#!/usr/bin/env python # -*- coding: utf-8 -*- """ Constants specific for RQC ReadQC pipeline (Illumina). Global constants are defined in a file under the directory lib/rqc_constants.py . Created: 7.29.2013 sulsj (ssul@lbl.gov) """ import os # from rqc_constants import * from common import get_run_path # from os_utility import get_tool_path # RQCReadQcConfig, RQCReadQc, ReadqcStats, RQCReadQcCommands # global configuration variables class RQCReadQcConfig: CFG = {} CFG["output_path"] = "" CFG["status_file"] = "" CFG["files_file"] = "" CFG["stats_file"] = "" CFG["log_file"] = "" CFG["no_cleanup"] = "" CFG["run_path"] = "" # ReadQC constants class RQCReadQc: ILLUMINA_SAMPLE_COUNT = 50000 ## Used in STEP13 ILLUMINA_SAMPLE_PERCENTAGE = 0.01 ## Used in STEP1 and STEP13 ILLUMINA_MER_SAMPLE_MER_SIZE = 25 ## Used in STEP2 (20 ==> 25 RQC-823 08102016) ILLUMINA_MER_SAMPLE_REPORT_FRQ = 25000 ## Used in STEP2 for mer sampling ILLUMINA_MIN_NUM_READS = 1000 ## Used in STEP1 to check min number of reads needed for processing #Reference databases class RQCReadQcReferenceDatabases: ## STEP10 ARTIFACT_FILE = "/global/dna/shared/rqc/ref_databases/qaqc/databases/illumina.artifacts/Illumina.artifacts.2012.04.fa" ## STEP12 for bbduk SCICLONE_RNA2 = "/global/projectb/sandbox/gaag/bbtools/data/sciclone_rna.fa" SCICLONE_DNA2 = "/global/projectb/sandbox/gaag/bbtools/data/sciclone_dna.fa" ## STEP17 END_OF_READ_ILLUMINA_ADAPTER_CHECK_DB = "/global/dna/shared/rqc/ref_databases/qaqc/databases/Artifacts.adapters_primers_only.fa" class RQCContamDb: # ARTIFACT_FILE_NO_SPIKEIN = '/global/dna/shared/rqc/ref_databases/qaqc/databases/illumina.artifacts/Illumina.artifacts.2012.10.no_DNA_RNA_spikeins.fa' #this db includes no DNA/RNA spike-in sequences ARTIFACT_FILE_NO_SPIKEIN = '/global/dna/shared/rqc/ref_databases/qaqc/databases/illumina.artifacts/Illumina.artifacts.2013.12.no_DNA_RNA_spikeins.fa' ARTIFACT_FILE_DNA_SPIKEIN = '/global/dna/shared/rqc/ref_databases/qaqc/databases/illumina.artifacts/DNA_spikeins.artifacts.2012.10.fa.bak' #this db has just DNA spike-in sequences ARTIFACT_FILE_RNA_SPIKEIN = '/global/dna/shared/rqc/ref_databases/qaqc/databases/illumina.artifacts/RNA_spikeins.artifacts.2012.10.NoPolyA.fa' #this db has just RNA spike-in sequences CONTAMINANTS = '/global/dna/shared/rqc/ref_databases/qaqc/databases/JGIContaminants.fa' ## '/home/blast_db2_admin/qaqc_db/2010-11-19/JGIContaminants.fa' FOSMID_VECTOR = '/global/dna/shared/rqc/ref_databases/qaqc/databases/pCC1Fos.ref.fa' PHIX = '/global/dna/shared/rqc/ref_databases/qaqc/databases/phix174_ill.ref.fa' GENERAL_RRNA_FILE = '/global/dna/shared/rqc/ref_databases/qaqc/databases/rRNA.fa' ## including Chlamy CHLOROPLAST_NCBI_REFSEQ = '/global/dna/shared/rqc/ref_databases/ncbi/CURRENT/refseq.plastid/refseq.plastid' MITOCHONDRION_NCBI_REFSEQ = '/global/dna/shared/rqc/ref_databases/ncbi/CURRENT/refseq.mitochondrion/refseq.mitochondrion' MICROBES = "/global/projectb/sandbox/gaag/bbtools/commonMicrobes/fusedERPBBmasked.fa.gz" ## non-synthetic contaminants SYNTHETIC = "/global/projectb/sandbox/gaag/bbtools/data/Illumina.artifacts.2013.12.no_DNA_RNA_spikeins.fa.gz" ## synthetic contaminants ADAPTERS = "/global/projectb/sandbox/gaag/bbtools/data/adapters.fa" ILLUMINA_READ_PERCENT_CONTAMINATION_ARTIFACT = "illumina read percent contamination artifact" ILLUMINA_READ_PERCENT_CONTAMINATION_ARTIFACT_50BP = "illumina read percent contamination artifact 50bp" ## 20131203 Added for 50bp contam ILLUMINA_READ_PERCENT_CONTAMINATION_ARTIFACT_20BP = "illumina read percent contamination artifact 20bp" ## 11092015 Added for 20bp contam for smRNA ILLUMINA_READ_PERCENT_CONTAMINATION_DNA_SPIKEIN = "illumina read percent contamination DNA spikein" ILLUMINA_READ_PERCENT_CONTAMINATION_RNA_SPIKEIN = "illumina read percent contamination RNA spikein" ILLUMINA_READ_PERCENT_CONTAMINATION_CONTAMINANTS = "illumina read percent contamination contaminants" # ILLUMINA_READ_PERCENT_CONTAMINATION_ECOLI_COMBINED = "illumina read percent contamination ecoli combined" ILLUMINA_READ_PERCENT_CONTAMINATION_FOSMID = "illumina read percent contamination fosmid" ILLUMINA_READ_PERCENT_CONTAMINATION_MITOCHONDRION = "illumina read percent contamination mitochondrion" ILLUMINA_READ_PERCENT_CONTAMINATION_PHIX = "illumina read percent contamination phix" ILLUMINA_READ_PERCENT_CONTAMINATION_PLASTID = "illumina read percent contamination plastid" ILLUMINA_READ_PERCENT_CONTAMINATION_RRNA = "illumina read percent contamination rrna" ILLUMINA_READ_PERCENT_CONTAMINATION_MICROBES = "illumina read percent contamination microbes" ## non-synthetic ILLUMINA_READ_PERCENT_CONTAMINATION_SYNTH = "illumina read percent contamination adapters" ILLUMINA_READ_PERCENT_CONTAMINATION_ADAPTERS = "illumina read percent contamination adapters" CONTAM_DBS = {} CONTAM_DBS['artifact'] = ARTIFACT_FILE_NO_SPIKEIN CONTAM_DBS['artifact_50bp'] = ARTIFACT_FILE_NO_SPIKEIN ## 20131203 Added for 50bp contam CONTAM_DBS['DNA_spikein'] = ARTIFACT_FILE_DNA_SPIKEIN CONTAM_DBS['RNA_spikein'] = ARTIFACT_FILE_RNA_SPIKEIN CONTAM_DBS['contaminants'] = CONTAMINANTS # CONTAM_DBS['ecoli_combined'] = ECOLI_COMBINED CONTAM_DBS['fosmid'] = FOSMID_VECTOR CONTAM_DBS['mitochondrion'] = MITOCHONDRION_NCBI_REFSEQ CONTAM_DBS['phix'] = PHIX CONTAM_DBS['plastid'] = CHLOROPLAST_NCBI_REFSEQ CONTAM_DBS['rrna'] = GENERAL_RRNA_FILE CONTAM_DBS['microbes'] = MICROBES ## non-synthetic CONTAM_DBS['synthetic'] = SYNTHETIC CONTAM_DBS['adapters'] = ADAPTERS CONTAM_KEYS = {} CONTAM_KEYS['artifact'] = ILLUMINA_READ_PERCENT_CONTAMINATION_ARTIFACT CONTAM_KEYS['artifact_50bp'] = ILLUMINA_READ_PERCENT_CONTAMINATION_ARTIFACT_50BP ## 12032013 Added for 50bp contam CONTAM_KEYS['artifact_20bp'] = ILLUMINA_READ_PERCENT_CONTAMINATION_ARTIFACT_20BP ## 11092015 Added for 20bp contam for smRNA CONTAM_KEYS['DNA_spikein'] = ILLUMINA_READ_PERCENT_CONTAMINATION_DNA_SPIKEIN CONTAM_KEYS['RNA_spikein'] = ILLUMINA_READ_PERCENT_CONTAMINATION_RNA_SPIKEIN CONTAM_KEYS['contaminants'] = ILLUMINA_READ_PERCENT_CONTAMINATION_CONTAMINANTS # CONTAM_KEYS['ecoli_combined'] = ILLUMINA_READ_PERCENT_CONTAMINATION_ECOLI_COMBINED CONTAM_KEYS['fosmid'] = ILLUMINA_READ_PERCENT_CONTAMINATION_FOSMID CONTAM_KEYS['mitochondrion'] = ILLUMINA_READ_PERCENT_CONTAMINATION_MITOCHONDRION CONTAM_KEYS['phix'] = ILLUMINA_READ_PERCENT_CONTAMINATION_PHIX CONTAM_KEYS['plastid'] = ILLUMINA_READ_PERCENT_CONTAMINATION_PLASTID CONTAM_KEYS['rrna'] = ILLUMINA_READ_PERCENT_CONTAMINATION_RRNA CONTAM_KEYS['microbes'] = ILLUMINA_READ_PERCENT_CONTAMINATION_MICROBES ## non-synthetic CONTAM_KEYS['synthetic'] = ILLUMINA_READ_PERCENT_CONTAMINATION_SYNTH CONTAM_KEYS['adapters'] = ILLUMINA_READ_PERCENT_CONTAMINATION_ADAPTERS ## Constants for reporting class ReadqcStats: ILLUMINA_READ_Q20_READ1 = "read q20 read1" ILLUMINA_READ_Q20_READ2 = "read q20 read2" ILLUMINA_READ_QHIST_TEXT = "read qhist text" ILLUMINA_READ_QHIST_PLOT = "read qhist plot" ILLUMINA_READ_QHIST_D3_HTML_PLOT = "ILLUMINA_READ_QHIST_D3_HTML_PLOT" ILLUMINA_READ_QUAL_POS_PLOT_1 = "read qual pos plot 1" ILLUMINA_READ_QUAL_POS_PLOT_2 = "read qual pos plot 2" ILLUMINA_READ_QUAL_POS_PLOT_MERGED = "read qual pos plot merged" ILLUMINA_READ_QUAL_POS_PLOT_MERGED_D3_HTML_PLOT = "ILLUMINA_READ_QUAL_POS_PLOT_MERGED_D3_HTML_PLOT" ILLUMINA_READ_QUAL_POS_QRPT_1 = "read qual pos qrpt 1" ILLUMINA_READ_QUAL_POS_QRPT_2 = "read qual pos qrpt 2" ILLUMINA_READ_QUAL_POS_QRPT_MERGED = "ILLUMINA_READ_QUAL_POS_QRPT_MERGED" ILLUMINA_READ_QUAL_POS_QRPT_BOXPLOT_1 = "ILLUMINA_READ_QUAL_POS_QRPT_BOXPLOT_1" ILLUMINA_READ_QUAL_POS_QRPT_BOXPLOT_2 = "ILLUMINA_READ_QUAL_POS_QRPT_BOXPLOT_2" ILLUMINA_READ_QUAL_POS_QRPT_D3_HTML_BOXPLOT_1 = "ILLUMINA_READ_QUAL_POS_QRPT_D3_HTML_BOXPLOT_1" ILLUMINA_READ_QUAL_POS_QRPT_D3_HTML_BOXPLOT_2 = "ILLUMINA_READ_QUAL_POS_QRPT_D3_HTML_BOXPLOT_2" ILLUMINA_READ_QUAL_POS_QRPT_BOXPLOT_TEXT = "ILLUMINA_READ_QUAL_POS_QRPT_BOXPLOT_TEXT" ILLUMINA_READ_BASE_COUNT_TEXT_1 = "read base count text 1" ILLUMINA_READ_BASE_COUNT_TEXT_2 = "read base count text 2" ILLUMINA_READ_BASE_COUNT_PLOT_1 = "read base count plot 1" ILLUMINA_READ_BASE_COUNT_PLOT_2 = "read base count plot 2" ILLUMINA_READ_BASE_COUNT_D3_HTML_PLOT_1 = "ILLUMINA_READ_BASE_COUNT_D3_HTML_PLOT_1" # cyclone nucleotide comp plot ILLUMINA_READ_BASE_COUNT_D3_HTML_PLOT_2 = "ILLUMINA_READ_BASE_COUNT_D3_HTML_PLOT_2" # cyclone nucleotide comp plot ILLUMINA_READ_BASE_PERCENTAGE_TEXT_1 = "read base percentage text 1" ILLUMINA_READ_BASE_PERCENTAGE_TEXT_2 = "read base percentage text 2" ILLUMINA_READ_BASE_PERCENTAGE_PLOT_1 = "read base percentage plot 1" ILLUMINA_READ_BASE_PERCENTAGE_PLOT_2 = "read base percentage plot 2" ILLUMINA_READ_BASE_PERCENTAGE_D3_HTML_PLOT_1 = "ILLUMINA_READ_BASE_PERCENTAGE_D3_HTML_PLOT_1" ILLUMINA_READ_BASE_PERCENTAGE_D3_HTML_PLOT_2 = "ILLUMINA_READ_BASE_PERCENTAGE_D3_HTML_PLOT_2" ILLUMINA_READ_20MER_SAMPLE_SIZE = "read 20mer sample size" ILLUMINA_READ_20MER_PERCENTAGE_STARTING_MERS = "read 20mer percentage starting mers" ILLUMINA_READ_20MER_PERCENTAGE_RANDOM_MERS = "read 20mer percentage random mers" ILLUMINA_READ_20MER_UNIQUENESS_TEXT = "read 20mer uniqueness text" ILLUMINA_READ_20MER_UNIQUENESS_PLOT = "read 20mer uniqueness plot" ILLUMINA_READ_BWA_ALIGNED = "read bwa aligned" ILLUMINA_READ_BWA_ALIGNED_DUPLICATE = "read bwa aligned duplicate" ILLUMINA_READ_BWA_ALIGNED_DUPLICATE_PERCENT = "read bwa aligned duplicate percent" ILLUMINA_READ_N_FREQUENCE = "read N frequence" ILLUMINA_READ_N_PATTERN = "read N pattern" ILLUMINA_READ_GC_MEAN = "read GC mean" ILLUMINA_READ_GC_STD = "read GC std" ILLUMINA_READ_GC_MED = "read GC median" ILLUMINA_READ_GC_MODE = "read GC mode" ILLUMINA_READ_GC_PLOT = "read GC plot" ILLUMINA_READ_GC_D3_HTML_PLOT = "ILLUMINA_READ_GC_D3_HTML_PLOT" ILLUMINA_READ_GC_TEXT = "read GC text hist" ILLUMINA_READ_LENGTH_1 = "read length 1" ILLUMINA_READ_LENGTH_2 = "read length 2" ILLUMINA_READ_BASE_COUNT = "read base count" ILLUMINA_READ_COUNT = "read count" ILLUMINA_READ_TOPHIT_FILE = "read tophit file of" ILLUMINA_READ_TOP100HIT_FILE = "read top100hit file of" ILLUMINA_READ_TAXLIST_FILE = "read taxlist file of" ILLUMINA_READ_TAX_SPECIES = "read tax species of" ILLUMINA_READ_TOP_HITS = "read top hits of" ILLUMINA_READ_TOP_100HITS = "read top 100 hits of" ILLUMINA_READ_PARSED_FILE = "read parsed file of" ILLUMINA_READ_MATCHING_HITS = "read matching hits of" ILLUMINA_READS_NUMBER = "reads number" ILLUMINA_READ_DEMULTIPLEX_STATS = "demultiplex stats" ILLUMINA_READ_DEMULTIPLEX_STATS_PLOT = "demultiplex stats plot" ILLUMINA_READ_DEMULTIPLEX_STATS_D3_HTML_PLOT = "ILLUMINA_READ_DEMULTIPLEX_STATS_D3_HTML_PLOT" ILLUMINA_READ_BASE_QUALITY_STATS = "read base quality stats" ILLUMINA_READ_BASE_QUALITY_STATS_PLOT = "read base quality stats plot" ILLUMINA_READ_PERCENT_CONTAMINATION_ARTIFACT = "illumina read percent contamination artifact" ILLUMINA_READ_PERCENT_CONTAMINATION_ARTIFACT_50BP = "illumina read percent contamination artifact 50bp" ## 20131203 Added for 50bp contam ILLUMINA_READ_PERCENT_CONTAMINATION_ARTIFACT_20BP = "illumina read percent contamination artifact 20bp" ## 11092015 Added for 20bp contam for smRNA ILLUMINA_READ_PERCENT_CONTAMINATION_DNA_SPIKEIN = "illumina read percent contamination DNA spikein" ILLUMINA_READ_PERCENT_CONTAMINATION_RNA_SPIKEIN = "illumina read percent contamination RNA spikein" ILLUMINA_READ_PERCENT_CONTAMINATION_CONTAMINANTS = "illumina read percent contamination contaminants" ILLUMINA_READ_PERCENT_CONTAMINATION_ECOLI_B = "illumina read percent contamination ecoli b" ILLUMINA_READ_PERCENT_CONTAMINATION_ECOLI_K12 = "illumina read percent contamination ecoli k12" # ILLUMINA_READ_PERCENT_CONTAMINATION_ECOLI_COMBINED = "illumina read percent contamination ecoli combined" ILLUMINA_READ_PERCENT_CONTAMINATION_FOSMID = "illumina read percent contamination fosmid" ILLUMINA_READ_PERCENT_CONTAMINATION_MITOCHONDRION = "illumina read percent contamination mitochondrion" ILLUMINA_READ_PERCENT_CONTAMINATION_PLASTID = "illumina read percent contamination plastid" ILLUMINA_READ_PERCENT_CONTAMINATION_PHIX = "illumina read percent contamination phix" ILLUMINA_READ_PERCENT_CONTAMINATION_RRNA = "illumina read percent contamination rrna" ILLUMINA_READ_SCICLONE_DNA_COUNT_FILE = "illumina read sciclone DNA count file" ILLUMINA_READ_SCICLONE_RNA_COUNT_FILE = "illumina read sciclone RNA count file" ILLUMINA_READ_SCICLONE_RNA_COUNT_TOTAL = "ILLUMINA_READ_SCICLONE_RNA_COUNT_TOTAL" ILLUMINA_READ_SCICLONE_RNA_COUNT_MATCHED = "ILLUMINA_READ_SCICLONE_RNA_COUNT_MATCHED" ILLUMINA_READ_SCICLONE_RNA_COUNT_MATCHED_PERC = "ILLUMINA_READ_SCICLONE_RNA_COUNT_MATCHED_PERC" ILLUMINA_READ_SCICLONE_DNA_COUNT_TOTAL = "ILLUMINA_READ_SCICLONE_DNA_COUNT_TOTAL" ILLUMINA_READ_SCICLONE_DNA_COUNT_MATCHED = "ILLUMINA_READ_SCICLONE_DNA_COUNT_MATCHED" ILLUMINA_READ_SCICLONE_DNA_COUNT_MATCHED_PERC = "ILLUMINA_READ_SCICLONE_DNA_COUNT_MATCHED_PERC" ILLUMINA_BASE_Q30 = 'base Q30' ILLUMINA_BASE_Q25 = 'base Q25' ILLUMINA_BASE_Q20 = 'base Q20' ILLUMINA_BASE_Q15 = 'base Q15' ILLUMINA_BASE_Q10 = 'base Q10' ILLUMINA_BASE_Q5 = 'base Q5' ILLUMINA_BASE_C30 = 'base C30' ILLUMINA_BASE_C25 = 'base C25' ILLUMINA_BASE_C20 = 'base C20' ILLUMINA_BASE_C15 = 'base C15' ILLUMINA_BASE_C10 = 'base C10' ILLUMINA_BASE_C5 = 'base C5' ILLUMINA_READ_Q30 = 'read Q30' ILLUMINA_READ_Q25 = 'read Q25' ILLUMINA_READ_Q20 = 'read Q20' ILLUMINA_READ_Q15 = 'read Q15' ILLUMINA_READ_Q10 = 'read Q10' ILLUMINA_READ_Q5 = 'read Q5' ILLUMINA_BASE_Q30_SCORE_MEAN = 'Q30 bases Q score mean' ILLUMINA_BASE_Q30_SCORE_STD = 'Q30 bases Q score std' ILLUMINA_BASE_OVERALL_BASES_Q_SCORE_MEAN = 'overall bases Q score mean' ILLUMINA_BASE_OVERALL_BASES_Q_SCORE_STD = 'overall bases Q score std' ## read qc step 1 ILLUMINA_TOO_SMALL_NUM_READS = "ILLUMINA_TOO_SMALL_NUM_READS" ## flag to notify too low number of reads ## read qc step 2 ILLUMINA_READ_20MER_UNIQUENESS_D3_HTML_PLOT = "ILLUMINA_READ_20MER_UNIQUENESS_D3_HTML_PLOT" ## read qc step 13, 14, 15 ILLUMINA_SKIP_BLAST = "ILLUMINA_SKIP_BLAST" ## to record the blast step was skipped ## read qc step 17 ILLUMINA_READ_END_OF_READ_ADAPTER_CHECK_DATA = "ILLUMINA_READ_END_OF_READ_ADAPTER_CHECK_DATA" ILLUMINA_READ_END_OF_READ_ADAPTER_CHECK_PLOT = "ILLUMINA_READ_END_OF_READ_ADAPTER_CHECK_PLOT" ILLUMINA_READ_END_OF_READ_ADAPTER_CHECK_D3_HTML_PLOT = "ILLUMINA_READ_END_OF_READ_ADAPTER_CHECK_D3_HTML_PLOT" ## read qc step 18 ILLUMINA_READ_INSERT_SIZE_HISTO_PLOT = "ILLUMINA_READ_INSERT_SIZE_HISTO_PLOT" ILLUMINA_READ_INSERT_SIZE_HISTO_DATA = "ILLUMINA_READ_INSERT_SIZE_HISTO_DATA" ILLUMINA_READ_INSERT_SIZE_HISTO_D3_HTML_PLOT = "ILLUMINA_READ_INSERT_SIZE_HISTO_D3_HTML_PLOT" ILLUMINA_READ_INSERT_SIZE_TOTAL_TIME = "ILLUMINA_READ_INSERT_SIZE_TOTAL_TIME" ILLUMINA_READ_INSERT_SIZE_NUM_READS = "ILLUMINA_READ_INSERT_SIZE_NUM_READS" ILLUMINA_READ_INSERT_SIZE_JOINED_NUM = "ILLUMINA_READ_INSERT_SIZE_JOINED_NUM" ILLUMINA_READ_INSERT_SIZE_JOINED_PERC = "ILLUMINA_READ_INSERT_SIZE_JOINED_PERC" ILLUMINA_READ_INSERT_SIZE_AMBIGUOUS_NUM = "ILLUMINA_READ_INSERT_SIZE_AMBIGUOUS_NUM" ILLUMINA_READ_INSERT_SIZE_AMBIGUOUS_PERC = "ILLUMINA_READ_INSERT_SIZE_AMBIGUOUS_PERC" ILLUMINA_READ_INSERT_SIZE_NO_SOLUTION_NUM = "ILLUMINA_READ_INSERT_SIZE_NO_SOLUTION_NUM" ILLUMINA_READ_INSERT_SIZE_NO_SOLUTION_PERC = "ILLUMINA_READ_INSERT_SIZE_NO_SOLUTION_PERC" ILLUMINA_READ_INSERT_SIZE_TOO_SHORT_NUM = "ILLUMINA_READ_INSERT_SIZE_TOO_SHORT_NUM" ILLUMINA_READ_INSERT_SIZE_TOO_SHORT_PERC = "ILLUMINA_READ_INSERT_SIZE_TOO_SHORT_PERC" ILLUMINA_READ_INSERT_SIZE_AVG_INSERT = "ILLUMINA_READ_INSERT_SIZE_AVG_INSERT" ILLUMINA_READ_INSERT_SIZE_STD_INSERT = "ILLUMINA_READ_INSERT_SIZE_STD_INSERT" ILLUMINA_READ_INSERT_SIZE_MODE_INSERT = "ILLUMINA_READ_INSERT_SIZE_MODE_INSERT" ILLUMINA_READ_INSERT_SIZE_INSERT_RANGE_START = "ILLUMINA_READ_INSERT_SIZE_INSERT_RANGE_START" ILLUMINA_READ_INSERT_SIZE_INSERT_RANGE_END = "ILLUMINA_READ_INSERT_SIZE_INSERT_RANGE_END" ILLUMINA_READ_INSERT_SIZE_90TH_PERC = "ILLUMINA_READ_INSERT_SIZE_90TH_PERC" ILLUMINA_READ_INSERT_SIZE_50TH_PERC = "ILLUMINA_READ_INSERT_SIZE_50TH_PERC" ILLUMINA_READ_INSERT_SIZE_10TH_PERC = "ILLUMINA_READ_INSERT_SIZE_10TH_PERC" ILLUMINA_READ_INSERT_SIZE_75TH_PERC = "ILLUMINA_READ_INSERT_SIZE_75TH_PERC" ILLUMINA_READ_INSERT_SIZE_25TH_PERC = "ILLUMINA_READ_INSERT_SIZE_25TH_PERC" ## step 19 GC_DIVERGENCE_CSV_FILE = "GC_DIVERGENCE_CSV_FILE" GC_DIVERGENCE_PLOT_FILE = "GC_DIVERGENCE_PLOT_FILE" GC_DIVERGENCE_COEFFICIENTS_CSV_FILE = "GC_DIVERGENCE_COEFFICIENTS_CSV_FILE" #GC_DIVERGENCE_VAL = "GC_DIVERGENCE_VAL" GC_DIVERGENCE_COEFF_R1_AT = "GC_DIVERGENCE_COEFF_R1_AT" GC_DIVERGENCE_COEFF_R1_ATCG = "GC_DIVERGENCE_COEFF_R1_ATCG" GC_DIVERGENCE_COEFF_R1_CG = "GC_DIVERGENCE_COEFF_R1_CG" GC_DIVERGENCE_COEFF_R2_AT = "GC_DIVERGENCE_COEFF_R2_AT" GC_DIVERGENCE_COEFF_R2_ATCG = "GC_DIVERGENCE_COEFF_R2_ATCG" GC_DIVERGENCE_COEFF_R2_CG = "GC_DIVERGENCE_COEFF_R2_CG" ## EOF