## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[./pipeline_output_destplus/US_Lou_Wes_1_2013-09-15/US_Lou_Wes_1_2013-09-15.sorted_merged.bam] OUTPUT=./pipeline_output_destplus/US_Lou_Wes_1_2013-09-15/US_Lou_Wes_1_2013-09-15.dedup.bam METRICS_FILE=./pipeline_output_destplus/US_Lou_Wes_1_2013-09-15/US_Lou_Wes_1_2013-09-15.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: Fri Jan 13 21:08:30 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	51579	2223566	0	0	4631	98839	0	0.04497	24264799

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	2007920	2007920
2.0	1.912436	93326	93326
3.0	2.744975	2530	2530
4.0	3.504614	90	90
5.0	4.197735	19	19
6.0	4.830164	7	7
7.0	5.407214	1	1
8.0	5.933736	2	2
9.0	6.414154	0	0
10.0	6.852503	2	2
11.0	7.25247	0	0
12.0	7.617413	0	0
13.0	7.950401	1	1
14.0	8.25423	0	0
15.0	8.531456	0	0
16.0	8.784406	0	0
17.0	9.015207	0	0
18.0	9.225798	0	0
19.0	9.417948	0	0
20.0	9.593273	0	0
21.0	9.753246	0	0
22.0	9.899211	0	0
23.0	10.032395	1	1
24.0	10.153917	0	0
25.0	10.264798	0	0
26.0	10.365969	0	0
27.0	10.458282	0	0
28.0	10.542511	0	0
29.0	10.619365	0	0
30.0	10.689489	0	0
31.0	10.753473	0	0
32.0	10.811854	0	0
33.0	10.865123	0	0
34.0	10.913727	0	0
35.0	10.958076	0	0
36.0	10.998541	0	0
37.0	11.035463	0	0
38.0	11.069152	0	0
39.0	11.099891	0	0
40.0	11.127938	0	0
41.0	11.153529	0	0
42.0	11.17688	0	0
43.0	11.198185	0	0
44.0	11.217626	0	0
45.0	11.235364	0	0
46.0	11.251548	0	0
47.0	11.266316	0	0
48.0	11.27979	0	0
49.0	11.292085	0	0
50.0	11.303303	0	0
51.0	11.313538	0	0
52.0	11.322878	0	0
53.0	11.331399	0	0
54.0	11.339175	0	0
55.0	11.346269	0	0
56.0	11.352743	0	0
57.0	11.358649	0	0
58.0	11.364038	0	0
59.0	11.368956	0	0
60.0	11.373443	0	0
61.0	11.377537	0	0
62.0	11.381272	0	0
63.0	11.38468	0	0
64.0	11.38779	0	0
65.0	11.390628	0	0
66.0	11.393217	0	0
67.0	11.395579	0	0
68.0	11.397735	0	0
69.0	11.399702	0	0
70.0	11.401496	0	0
71.0	11.403134	0	0
72.0	11.404628	0	0
73.0	11.405991	0	0
74.0	11.407235	0	0
75.0	11.40837	0	0
76.0	11.409405	0	0
77.0	11.41035	0	0
78.0	11.411212	0	0
79.0	11.411999	0	0
80.0	11.412717	0	0
81.0	11.413372	0	0
82.0	11.413969	0	0
83.0	11.414515	0	0
84.0	11.415012	0	0
85.0	11.415466	0	0
86.0	11.41588	0	0
87.0	11.416258	0	0
88.0	11.416603	0	0
89.0	11.416918	0	0
90.0	11.417205	0	0
91.0	11.417467	0	0
92.0	11.417706	0	0
93.0	11.417924	0	0
94.0	11.418123	0	0
95.0	11.418304	0	0
96.0	11.41847	0	0
97.0	11.418621	0	0
98.0	11.418759	0	0
99.0	11.418885	0	0
100.0	11.419	0	0