## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[P07-male_bleached_K5.sorted.bam] OUTPUT=P07-male_bleached_K5.sorted.dedup.bam METRICS_FILE=P07-male_bleached_K5-picard_metrics.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT    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 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: Thu Jul 18 14:35:51 PDT 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	704944	24839879	0	1428562	407752	7110946	743010	0.290359	37145537

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.021689	13369326	0	13680921
2.0	1.545167	2957292	589601	2845085
3.0	1.813379	853257	57586	759102
4.0	1.950801	295505	9050	243963
5.0	2.021212	118288	1805	92049
6.0	2.057288	53911	454	40981
7.0	2.075772	27273	128	20783
8.0	2.085242	15326	41	12019
9.0	2.090095	9386	23	7722
10.0	2.092581	6188	9	5298
11.0	2.093855	4415	2	3779
12.0	2.094507	3149	2	2817
13.0	2.094842	2464	3	2176
14.0	2.095013	1838	1	1744
15.0	2.095101	1526	1	1419
16.0	2.095146	1233	2	1147
17.0	2.095169	1064	0	975
18.0	2.095181	858	1	759
19.0	2.095187	757	1	691
20.0	2.09519	589	3	551
21.0	2.095191	513	0	486
22.0	2.095192	443	0	439
23.0	2.095193	393	1	348
24.0	2.095193	333	0	301
25.0	2.095193	274	0	280
26.0	2.095193	271	0	244
27.0	2.095193	234	0	206
28.0	2.095193	207	0	205
29.0	2.095193	170	1	171
30.0	2.095193	179	0	135
31.0	2.095193	142	0	152
32.0	2.095193	141	0	132
33.0	2.095193	142	0	99
34.0	2.095193	119	0	122
35.0	2.095193	102	0	109
36.0	2.095193	98	0	96
37.0	2.095193	86	0	80
38.0	2.095193	78	0	67
39.0	2.095193	75	0	69
40.0	2.095193	64	0	66
41.0	2.095193	61	0	58
42.0	2.095193	52	0	47
43.0	2.095193	54	0	62
44.0	2.095193	58	0	47
45.0	2.095193	63	0	55
46.0	2.095193	40	0	43
47.0	2.095193	48	0	46
48.0	2.095193	46	0	43
49.0	2.095193	34	0	41
50.0	2.095193	43	0	36
51.0	2.095193	36	0	38
52.0	2.095193	43	0	35
53.0	2.095193	33	0	34
54.0	2.095193	31	0	19
55.0	2.095193	27	0	41
56.0	2.095193	32	0	25
57.0	2.095193	19	0	19
58.0	2.095193	24	0	21
59.0	2.095193	19	0	22
60.0	2.095193	22	0	19
61.0	2.095193	27	0	10
62.0	2.095193	17	0	14
63.0	2.095193	12	0	13
64.0	2.095193	15	0	13
65.0	2.095193	12	0	20
66.0	2.095193	22	0	13
67.0	2.095193	19	0	12
68.0	2.095193	10	0	7
69.0	2.095193	8	0	11
70.0	2.095193	6	0	11
71.0	2.095193	9	0	10
72.0	2.095193	5	0	2
73.0	2.095193	10	0	2
74.0	2.095193	2	0	9
75.0	2.095193	6	0	7
76.0	2.095193	9	0	6
77.0	2.095193	9	0	6
78.0	2.095193	6	0	6
79.0	2.095193	6	0	9
80.0	2.095193	8	0	7
81.0	2.095193	6	0	6
82.0	2.095193	8	0	3
83.0	2.095193	4	0	6
84.0	2.095193	6	0	6
85.0	2.095193	5	0	11
86.0	2.095193	2	0	6
87.0	2.095193	7	0	4
88.0	2.095193	9	0	7
89.0	2.095193	4	0	6
90.0	2.095193	15	0	6
91.0	2.095193	5	0	1
92.0	2.095193	1	0	2
93.0	2.095193	2	0	1
94.0	2.095193	1	0	3
95.0	2.095193	3	0	3
96.0	2.095193	2	0	5
97.0	2.095193	3	0	3
98.0	2.095193	3	0	5
99.0	2.095193	5	0	2
100.0	2.095193	6	0	5
101.0	0	1	0	4
102.0	0	5	0	3
103.0	0	5	0	5
104.0	0	2	0	2
105.0	0	4	0	3
106.0	0	2	0	3
107.0	0	1	0	2
108.0	0	1	0	1
109.0	0	4	0	1
110.0	0	3	0	2
111.0	0	1	0	2
112.0	0	3	0	6
113.0	0	4	0	4
114.0	0	2	0	1
115.0	0	4	0	3
116.0	0	5	0	2
117.0	0	1	0	4
118.0	0	3	0	1
119.0	0	3	0	0
120.0	0	1	0	2
121.0	0	2	0	1
123.0	0	2	0	2
125.0	0	1	0	0
126.0	0	0	0	1
127.0	0	3	0	3
128.0	0	1	0	2
129.0	0	2	0	3
130.0	0	1	0	0
131.0	0	2	0	0
132.0	0	2	0	0
134.0	0	0	0	2
135.0	0	0	0	1
138.0	0	1	0	0
139.0	0	1	0	0
140.0	0	1	0	2
141.0	0	0	0	1
142.0	0	2	0	0
143.0	0	0	0	1
146.0	0	1	0	0
147.0	0	1	0	2
149.0	0	1	0	0
150.0	0	0	0	1
151.0	0	1	0	0
152.0	0	1	0	1
154.0	0	0	0	1
155.0	0	1	0	0
156.0	0	0	0	1
157.0	0	1	0	0
159.0	0	1	0	0
160.0	0	0	0	1
162.0	0	0	0	1
163.0	0	1	0	0
164.0	0	0	0	1
165.0	0	0	0	1
166.0	0	1	0	0
167.0	0	0	0	1
168.0	0	2	0	0
169.0	0	0	0	1
171.0	0	1	0	0
174.0	0	1	0	0
177.0	0	1	0	0
178.0	0	0	0	2
179.0	0	1	0	1
182.0	0	1	0	1
185.0	0	1	0	0
186.0	0	0	0	1
188.0	0	1	0	0
190.0	0	1	0	0
199.0	0	0	0	1
201.0	0	0	0	1
202.0	0	1	0	0
203.0	0	0	0	1
204.0	0	0	0	1
206.0	0	0	0	1
208.0	0	1	0	1
209.0	0	2	0	0
210.0	0	0	0	1
212.0	0	1	0	0
213.0	0	0	0	1
216.0	0	0	0	1
217.0	0	1	0	0
220.0	0	1	0	0
221.0	0	1	0	0
225.0	0	1	0	0
230.0	0	0	0	1
233.0	0	1	0	1
236.0	0	1	0	0
237.0	0	0	0	1
241.0	0	0	0	1
243.0	0	1	0	1
244.0	0	1	0	0
248.0	0	0	0	1
252.0	0	1	0	0
258.0	0	1	0	0
271.0	0	0	0	1
277.0	0	1	0	0
278.0	0	0	0	2
282.0	0	1	0	1
283.0	0	1	0	0
294.0	0	1	0	0
299.0	0	0	0	1
301.0	0	1	0	0
306.0	0	0	0	1
321.0	0	1	0	0
390.0	0	0	0	1
402.0	0	0	0	1
408.0	0	1	0	0
421.0	0	1	0	0
486.0	0	0	0	1
489.0	0	0	0	1
505.0	0	1	0	0
506.0	0	1	0	0
543.0	0	0	0	1
562.0	0	1	0	0
632.0	0	0	0	1
649.0	0	0	0	1
654.0	0	1	0	0
677.0	0	1	0	0