## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[./pipeline_output_destplus/AU_Que_Inn_3_2014-02-15/AU_Que_Inn_3_2014-02-15.sorted_merged.bam] OUTPUT=./pipeline_output_destplus/AU_Que_Inn_3_2014-02-15/AU_Que_Inn_3_2014-02-15.dedup.bam METRICS_FILE=./pipeline_output_destplus/AU_Que_Inn_3_2014-02-15/AU_Que_Inn_3_2014-02-15.mark_duplicates_report.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Sat Jan 14 01:43:04 UTC 2023

## METRICS CLASS	picard.sam.DuplicationMetrics
LIBRARY	UNPAIRED_READS_EXAMINED	READ_PAIRS_EXAMINED	SECONDARY_OR_SUPPLEMENTARY_RDS	UNMAPPED_READS	UNPAIRED_READ_DUPLICATES	READ_PAIR_DUPLICATES	READ_PAIR_OPTICAL_DUPLICATES	PERCENT_DUPLICATION	ESTIMATED_LIBRARY_SIZE
lib1	349143	14347938	0	0	200634	7226311	0	0.504502	8893416

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	903	903
2.0	1.199225	6748254	6748254
3.0	1.238915	55	55
4.0	1.246823	152401	152401
5.0	1.248398	17	17
6.0	1.248712	2964	2964
7.0	1.248774	6	6
8.0	1.248787	281	281
9.0	1.248789	3	3
10.0	1.24879	111	111
11.0	1.24879	3	3
12.0	1.24879	55	55
13.0	1.24879	0	0
14.0	1.24879	31	31
15.0	1.24879	0	0
16.0	1.24879	14	14
17.0	1.24879	0	0
18.0	1.24879	12	12
19.0	1.24879	3	3
20.0	1.24879	12	12
21.0	1.24879	0	0
22.0	1.24879	6	6
23.0	1.24879	0	0
24.0	1.24879	6	6
25.0	1.24879	0	0
26.0	1.24879	6	6
27.0	1.24879	0	0
28.0	1.24879	2	2
29.0	1.24879	0	0
30.0	1.24879	5	5
31.0	1.24879	0	0
32.0	1.24879	2	2
33.0	1.24879	0	0
34.0	1.24879	1	1
35.0	1.24879	0	0
36.0	1.24879	0	0
37.0	1.24879	0	0
38.0	1.24879	0	0
39.0	1.24879	0	0
40.0	1.24879	0	0
41.0	1.24879	0	0
42.0	1.24879	1	1
43.0	1.24879	0	0
44.0	1.24879	1	1
45.0	1.24879	1	1
46.0	1.24879	0	0
47.0	1.24879	0	0
48.0	1.24879	0	0
49.0	1.24879	0	0
50.0	1.24879	1	1
51.0	1.24879	0	0
52.0	1.24879	0	0
53.0	1.24879	0	0
54.0	1.24879	0	0
55.0	1.24879	0	0
56.0	1.24879	0	0
57.0	1.24879	0	0
58.0	1.24879	1	1
59.0	1.24879	0	0
60.0	1.24879	0	0
61.0	1.24879	0	0
62.0	1.24879	0	0
63.0	1.24879	0	0
64.0	1.24879	0	0
65.0	1.24879	0	0
66.0	1.24879	0	0
67.0	1.24879	0	0
68.0	1.24879	0	0
69.0	1.24879	0	0
70.0	1.24879	0	0
71.0	1.24879	0	0
72.0	1.24879	0	0
73.0	1.24879	0	0
74.0	1.24879	1	1
75.0	1.24879	0	0
76.0	1.24879	0	0
77.0	1.24879	0	0
78.0	1.24879	0	0
79.0	1.24879	0	0
80.0	1.24879	0	0
81.0	1.24879	0	0
82.0	1.24879	1	1
83.0	1.24879	0	0
84.0	1.24879	0	0
85.0	1.24879	0	0
86.0	1.24879	0	0
87.0	1.24879	0	0
88.0	1.24879	0	0
89.0	1.24879	0	0
90.0	1.24879	0	0
91.0	1.24879	0	0
92.0	1.24879	0	0
93.0	1.24879	0	0
94.0	1.24879	0	0
95.0	1.24879	0	0
96.0	1.24879	0	0
97.0	1.24879	0	0
98.0	1.24879	0	0
99.0	1.24879	0	0
100.0	1.24879	0	0