1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
|
#!/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
|
