## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[./pipeline_output_destplus/US_Lou_Wes_10_2013-09-15/US_Lou_Wes_10_2013-09-15.sorted_merged.bam] OUTPUT=./pipeline_output_destplus/US_Lou_Wes_10_2013-09-15/US_Lou_Wes_10_2013-09-15.dedup.bam METRICS_FILE=./pipeline_output_destplus/US_Lou_Wes_10_2013-09-15/US_Lou_Wes_10_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 21:10:26 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	79071	2827893	0	0	6791	170207	0	0.060543	22539517

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	2465158	2465158
2.0	1.882088	158724	158724
3.0	2.660166	5450	5450
4.0	3.3465	170	170
5.0	3.951907	8	8
6.0	4.485928	1	1
7.0	4.956982	1	1
8.0	5.372493	0	0
9.0	5.73901	1	1
10.0	6.06231	1	1
11.0	6.347489	0	0
12.0	6.599042	0	0
13.0	6.820934	0	0
14.0	7.016662	1	1
15.0	7.189312	0	0
16.0	7.341603	0	0
17.0	7.475938	0	0
18.0	7.594433	0	0
19.0	7.698956	0	0
20.0	7.791155	0	0
21.0	7.872482	0	0
22.0	7.944219	0	0
23.0	8.007498	0	0
24.0	8.063316	0	0
25.0	8.112552	0	0
26.0	8.155982	0	0
27.0	8.194292	0	0
28.0	8.228084	0	0
29.0	8.257892	0	0
30.0	8.284185	0	0
31.0	8.307378	0	0
32.0	8.327836	0	0
33.0	8.345882	0	0
34.0	8.3618	0	0
35.0	8.375841	0	0
36.0	8.388226	0	0
37.0	8.399151	0	0
38.0	8.408788	0	0
39.0	8.417289	0	0
40.0	8.424787	0	0
41.0	8.431401	0	0
42.0	8.437235	0	0
43.0	8.442382	0	0
44.0	8.446921	0	0
45.0	8.450925	0	0
46.0	8.454457	0	0
47.0	8.457573	0	0
48.0	8.460321	0	0
49.0	8.462745	0	0
50.0	8.464884	0	0
51.0	8.46677	0	0
52.0	8.468434	0	0
53.0	8.469901	0	0
54.0	8.471196	0	0
55.0	8.472338	0	0
56.0	8.473345	0	0
57.0	8.474234	0	0
58.0	8.475017	0	0
59.0	8.475709	0	0
60.0	8.476318	0	0
61.0	8.476856	0	0
62.0	8.477331	0	0
63.0	8.477749	0	0
64.0	8.478119	0	0
65.0	8.478444	0	0
66.0	8.478731	0	0
67.0	8.478985	0	0
68.0	8.479208	0	0
69.0	8.479405	0	0
70.0	8.479579	0	0
71.0	8.479733	0	0
72.0	8.479868	0	0
73.0	8.479987	0	0
74.0	8.480093	0	0
75.0	8.480186	0	0
76.0	8.480268	0	0
77.0	8.48034	0	0
78.0	8.480404	0	0
79.0	8.48046	0	0
80.0	8.480509	0	0
81.0	8.480553	0	0
82.0	8.480592	0	0
83.0	8.480626	0	0
84.0	8.480656	0	0
85.0	8.480682	0	0
86.0	8.480706	0	0
87.0	8.480726	0	0
88.0	8.480744	0	0
89.0	8.48076	0	0
90.0	8.480775	0	0
91.0	8.480787	0	0
92.0	8.480798	0	0
93.0	8.480808	0	0
94.0	8.480816	0	0
95.0	8.480824	0	0
96.0	8.480831	0	0
97.0	8.480836	0	0
98.0	8.480842	0	0
99.0	8.480846	0	0
100.0	8.48085	0	0