## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[P11-female_bleached_44.sorted.bam] OUTPUT=P11-female_bleached_44.sorted.dedup.bam METRICS_FILE=P11-female_bleached_44-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 17:34:00 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	823092	20668023	0	1719198	455804	5060495	732637	0.250878	38995912

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.027891	12454154	0	12824521
2.0	1.63291	2237434	576944	2054681
3.0	1.989025	567809	58215	463492
4.0	2.198635	183311	8946	137045
5.0	2.322012	71104	1899	51624
6.0	2.394632	32743	468	24268
7.0	2.437376	17626	147	13651
8.0	2.462536	10298	52	8546
9.0	2.477345	6858	34	5869
10.0	2.486061	4766	20	4221
11.0	2.491192	3490	6	3091
12.0	2.494212	2749	9	2509
13.0	2.495989	2168	5	1940
14.0	2.497035	1767	13	1622
15.0	2.497651	1368	5	1288
16.0	2.498014	1126	0	1029
17.0	2.498227	959	2	889
18.0	2.498353	848	5	800
19.0	2.498426	707	1	633
20.0	2.49847	565	0	535
21.0	2.498496	518	0	477
22.0	2.498511	440	0	408
23.0	2.49852	402	2	380
24.0	2.498525	349	1	337
25.0	2.498528	291	0	299
26.0	2.49853	293	1	248
27.0	2.498531	252	1	254
28.0	2.498531	232	0	180
29.0	2.498532	183	0	205
30.0	2.498532	213	1	183
31.0	2.498532	164	0	154
32.0	2.498532	164	0	143
33.0	2.498532	144	0	132
34.0	2.498532	126	0	101
35.0	2.498532	117	0	101
36.0	2.498532	97	0	91
37.0	2.498532	103	0	114
38.0	2.498532	83	0	80
39.0	2.498532	85	0	64
40.0	2.498532	77	0	62
41.0	2.498532	67	0	69
42.0	2.498532	69	0	59
43.0	2.498532	53	0	48
44.0	2.498532	44	0	51
45.0	2.498532	57	0	57
46.0	2.498532	57	0	42
47.0	2.498532	42	0	42
48.0	2.498532	34	0	29
49.0	2.498532	33	0	29
50.0	2.498532	37	0	36
51.0	2.498532	30	0	28
52.0	2.498532	32	1	35
53.0	2.498532	27	0	28
54.0	2.498532	28	0	23
55.0	2.498532	28	0	32
56.0	2.498532	29	0	34
57.0	2.498532	24	0	25
58.0	2.498532	25	0	17
59.0	2.498532	35	0	33
60.0	2.498532	23	0	24
61.0	2.498532	24	0	17
62.0	2.498532	24	0	16
63.0	2.498532	10	0	8
64.0	2.498532	15	0	19
65.0	2.498532	26	0	23
66.0	2.498532	16	0	18
67.0	2.498532	20	0	22
68.0	2.498532	19	0	9
69.0	2.498532	13	0	9
70.0	2.498532	13	0	15
71.0	2.498532	10	0	14
72.0	2.498532	7	0	10
73.0	2.498532	9	0	13
74.0	2.498532	14	0	9
75.0	2.498532	6	0	5
76.0	2.498532	7	0	9
77.0	2.498532	13	0	7
78.0	2.498532	9	0	7
79.0	2.498532	5	0	6
80.0	2.498532	10	0	13
81.0	2.498532	13	0	8
82.0	2.498532	10	0	6
83.0	2.498532	8	0	11
84.0	2.498532	9	0	0
85.0	2.498532	6	0	6
86.0	2.498532	4	0	9
87.0	2.498532	6	0	4
88.0	2.498532	6	0	5
89.0	2.498532	7	0	1
90.0	2.498532	2	0	7
91.0	2.498532	3	0	8
92.0	2.498532	3	0	8
93.0	2.498532	7	0	3
94.0	2.498532	3	0	4
95.0	2.498532	5	0	3
96.0	2.498532	7	0	7
97.0	2.498532	4	0	3
98.0	2.498532	6	0	7
99.0	2.498532	5	0	4
100.0	2.498532	8	0	5
101.0	0	2	0	2
102.0	0	6	0	4
103.0	0	4	0	2
104.0	0	3	0	3
105.0	0	6	0	2
106.0	0	2	0	3
107.0	0	4	0	2
108.0	0	1	0	1
109.0	0	2	0	2
110.0	0	2	0	1
111.0	0	3	0	3
112.0	0	0	0	4
113.0	0	3	0	5
114.0	0	1	0	1
115.0	0	4	0	3
116.0	0	0	0	1
117.0	0	1	0	3
118.0	0	4	0	1
119.0	0	4	0	2
120.0	0	3	0	2
121.0	0	3	0	2
122.0	0	1	0	0
123.0	0	3	0	1
124.0	0	1	0	1
125.0	0	1	0	3
126.0	0	0	0	3
127.0	0	1	0	2
128.0	0	3	0	1
129.0	0	1	0	1
131.0	0	0	0	4
132.0	0	6	0	6
133.0	0	4	0	4
134.0	0	3	0	1
135.0	0	2	0	2
136.0	0	1	0	0
137.0	0	4	0	1
138.0	0	2	0	1
139.0	0	0	0	2
140.0	0	0	0	2
141.0	0	2	0	2
142.0	0	1	0	1
143.0	0	2	0	1
144.0	0	3	0	1
145.0	0	3	0	2
146.0	0	2	0	1
147.0	0	0	0	3
149.0	0	1	0	1
150.0	0	1	0	1
151.0	0	0	0	1
152.0	0	4	0	1
153.0	0	2	0	2
154.0	0	1	0	0
155.0	0	2	0	0
156.0	0	0	0	2
157.0	0	4	0	0
159.0	0	0	0	3
161.0	0	1	0	2
163.0	0	1	0	0
164.0	0	2	0	0
165.0	0	0	0	1
167.0	0	1	0	1
168.0	0	1	0	2
169.0	0	0	0	1
170.0	0	0	0	1
172.0	0	3	0	1
176.0	0	1	0	2
177.0	0	1	0	1
179.0	0	2	0	0
180.0	0	1	0	2
182.0	0	0	0	2
183.0	0	2	0	1
185.0	0	1	0	2
186.0	0	1	0	1
187.0	0	2	0	0
188.0	0	0	0	2
191.0	0	1	0	0
193.0	0	1	0	1
194.0	0	1	0	0
196.0	0	1	0	0
199.0	0	2	0	1
200.0	0	0	0	1
203.0	0	0	0	1
205.0	0	0	0	1
209.0	0	0	0	1
211.0	0	1	0	0
212.0	0	2	0	0
213.0	0	2	0	0
214.0	0	1	0	0
218.0	0	0	0	1
221.0	0	1	0	0
222.0	0	0	0	1
231.0	0	0	0	1
233.0	0	1	0	1
235.0	0	1	0	0
237.0	0	1	0	0
239.0	0	0	0	1
242.0	0	1	0	0
243.0	0	0	0	1
246.0	0	0	0	1
247.0	0	1	0	0
251.0	0	1	0	0
255.0	0	0	0	1
257.0	0	1	0	1
261.0	0	0	0	1
264.0	0	0	0	1
272.0	0	1	0	0
274.0	0	1	0	0
275.0	0	0	0	1
277.0	0	1	0	0
278.0	0	1	0	0
295.0	0	0	0	1
299.0	0	0	0	1
301.0	0	0	0	1
302.0	0	0	0	1
304.0	0	1	0	0
305.0	0	0	0	1
312.0	0	1	0	0
314.0	0	1	0	0
317.0	0	1	0	0
319.0	0	0	0	1
320.0	0	0	0	1
330.0	0	1	0	0
331.0	0	1	0	0
332.0	0	1	0	0
352.0	0	0	0	1
361.0	0	1	0	0
373.0	0	0	0	1
379.0	0	0	0	1
390.0	0	1	0	0
430.0	0	1	0	0
455.0	0	0	0	1
459.0	0	0	0	1
473.0	0	1	0	0
475.0	0	1	0	0
504.0	0	0	0	1
527.0	0	1	0	0
531.0	0	0	0	1
545.0	0	1	0	0
610.0	0	0	0	1
613.0	0	0	0	1
635.0	0	2	0	0