32.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_33.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_34.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_35.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_36.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_37.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_38.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_39.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_4.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_40.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_5.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_6.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_7.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_8.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_9.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s01_AbySS_Asobara_Japonica_AM1_73_AM1_73.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s01_AbySS_Asobara_Japonica_AM1_75_AM1_75.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s01_AbySS_Asobara_Japonica_AM1_77_AM1_77.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s01_AbySS_Asobara_Japonica_AM1_79_AM1_79.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s01_AbySS_Asobara_Japonica_AM1_81_AM1_81.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s01_AbySS_Asobara_Japonica_KG1_73_KG1_73.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s01_AbySS_Asobara_Japonica_KG1_75_KG1_75.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s01_AbySS_Asobara_Japonica_KG1_77_KG1_77.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s01_AbySS_Asobara_Japonica_KG1_79_KG1_79.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/s01_AbySS_Asobara_Japonica_KG1_81_KG1_81.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/submit.sh
# new file: modules/compute/demo/debugCompute4/assembly/scripts/workflow.csv
# new file: modules/compute/demo/debugCompute4/assembly/system
# new file: modules/compute/demo/debugCompute4/assembly/templates_/templ-cluster.ftl
# new file: modules/compute/demo/debugCompute4/assembly/templates_/templ-download-grid.ftl
# new file: modules/compute/demo/debugCompute4/assembly/templates_/templ-errorfile.ftl
# new file: modules/compute/demo/debugCompute4/assembly/templates_/templ-exe-grid-dir.ftl
# new file: modules/compute/demo/debugCompute4/assembly/templates_/templ-exe-grid.ftl
# new file: modules/compute/demo/debugCompute4/assembly/templates_/templ-extrafile.ftl
# new file: modules/compute/demo/debugCompute4/assembly/templates_/templ-jdl-grid.ftl
# new file: modules/compute/demo/debugCompute4/assembly/templates_/templ-logfile.ftl
# new file: modules/compute/demo/debugCompute4/assembly/templates_/templ-outfile.ftl
# new file: modules/compute/demo/debugCompute4/assembly/templates_/templ-submit.ftl
# new file: modules/compute/demo/debugCompute4/assembly/templates_/templ-upload-grid.ftl
# new file: modules/compute/demo/debugCompute4/assembly/workflow.csv
# new file: modules/compute/demo/debugCompute4/output/parameters.csv
# new file: modules/compute/demo/debugCompute4/output/runlocal.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_1.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_10.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_11.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_12.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_13.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_14.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_15.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_16.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_17.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_18.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_19.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_2.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_20.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_21.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_22.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_23.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_24.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_25.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_26.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_27.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_28.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_29.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_3.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_30.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_31.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_32.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_33.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_34.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_35.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_36.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_37.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_38.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_39.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_4.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_40.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_5.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_6.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_7.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_8.sh
# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_9.sh
# new file: modules/compute/demo/debugCompute4/output/s01_AbySS_Asobara_Japonica_AM1_73_AM1_73.sh
# new file: modules/compute/demo/debugCompute4/output/s01_AbySS_Asobara_Japonica_AM1_75_AM1_75.sh
# new file: modules/compute/demo/debugCompute4/output/s01_AbySS_Asobara_Japonica_AM1_77_AM1_77.sh
# new file: modules/compute/demo/debugCompute4/output/s01_AbySS_Asobara_Japonica_AM1_79_AM1_79.sh
# new file: modules/compute/demo/debugCompute4/output/s01_AbySS_Asobara_Japonica_AM1_81_AM1_81.sh
# new file: modules/compute/demo/debugCompute4/output/s01_AbySS_Asobara_Japonica_KG1_73_KG1_73.sh
# new file: modules/compute/demo/debugCompute4/output/s01_AbySS_Asobara_Japonica_KG1_75_KG1_75.sh
# new file: modules/compute/demo/debugCompute4/output/s01_AbySS_Asobara_Japonica_KG1_77_KG1_77.sh
# new file: modules/compute/demo/debugCompute4/output/s01_AbySS_Asobara_Japonica_KG1_79_KG1_79.sh
# new file: modules/compute/demo/debugCompute4/output/s01_AbySS_Asobara_Japonica_KG1_81_KG1_81.sh
# new file: modules/compute/demo/debugCompute4/output/submit.sh
# new file: modules/compute/demo/debugCompute4/output/workflow.csv
# new file: modules/compute/demo/debugCompute4/output/worksheet.csv
# new file: modules/compute/demo/debugCompute4/parameters.csv
# new file: modules/compute/demo/debugCompute4/protocols/Abyss.ftl
# new file: modules/compute/demo/debugCompute4/protocols/Fastqc.ftl
# new file: modules/compute/demo/debugCompute4/protocols/Footer.ftl
# new file: modules/compute/demo/debugCompute4/protocols/Header.ftl
# new file: modules/compute/demo/debugCompute4/protocols/Helpers.ftl
# new file: modules/compute/demo/debugCompute4/protocols/Macros.ftl
# new file: modules/compute/demo/debugCompute4/protocols/NGSHeader.ftl
# new file: modules/compute/demo/debugCompute4/protocols/PBSHeader.ftl
# new file: modules/compute/demo/debugCompute4/protocols/Submit.sh.ftl
# new file: modules/compute/demo/debugCompute4/workflow.csv
# new file: modules/compute/demo/debugCompute4/worksheet.csv
# new file: modules/compute/demo/debugFolding/inputdir/workflow_QCReport.csv
# new file: modules/compute/demo/demoWorkflow/parameters.csv
# new file: modules/compute/demo/demoWorkflow/protocols/BwaAlignLeft.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/BwaAlignRight.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/BwaSampe.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/Covariates.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/CovariatesAfter.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/CovariatesBefore.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/Coverage.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/CreateInhouseProjects.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/DataTransfer.sh.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/DeployDbsnpIndelResources.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/Fixmates.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/GenerateReference.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/GenomicAnnotator.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/Helpers.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/IndexReference.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/Initialize.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/InstallTools.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/InstallWget.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/Markduplicates.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/MergeBam.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/PicardQC.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/PicardQCrecal.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/QCReport.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/QCReportTemplate.tex
# new file: modules/compute/demo/demoWorkflow/protocols/Realign.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/RealignTargetCreator.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/Recalibrate.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/SamSort.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/SamSortRecal.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/SamToBam.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/Submit.sh.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/UnifiedGenotyper.ftl
# new file: modules/compute/demo/demoWorkflow/protocols/VariantAnnotator.ftl
# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/qc/dedupmetrics.txt
# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/qc/projectName_QCReport.aux
# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/qc/projectName_QCReport.log
# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/qc/projectName_QCReport.tex
# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/qc/projectName_QCReport.toc
# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/qc/projectName_QCStatistics.csv
# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/qc/projectName_qcstatisticsdescription.tex
# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/qc/projectName_qcstatisticstable.tex
# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/qc/projectName_workflow.png
# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/qc/projectbaitset.txt
# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/rawdata/ngs/20130129_simMachine_0001_FLOWCELL_L1_None_1.fq.gz
# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/rawdata/ngs/20130129_simMachine_0001_FLOWCELL_L1_None_1.fq.md5
# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/rawdata/ngs/20130129_simMachine_0001_FLOWCELL_L1_None_2.fq.gz
# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/rawdata/ngs/20130129_simMachine_0001_FLOWCELL_L1_None_2.fq.md5
# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/rawdata/ngs/20130129_simMachine_0001_FLOWCELL/20130129_simMachine_0001_FLOWCELL_L1_1.fq.gz
# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/rawdata/ngs/20130129_simMachine_0001_FLOWCELL/20130129_simMachine_0001_FLOWCELL_L1_2.fq.gz
# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/dbsnp/dbSNP135.tabdelim.table
# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/dbsnp/dbSNP135.tabdelim.table.idx
# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/dbsnp/dbsnp_129_b37_human_g1k_v37.rod
# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/dbsnp/dbsnp_129_b37_human_g1k_v37.rod.idx
# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indels/1kg_pilot_release_merged_indels_sites_hg19_human_g1k_v37.vcf
# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indels/1kg_pilot_release_merged_indels_sites_hg19_human_g1k_v37.vcf.idx
# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indices/simulatedReferenceGenome.dict
# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indices/simulatedReferenceGenome.fa
# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indices/simulatedReferenceGenome.fa.amb
# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indices/simulatedReferenceGenome.fa.ann
# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indices/simulatedReferenceGenome.fa.bwt
# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indices/simulatedReferenceGenome.fa.fai
# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indices/simulatedReferenceGenome.fa.pac
# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indices/simulatedReferenceGenome.fa.rbwt
# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indices/simulatedReferenceGenome.fa.rpac
# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indices/simulatedReferenceGenome.fa.rsa
# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indices/simulatedReferenceGenome.fa.sa
# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indices/visualization.txt
# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/intervals/#simulated_baits.interval_list#
# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/intervals/simulated_baits.interval_list
# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/intervals/simulated_baits_hg19_simulatedReferenceGenome.bed
# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/intervals/simulated_targets.interval_list
# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/intervals/simulated_targets_hg19_simulatedReferenceGenome.bed
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/Aligner.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/AnalyzeCovariates.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/CountRecords.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/GenomeAnalysisTK.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/IndexToTable.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/Jama-1.0.2.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/StingUtils.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/activation-1.1.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/annotations-1.3.2.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/aopalliance-1.0.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/bcel-5.2.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/bsh-2.0b4.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/colt-1.2.0.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/commons-email-1.2.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/commons-io-2.0.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/commons-jexl-2.0.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/commons-lang-2.5.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/commons-logging-1.1.1.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/concurrent-1.3.4.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/dom4j-1.6.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/google-collections-1.0.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/gson-1.4.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/guice-2.0.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/jakarta-regexp-1.4.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/javassist-3.7.ga.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/javassist-3.8.0.GA.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/jcommander-1.7.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/jgrapht-jdk1.5-0.7.3.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/jna-3.2.7.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/jsr305-1.3.2.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/junit-3.8.1.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/lucene-core-3.0.3.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/mail-1.4.1.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/picard-1.37.686.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/picard-private-parts-1702.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/reflections-0.9.5-RC2.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/sam-1.37.686.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/scala-compiler-2.8.1.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/scala-library-2.8.1.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/simple-xml-2.0.4.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/slf4j-api-1.5.0.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/snakeyaml-1.7.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/stax-1.2.0.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/stax-api-1.0.1.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/testng-5.14.1.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/testng-5.5-jdk15.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/tribble-0.1.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/xml-apis-1.0.b2.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/LICENSE
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/build.xml
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/Aligner.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/AnalyzeCovariates.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/GenomeAnalysisTK.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/Jama-1.0.2.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/StingUtils.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/activation-1.1.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/asm-all-3.3.1.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/bcel-5.2.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/cofoja-1.0-20110609.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/colt-1.2.0.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/commons-codec-1.5.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/commons-email-1.2.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/commons-httpclient-3.1.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/commons-io-2.0.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/commons-jexl-2.0.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/commons-lang-2.5.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/commons-logging-1.1.1.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/commons-math-2.2.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/concurrent-1.3.4.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/dom4j-1.6.1.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/drmaa-6.2u5p2.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/freemarker-2.3.18.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/google-collections-1.0.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/gson-1.4.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/jakarta-regexp-1.4.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/java-xmlbuilder-0.4.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/javassist-3.7.ga.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/javassist-3.8.0.GA.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/jets3t-0.8.0.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/jgrapht-jdk1.5-0.7.3.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/jna-3.2.7.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/lucene-core-3.0.3.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/mail-1.4.4.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/picard-1.55.985.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/picard-private-parts-2068.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/poi-3.8-beta3.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/poi-ooxml-3.8-beta3.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/poi-ooxml-schemas-3.8-beta3.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/reflections-0.9.5-RC2.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/sam-1.55.985.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/scala-compiler-2.8.1.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/scala-library-2.8.1.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/simple-xml-2.0.4.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/slf4j-api-1.5.0.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/snakeyaml-1.7.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/snpeff-2.0.2.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/stax-1.2.0.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/stax-api-1.0.1.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/tribble-40.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/vcf.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/xml-apis-1.0.b2.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/xmlbeans-2.3.0.jar
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/DESCRIPTION
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/INDEX
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/Meta/Rd.rds
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/Meta/data.rds
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/Meta/hsearch.rds
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/Meta/links.rds
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/Meta/package.rds
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/NAMESPACE
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/R/gsalib
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/R/gsalib.rdb
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/R/gsalib.rdx
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/data/tearsheetdrop.jpg
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/gsalib/DESCRIPTION
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/gsalib/INDEX
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/gsalib/Meta/Rd.rds
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# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/BWAAligner.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/BWAConfiguration.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/c/BWAPath.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentState.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/java/LowerBound.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/package-info.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/AMBWriter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/ANNWriter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTSupplementaryFileGenerator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SequenceBlock.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/packing/CreatePACFromReference.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedInputStream.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedOutputStream.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalysisDataManager.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/analyzecovariates/package-info.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/Advanced.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/Argument.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentCollection.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinition.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentException.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentIOType.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentMatch.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentMatchSite.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentMatchSource.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentMatchSourceType.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentMatches.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ClassType.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/EnumerationArgumentDefault.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/Gather.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/Gatherer.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/Hidden.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/Input.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/IntervalBinding.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/MissingArgumentValueException.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/Output.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/RodBinding.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/Tags.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/package-info.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/DownsampleType.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/DownsamplingMethod.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/ReadProperties.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/arguments/ValidationExclusion.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/package-info.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusView.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/InvalidPositionException.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RODMetaDataContainer.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedView.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/View.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/package-info.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMBlockStartIterator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMIndexContent.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMOverlap.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShardStrategy.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShard.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShardStrategy.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardStrategy.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReaderBin.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderID.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/Shard.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardStrategy.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardStrategyFactory.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/package-info.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/FindLargeShards.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBAMRegion.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/UnzipSingleBlock.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/package-info.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/package-info.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/DataStreamSegment.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/EntireStream.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/MappedStreamSegment.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPool.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataSource.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/package-info.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/examples/GATKDocsExample.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroSchedulerMBean.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/MicroSchedulerMBean.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/OutputMergeTask.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/ReduceTree.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/package-info.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckFilter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityFilter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableFilter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityZeroFilter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/MateSameStrandFilter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentFilter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilterHelper.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/ReadNameFilter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/ReassignMappingQualityFilter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/package-info.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/DirectOutputTracker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/storage/Storage.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/stubs/Stub.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/DownsampleIterator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/GenomeLocusIterator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/IterableIterator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIterator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/NullSAMIterator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/PeekingIterator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/PositionTrackingIterator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/PushbackIterator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/package-info.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/package-info.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/ReadMetaDataTracker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceDependentFeatureCodec.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedDatum.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/SelfScopingFeatureCodec.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/package-info.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/IndexDictionaryUtils.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/FlashBackIterator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/RMDTriplet.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/RODRecordList.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumn.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumns.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportVersion.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/samples/Affection.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/samples/Gender.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/samples/PedReader.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/samples/PedigreeValidationType.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/samples/Sample.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDBBuilder.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/traversals/package-info.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Allows.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Attribution.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/BAQMode.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/By.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/DataSource.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Downsample.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/DuplicateWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Multiplex.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Multiplexer.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/PartitionBy.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/PartitionType.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/RMD.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadFilters.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadPairWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/RefWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Reference.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Requires.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/RodWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/TreeReducible.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/WalkerName.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Window.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatibleWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByIntervalWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStatsWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BaseMismatchModel.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BiallelicGenotypeLikelihoods.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidIndelGenotypePriors.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypePriors.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypePriors.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiallelicGenotypeLikelihoods.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SAMRecordCoordinateComparatorWithUnmappedReads.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/package-info.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CloneableIteratorLinkedList.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/Haplotype.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraph.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraphEdge.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBase.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBasesAtPosition.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/RefSeqDataParser.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMalesWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRefWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/DocumentationTest.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesGatherer.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/Covariate.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/Dinuc.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/GCContentCovariate.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/HomopolymerCovariate.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MappingQualityCovariate.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PositionCovariate.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PrimerRoundCovariate.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/QualityScoreCovariate.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ReadGroupCovariate.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDatum.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDatumOptimized.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PhaseStats.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java
# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java