## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[./pipeline_output_destplus/US_Rho_Pro_12_2015-06-11/US_Rho_Pro_12_2015-06-11.sorted_merged.bam] OUTPUT=./pipeline_output_destplus/US_Rho_Pro_12_2015-06-11/US_Rho_Pro_12_2015-06-11.dedup.bam METRICS_FILE=./pipeline_output_destplus/US_Rho_Pro_12_2015-06-11/US_Rho_Pro_12_2015-06-11.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 00:51:52 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	318482	9213992	0	0	33575	81202	0	0.010454	519680033

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	8827859	8827859
2.0	1.982426	68193	68193
3.0	2.947587	333	333
4.0	3.895787	94	94
5.0	4.827323	79	79
6.0	5.742488	73	73
7.0	6.64157	37	37
8.0	7.524852	45	45
9.0	8.392611	41	41
10.0	9.245121	36	36
11.0	10.082648	16	16
12.0	10.905457	17	17
13.0	11.713806	27	27
14.0	12.507949	22	22
15.0	13.288136	18	18
16.0	14.054612	26	26
17.0	14.807618	11	11
18.0	15.547391	11	11
19.0	16.274163	17	17
20.0	16.988163	12	12
21.0	17.689615	12	12
22.0	18.37874	12	12
23.0	19.055754	13	13
24.0	19.720871	10	10
25.0	20.374299	7	7
26.0	21.016244	13	13
27.0	21.646907	5	5
28.0	22.266487	3	3
29.0	22.875179	2	2
30.0	23.473173	5	5
31.0	24.060659	4	4
32.0	24.63782	4	4
33.0	25.204838	7	7
34.0	25.761891	6	6
35.0	26.309155	4	4
36.0	26.846801	1	1
37.0	27.374999	3	3
38.0	27.893914	1	1
39.0	28.40371	1	1
40.0	28.904547	6	6
41.0	29.396582	3	3
42.0	29.879971	2	2
43.0	30.354864	1	1
44.0	30.821411	0	0
45.0	31.27976	2	2
46.0	31.730053	0	0
47.0	32.172434	0	0
48.0	32.607039	3	3
49.0	33.034007	2	2
50.0	33.453472	3	3
51.0	33.865565	1	1
52.0	34.270416	4	4
53.0	34.668152	3	3
54.0	35.058898	4	4
55.0	35.442778	1	1
56.0	35.819911	2	2
57.0	36.190417	1	1
58.0	36.554411	1	1
59.0	36.912008	1	1
60.0	37.263321	1	1
61.0	37.608461	2	2
62.0	37.947534	0	0
63.0	38.280649	1	1
64.0	38.60791	0	0
65.0	38.92942	0	0
66.0	39.245279	0	0
67.0	39.555588	0	0
68.0	39.860443	0	0
69.0	40.15994	1	1
70.0	40.454175	1	1
71.0	40.743238	0	0
72.0	41.027222	0	0
73.0	41.306215	0	0
74.0	41.580305	0	0
75.0	41.849578	0	0
76.0	42.114119	0	0
77.0	42.374011	0	0
78.0	42.629335	1	1
79.0	42.880173	0	0
80.0	43.126602	0	0
81.0	43.368701	1	1
82.0	43.606545	0	0
83.0	43.840209	0	0
84.0	44.069767	0	0
85.0	44.29529	0	0
86.0	44.516851	1	1
87.0	44.734517	0	0
88.0	44.948359	0	0
89.0	45.158442	1	1
90.0	45.364833	0	0
91.0	45.567598	0	0
92.0	45.766798	0	0
93.0	45.962499	1	1
94.0	46.15476	0	0
95.0	46.343642	0	0
96.0	46.529205	1	1
97.0	46.711506	0	0
98.0	46.890604	0	0
99.0	47.066555	0	0
100.0	47.239413	0	0
103.0	0	1	1
108.0	0	1	1
111.0	0	1	1
113.0	0	1	1
148.0	0	1	1
275.0	0	1	1
498.0	0	1	1
612.0	0	1	1