## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[rep2-R1.subsampled.50.merged.filt.bam] OUTPUT=rep2-R1.subsampled.50.merged.dupmark.bam METRICS_FILE=rep2-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 23:28:28 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	27068	0	0	0	52	1	0.001921	7173548

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000037	26965	0	26966
2.0	1.996307	50	1	49
3.0	2.988826	1	0	1
4.0	3.977606	0	0	0
5.0	4.962663	0	0	0
6.0	5.944009	0	0	0
7.0	6.92166	0	0	0
8.0	7.895628	0	0	0
9.0	8.865929	0	0	0
10.0	9.832575	0	0	0
11.0	10.79558	0	0	0
12.0	11.754959	0	0	0
13.0	12.710724	0	0	0
14.0	13.66289	0	0	0
15.0	14.61147	0	0	0
16.0	15.556477	0	0	0
17.0	16.497925	0	0	0
18.0	17.435827	0	0	0
19.0	18.370197	0	0	0
20.0	19.301049	0	0	0
21.0	20.228394	0	0	0
22.0	21.152247	0	0	0
23.0	22.07262	0	0	0
24.0	22.989527	0	0	0
25.0	23.902981	0	0	0
26.0	24.812994	0	0	0
27.0	25.719581	0	0	0
28.0	26.622752	0	0	0
29.0	27.522523	0	0	0
30.0	28.418904	0	0	0
31.0	29.31191	0	0	0
32.0	30.201553	0	0	0
33.0	31.087844	0	0	0
34.0	31.970798	0	0	0
35.0	32.850427	0	0	0
36.0	33.726743	0	0	0
37.0	34.599758	0	0	0
38.0	35.469485	0	0	0
39.0	36.335937	0	0	0
40.0	37.199126	0	0	0
41.0	38.059063	0	0	0
42.0	38.915762	0	0	0
43.0	39.769235	0	0	0
44.0	40.619493	0	0	0
45.0	41.466549	0	0	0
46.0	42.310414	0	0	0
47.0	43.151102	0	0	0
48.0	43.988623	0	0	0
49.0	44.82299	0	0	0
50.0	45.654215	0	0	0
51.0	46.482309	0	0	0
52.0	47.307284	0	0	0
53.0	48.129153	0	0	0
54.0	48.947926	0	0	0
55.0	49.763615	0	0	0
56.0	50.576232	0	0	0
57.0	51.385789	0	0	0
58.0	52.192297	0	0	0
59.0	52.995767	0	0	0
60.0	53.796212	0	0	0
61.0	54.593641	0	0	0
62.0	55.388068	0	0	0
63.0	56.179502	0	0	0
64.0	56.967956	0	0	0
65.0	57.75344	0	0	0
66.0	58.535966	0	0	0
67.0	59.315545	0	0	0
68.0	60.092188	0	0	0
69.0	60.865906	0	0	0
70.0	61.63671	0	0	0
71.0	62.404611	0	0	0
72.0	63.16962	0	0	0
73.0	63.931747	0	0	0
74.0	64.691004	0	0	0
75.0	65.447402	0	0	0
76.0	66.200951	0	0	0
77.0	66.951662	0	0	0
78.0	67.699546	0	0	0
79.0	68.444613	0	0	0
80.0	69.186874	0	0	0
81.0	69.92634	0	0	0
82.0	70.66302	0	0	0
83.0	71.396926	0	0	0
84.0	72.128068	0	0	0
85.0	72.856456	0	0	0
86.0	73.582101	0	0	0
87.0	74.305014	0	0	0
88.0	75.025203	0	0	0
89.0	75.74268	0	0	0
90.0	76.457455	0	0	0
91.0	77.169538	0	0	0
92.0	77.87894	0	0	0
93.0	78.585669	0	0	0
94.0	79.289737	0	0	0
95.0	79.991153	0	0	0
96.0	80.689927	0	0	0
97.0	81.38607	0	0	0
98.0	82.079591	0	0	0
99.0	82.7705	0	0	0
100.0	83.458807	0	0	0