## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT DE-CTCF_R1.target.filtered.sorted.bam --OUTPUT DE-CTCF_R1.target.markdup.bam --METRICS_FILE DE-CTCF_R1.target.markdup.MarkDuplicates.metrics.txt --REMOVE_DUPLICATES false --ASSUME_SORT_ORDER coordinate --TMP_DIR tmp --VALIDATION_STRINGENCY LENIENT --REFERENCE_SEQUENCE GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna --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 --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --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 --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
## htsjdk.samtools.metrics.StringHeader
# Started on: Thu Jun 15 15:09:16 GMT 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
Unknown Library	0	9953349	0	0	0	302881	1440	0.03043	160944078

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.00014	9356826	0	9358142
2.0	1.940302	285033	1440	283838
3.0	2.824082	8192	0	8074
4.0	3.654862	321	0	318
5.0	4.43582	59	0	59
6.0	5.169944	15	0	15
7.0	5.860043	2	0	2
8.0	6.508756	8	0	8
9.0	7.118566	5	0	5
10.0	7.691806	4	0	4
11.0	8.230668	0	0	0
12.0	8.737215	2	0	2
13.0	9.213384	0	0	0
14.0	9.660998	0	0	0
15.0	10.081767	0	0	0
16.0	10.477304	0	0	0
17.0	10.84912	0	0	0
18.0	11.198638	0	0	0
19.0	11.527196	0	0	0
20.0	11.83605	0	0	0
21.0	12.126382	0	0	0
22.0	12.399302	0	0	0
23.0	12.655856	0	0	0
24.0	12.897024	0	0	0
25.0	13.123729	1	0	1
26.0	13.336839	0	0	0
27.0	13.537169	0	0	0
28.0	13.725485	0	0	0
29.0	13.902507	0	0	0
30.0	14.068914	0	0	0
31.0	14.225341	0	0	0
32.0	14.372387	0	0	0
33.0	14.510615	0	0	0
34.0	14.640553	0	0	0
35.0	14.762699	0	0	0
36.0	14.877519	0	0	0
37.0	14.985454	0	0	0
38.0	15.086916	0	0	0
39.0	15.182294	0	0	0
40.0	15.271951	0	0	0
41.0	15.356232	0	0	0
42.0	15.435459	0	0	0
43.0	15.509934	0	0	0
44.0	15.579943	0	0	0
45.0	15.645754	0	0	0
46.0	15.707618	0	0	0
47.0	15.765771	0	0	0
48.0	15.820438	0	0	0
49.0	15.871826	0	0	0
50.0	15.920132	0	0	0
51.0	15.965542	0	0	0
52.0	16.008228	0	0	0
53.0	16.048354	0	0	0
54.0	16.086074	0	0	0
55.0	16.121532	0	0	0
56.0	16.154864	0	0	0
57.0	16.186196	0	0	0
58.0	16.21565	0	0	0
59.0	16.243337	0	0	0
60.0	16.269364	0	0	0
61.0	16.29383	0	0	0
62.0	16.316828	0	0	0
63.0	16.338448	0	0	0
64.0	16.358771	0	0	0
65.0	16.377875	0	0	0
66.0	16.395834	0	0	0
67.0	16.412715	0	0	0
68.0	16.428585	0	0	0
69.0	16.443502	0	0	0
70.0	16.457525	0	0	0
71.0	16.470707	0	0	0
72.0	16.483098	0	0	0
73.0	16.494747	0	0	0
74.0	16.505696	0	0	0
75.0	16.51599	0	0	0
76.0	16.525665	0	0	0
77.0	16.534761	0	0	0
78.0	16.543311	0	0	0
79.0	16.551348	0	0	0
80.0	16.558904	0	0	0
81.0	16.566006	0	0	0
82.0	16.572682	0	0	0
83.0	16.578958	0	0	0
84.0	16.584858	0	0	0
85.0	16.590404	0	0	0
86.0	16.595617	0	0	0
87.0	16.600518	0	0	0
88.0	16.605124	0	0	0
89.0	16.609455	0	0	0
90.0	16.613525	0	0	0
91.0	16.617352	0	0	0
92.0	16.620949	0	0	0
93.0	16.62433	0	0	0
94.0	16.627509	0	0	0
95.0	16.630497	0	0	0
96.0	16.633306	0	0	0
97.0	16.635946	0	0	0
98.0	16.638428	0	0	0
99.0	16.640761	0	0	0
100.0	16.642955	0	0	0