## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[ctl2-R1.subsampled.80.merged.filt.bam] OUTPUT=ctl2-R1.subsampled.80.merged.dupmark.bam METRICS_FILE=ctl2-R1.subsampled.80.merged.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT USE_JDK_DEFLATER=true USE_JDK_INFLATER=true    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 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
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Nov 15 23:27:19 UTC 2019

## 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	15944	0	0	0	44	0	0.00276	2883445

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	15858	15858
2.0	1.994486	40	40
3.0	2.983488	2	2
4.0	3.967036	0	0
5.0	4.945161	0	0
6.0	5.917892	0	0
7.0	6.885259	0	0
8.0	7.847292	0	0
9.0	8.804021	0	0
10.0	9.755473	0	0
11.0	10.701679	0	0
12.0	11.642668	0	0
13.0	12.578467	0	0
14.0	13.509106	0	0
15.0	14.434614	0	0
16.0	15.355018	0	0
17.0	16.270347	0	0
18.0	17.180628	0	0
19.0	18.08589	0	0
20.0	18.98616	0	0
21.0	19.881466	0	0
22.0	20.771835	0	0
23.0	21.657294	0	0
24.0	22.537871	0	0
25.0	23.413592	0	0
26.0	24.284484	0	0
27.0	25.150573	0	0
28.0	26.011887	0	0
29.0	26.868451	0	0
30.0	27.720292	0	0
31.0	28.567436	0	0
32.0	29.409908	0	0
33.0	30.247735	0	0
34.0	31.080942	0	0
35.0	31.909554	0	0
36.0	32.733597	0	0
37.0	33.553097	0	0
38.0	34.368077	0	0
39.0	35.178563	0	0
40.0	35.98458	0	0
41.0	36.786153	0	0
42.0	37.583305	0	0
43.0	38.376062	0	0
44.0	39.164447	0	0
45.0	39.948485	0	0
46.0	40.7282	0	0
47.0	41.503615	0	0
48.0	42.274754	0	0
49.0	43.041641	0	0
50.0	43.804299	0	0
51.0	44.562752	0	0
52.0	45.317022	0	0
53.0	46.067133	0	0
54.0	46.813108	0	0
55.0	47.55497	0	0
56.0	48.29274	0	0
57.0	49.026443	0	0
58.0	49.756099	0	0
59.0	50.481732	0	0
60.0	51.203364	0	0
61.0	51.921016	0	0
62.0	52.634712	0	0
63.0	53.344471	0	0
64.0	54.050317	0	0
65.0	54.752271	0	0
66.0	55.450354	0	0
67.0	56.144588	0	0
68.0	56.834993	0	0
69.0	57.521591	0	0
70.0	58.204404	0	0
71.0	58.883451	0	0
72.0	59.558753	0	0
73.0	60.230332	0	0
74.0	60.898208	0	0
75.0	61.562401	0	0
76.0	62.222931	0	0
77.0	62.879819	0	0
78.0	63.533085	0	0
79.0	64.182748	0	0
80.0	64.828829	0	0
81.0	65.471348	0	0
82.0	66.110323	0	0
83.0	66.745775	0	0
84.0	67.377723	0	0
85.0	68.006187	0	0
86.0	68.631184	0	0
87.0	69.252736	0	0
88.0	69.87086	0	0
89.0	70.485575	0	0
90.0	71.096901	0	0
91.0	71.704856	0	0
92.0	72.309458	0	0
93.0	72.910727	0	0
94.0	73.50868	0	0
95.0	74.103335	0	0
96.0	74.694712	0	0
97.0	75.282828	0	0
98.0	75.8677	0	0
99.0	76.449348	0	0
100.0	77.027788	0	0