## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1048576 INPUT=[unique.bam] OUTPUT=sampleA/bam/markDups.bam METRICS_FILE=sampleA/duplicates.txt TMP_DIR=[tmp] VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 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 REMOVE_DUPLICATES=false 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: Wed Jul 20 10:17:12 PDT 2022

## 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	12	1447064	0	0	1	121	0	0.000084	8652386350

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	1435404	1435404
2.0	1.999833	121	121
3.0	2.999498	0	0
4.0	3.998997	0	0
5.0	4.998328	0	0
6.0	5.997492	0	0
7.0	6.996489	0	0
8.0	7.995319	0	0
9.0	8.993982	0	0
10.0	9.992478	0	0
11.0	10.990807	0	0
12.0	11.988969	0	0
13.0	12.986964	0	0
14.0	13.984792	0	0
15.0	14.982454	0	0
16.0	15.979948	0	0
17.0	16.977276	0	0
18.0	17.974437	0	0
19.0	18.971431	0	0
20.0	19.968258	0	0
21.0	20.964919	0	0
22.0	21.961413	0	0
23.0	22.95774	0	0
24.0	23.953901	0	0
25.0	24.949895	0	0
26.0	25.945723	0	0
27.0	26.941384	0	0
28.0	27.936878	0	0
29.0	28.932206	0	0
30.0	29.927368	0	0
31.0	30.922363	0	0
32.0	31.917192	0	0
33.0	32.911855	0	0
34.0	33.906351	0	0
35.0	34.900681	0	0
36.0	35.894844	0	0
37.0	36.888841	0	0
38.0	37.882673	0	0
39.0	38.876337	0	0
40.0	39.869836	0	0
41.0	40.863169	0	0
42.0	41.856335	0	0
43.0	42.849335	0	0
44.0	43.84217	0	0
45.0	44.834838	0	0
46.0	45.82734	0	0
47.0	46.819676	0	0
48.0	47.811847	0	0
49.0	48.803851	0	0
50.0	49.79569	0	0
51.0	50.787362	0	0
52.0	51.778869	0	0
53.0	52.77021	0	0
54.0	53.761385	0	0
55.0	54.752395	0	0
56.0	55.743239	0	0
57.0	56.733917	0	0
58.0	57.724429	0	0
59.0	58.714776	0	0
60.0	59.704957	0	0
61.0	60.694972	0	0
62.0	61.684822	0	0
63.0	62.674507	0	0
64.0	63.664025	0	0
65.0	64.653379	0	0
66.0	65.642567	0	0
67.0	66.631589	0	0
68.0	67.620447	0	0
69.0	68.609138	0	0
70.0	69.597665	0	0
71.0	70.586026	0	0
72.0	71.574222	0	0
73.0	72.562253	0	0
74.0	73.550118	0	0
75.0	74.537818	0	0
76.0	75.525353	0	0
77.0	76.512723	0	0
78.0	77.499928	0	0
79.0	78.486967	0	0
80.0	79.473842	0	0
81.0	80.460551	0	0
82.0	81.447096	0	0
83.0	82.433476	0	0
84.0	83.41969	0	0
85.0	84.40574	0	0
86.0	85.391625	0	0
87.0	86.377345	0	0
88.0	87.3629	0	0
89.0	88.34829	0	0
90.0	89.333515	0	0
91.0	90.318576	0	0
92.0	91.303472	0	0
93.0	92.288203	0	0
94.0	93.27277	0	0
95.0	94.257172	0	0
96.0	95.241409	0	0
97.0	96.225482	0	0
98.0	97.20939	0	0
99.0	98.193134	0	0
100.0	99.176713	0	0