## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[md5638.sorted.bam] OUTPUT=md5638.markdup.bam METRICS_FILE=md5638.metrics.txt    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 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 VALIDATION_STRINGENCY=STRICT 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 Sep 06 10:33:27 BST 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	1226	195184	1013	1226	358	33490	12796	0.171959	741723

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.061355	136262	0	144022
2.0	1.87714	20041	9036	15250
3.0	2.504175	3826	1147	1980
4.0	2.986131	971	259	337
5.0	3.356576	342	85	72
6.0	3.641309	128	45	20
7.0	3.860163	62	13	9
8.0	4.02838	37	4	1
9.0	4.157677	10	0	3
10.0	4.257057	6	2	0
11.0	4.333444	4	0	0
12.0	4.392156	0	0	0
13.0	4.437285	2	0	0
14.0	4.471971	0	0	0
15.0	4.498633	0	0	0
16.0	4.519125	2	0	0
17.0	4.534876	0	0	0
18.0	4.546983	1	0	0
19.0	4.556288	0	0	0
20.0	4.563441	0	0	0
21.0	4.568939	0	0	0
22.0	4.573164	0	0	0
23.0	4.576412	0	0	0
24.0	4.578909	0	0	0
25.0	4.580827	0	0	0
26.0	4.582302	0	0	0
27.0	4.583436	0	0	0
28.0	4.584307	0	0	0
29.0	4.584977	0	0	0
30.0	4.585492	0	0	0
31.0	4.585887	0	0	0
32.0	4.586191	0	0	0
33.0	4.586425	0	0	0
34.0	4.586605	0	0	0
35.0	4.586743	0	0	0
36.0	4.586849	0	0	0
37.0	4.586931	0	0	0
38.0	4.586993	0	0	0
39.0	4.587042	0	0	0
40.0	4.587079	0	0	0
41.0	4.587107	0	0	0
42.0	4.587129	0	0	0
43.0	4.587146	0	0	0
44.0	4.587159	0	0	0
45.0	4.587169	0	0	0
46.0	4.587176	0	0	0
47.0	4.587182	0	0	0
48.0	4.587187	0	0	0
49.0	4.58719	0	0	0
50.0	4.587193	0	0	0
51.0	4.587195	0	0	0
52.0	4.587197	0	0	0
53.0	4.587198	0	0	0
54.0	4.587199	0	0	0
55.0	4.587199	0	0	0
56.0	4.5872	0	0	0
57.0	4.5872	0	0	0
58.0	4.587201	0	0	0
59.0	4.587201	0	0	0
60.0	4.587201	0	0	0
61.0	4.587201	0	0	0
62.0	4.587201	0	0	0
63.0	4.587201	0	0	0
64.0	4.587202	0	0	0
65.0	4.587202	0	0	0
66.0	4.587202	0	0	0
67.0	4.587202	0	0	0
68.0	4.587202	0	0	0
69.0	4.587202	0	0	0
70.0	4.587202	0	0	0
71.0	4.587202	0	0	0
72.0	4.587202	0	0	0
73.0	4.587202	0	0	0
74.0	4.587202	0	0	0
75.0	4.587202	0	0	0
76.0	4.587202	0	0	0
77.0	4.587202	0	0	0
78.0	4.587202	0	0	0
79.0	4.587202	0	0	0
80.0	4.587202	0	0	0
81.0	4.587202	0	0	0
82.0	4.587202	0	0	0
83.0	4.587202	0	0	0
84.0	4.587202	0	0	0
85.0	4.587202	0	0	0
86.0	4.587202	0	0	0
87.0	4.587202	0	0	0
88.0	4.587202	0	0	0
89.0	4.587202	0	0	0
90.0	4.587202	0	0	0
91.0	4.587202	0	0	0
92.0	4.587202	0	0	0
93.0	4.587202	0	0	0
94.0	4.587202	0	0	0
95.0	4.587202	0	0	0
96.0	4.587202	0	0	0
97.0	4.587202	0	0	0
98.0	4.587202	0	0	0
99.0	4.587202	0	0	0
100.0	4.587202	0	0	0