## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[rep1-R1.subsampled.50.merged.filt.bam] OUTPUT=rep1-R1.subsampled.50.merged.dupmark.bam METRICS_FILE=rep1-R1.subsampled.50.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 23:27:56 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	28515	0	0	0	95	0	0.003332	4269990

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	28325	28325
2.0	1.993344	95	95
3.0	2.980077	0	0
4.0	3.960242	0	0
5.0	4.933884	0	0
6.0	5.901045	0	0
7.0	6.861769	0	0
8.0	7.816099	0	0
9.0	8.764077	0	0
10.0	9.705746	0	0
11.0	10.641147	0	0
12.0	11.570322	0	0
13.0	12.493312	0	0
14.0	13.41016	0	0
15.0	14.320905	0	0
16.0	15.225589	0	0
17.0	16.124251	0	0
18.0	17.016932	0	0
19.0	17.903672	0	0
20.0	18.784509	0	0
21.0	19.659484	0	0
22.0	20.528635	0	0
23.0	21.392002	0	0
24.0	22.249622	0	0
25.0	23.101534	0	0
26.0	23.947776	0	0
27.0	24.788385	0	0
28.0	25.6234	0	0
29.0	26.452857	0	0
30.0	27.276793	0	0
31.0	28.095246	0	0
32.0	28.908251	0	0
33.0	29.715845	0	0
34.0	30.518063	0	0
35.0	31.314942	0	0
36.0	32.106518	0	0
37.0	32.892825	0	0
38.0	33.673898	0	0
39.0	34.449773	0	0
40.0	35.220484	0	0
41.0	35.986065	0	0
42.0	36.746551	0	0
43.0	37.501975	0	0
44.0	38.252371	0	0
45.0	38.997773	0	0
46.0	39.738213	0	0
47.0	40.473725	0	0
48.0	41.204342	0	0
49.0	41.930096	0	0
50.0	42.65102	0	0
51.0	43.367145	0	0
52.0	44.078504	0	0
53.0	44.785128	0	0
54.0	45.48705	0	0
55.0	46.184299	0	0
56.0	46.876908	0	0
57.0	47.564907	0	0
58.0	48.248326	0	0
59.0	48.927197	0	0
60.0	49.60155	0	0
61.0	50.271414	0	0
62.0	50.93682	0	0
63.0	51.597797	0	0
64.0	52.254375	0	0
65.0	52.906583	0	0
66.0	53.55445	0	0
67.0	54.198005	0	0
68.0	54.837276	0	0
69.0	55.472293	0	0
70.0	56.103083	0	0
71.0	56.729674	0	0
72.0	57.352096	0	0
73.0	57.970374	0	0
74.0	58.584538	0	0
75.0	59.194614	0	0
76.0	59.800629	0	0
77.0	60.402611	0	0
78.0	61.000586	0	0
79.0	61.594581	0	0
80.0	62.184623	0	0
81.0	62.770737	0	0
82.0	63.352951	0	0
83.0	63.931289	0	0
84.0	64.505778	0	0
85.0	65.076443	0	0
86.0	65.643311	0	0
87.0	66.206405	0	0
88.0	66.765752	0	0
89.0	67.321375	0	0
90.0	67.873301	0	0
91.0	68.421553	0	0
92.0	68.966156	0	0
93.0	69.507134	0	0
94.0	70.044512	0	0
95.0	70.578313	0	0
96.0	71.108561	0	0
97.0	71.63528	0	0
98.0	72.158493	0	0
99.0	72.678224	0	0
100.0	73.194496	0	0