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ref_files.txt
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/global/dna/shared/rqc/ref_databases/qaqc/databases/illumina.artifacts/Illumina.artifacts.2013.12.no_DNA_RNA_spikeins.fa
/global/dna/shared/rqc/ref_databases/qaqc/databases/illumina.artifacts/DNA_spikeins.artifacts.2012.10.fa
/global/dna/shared/rqc/ref_databases/qaqc/databases/phix174_ill.ref.fa
/global/dna/shared/rqc/ref_databases/qaqc/databases/lambda.fa.gz
/global/dna/shared/rqc/ref_databases/qaqc/databases/pJET1.2.fasta
private String mainArtifactFile = "/global/dna/shared/rqc/ref_databases/qaqc/databases/illumina.artifacts/Illumina.artifacts.2013.12.no_DNA_RNA_spikeins.fa";
private String artifactFileRna = "/global/dna/shared/rqc/ref_databases/qaqc/databases/illumina.artifacts/RNA_spikeins.artifacts.2012.10.NoPolyA.fa";
private String artifactFileDna = "/global/dna/shared/rqc/ref_databases/qaqc/databases/illumina.artifacts/DNA_spikeins.artifacts.2012.10.fa";
private String phixRef = "/global/dna/shared/rqc/ref_databases/qaqc/databases/phix174_ill.ref.fa";
private String lambdaRef = "/global/dna/shared/rqc/ref_databases/qaqc/databases/lambda.fa.gz";
private String pjetRef = "/global/dna/shared/rqc/ref_databases/qaqc/databases/pJET1.2.fasta";
private String allArtifactsLatest = "/global/projectb/sandbox/rqc/qcdb/illumina.artifacts/Illumina.artifacts.fa";
private String fragAdapters = "/global/projectb/sandbox/gaag/bbtools/data/adapters.fa";
private String rnaAdapter = "/global/projectb/sandbox/gaag/bbtools/data/truseq_rna.fa.gz";
private String indexPath = "/global/projectb/sandbox/gaag/bbtools/hg19/";
private String mapRef = null;