## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-42-TP1.bam --OUTPUT POC-42-TP1.md.bam --METRICS_FILE POC-42-TP1.md.MarkDuplicates.metrics.txt --ASSUME_SORTED true --VALIDATION_STRINGENCY LENIENT --REFERENCE_SEQUENCE Pocillopora_meandrina_HIv1.assembly.fasta --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 --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES 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 --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
## htsjdk.samtools.metrics.StringHeader
# Started on: Tue Jul 22 02:39:49 GMT 2025

## 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	315	13275326	2885050	0	214	6698493	3458071	0.504584	11377883

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.191322	3429748	0	4415243
2.0	1.562267	1599213	960433	1524380
3.0	1.677768	744694	377127	442185
4.0	1.713733	361697	185292	123229
5.0	1.724931	186422	99294	37088
6.0	1.728418	101884	54418	13675
7.0	1.729503	57821	30303	6460
8.0	1.729841	34339	16902	3735
9.0	1.729947	21108	9742	2400
10.0	1.729979	13198	5556	1614
11.0	1.72999	8169	3262	1181
12.0	1.729993	5323	1896	913
13.0	1.729994	3477	1069	657
14.0	1.729994	2320	610	568
15.0	1.729994	1599	364	457
16.0	1.729994	1152	220	361
17.0	1.729994	770	126	244
18.0	1.729994	556	79	271
19.0	1.729994	431	51	218
20.0	1.729994	347	32	167
21.0	1.729994	271	22	155
22.0	1.729994	219	17	128
23.0	1.729994	190	17	107
24.0	1.729994	171	5	109
25.0	1.729994	144	6	97
26.0	1.729994	137	3	78
27.0	1.729994	107	2	75
28.0	1.729994	96	3	56
29.0	1.729994	97	3	67
30.0	1.729994	90	4	62
31.0	1.729994	50	0	62
32.0	1.729994	67	1	43
33.0	1.729994	56	0	38
34.0	1.729994	52	2	41
35.0	1.729994	50	0	33
36.0	1.729994	42	1	35
37.0	1.729994	34	0	25
38.0	1.729994	26	4	30
39.0	1.729994	36	1	27
40.0	1.729994	28	0	20
41.0	1.729994	31	0	17
42.0	1.729994	20	1	21
43.0	1.729994	21	0	17
44.0	1.729994	25	0	21
45.0	1.729994	17	0	20
46.0	1.729994	21	0	15
47.0	1.729994	14	0	9
48.0	1.729994	17	2	12
49.0	1.729994	14	0	19
50.0	1.729994	20	0	10
51.0	1.729994	14	0	12
52.0	1.729994	15	0	3
53.0	1.729994	15	0	11
54.0	1.729994	12	0	5
55.0	1.729994	11	2	9
56.0	1.729994	6	0	4
57.0	1.729994	6	0	6
58.0	1.729994	11	0	9
59.0	1.729994	5	0	11
60.0	1.729994	8	0	8
61.0	1.729994	6	1	9
62.0	1.729994	14	0	3
63.0	1.729994	10	0	6
64.0	1.729994	3	0	3
65.0	1.729994	3	0	6
66.0	1.729994	8	0	8
67.0	1.729994	10	0	7
68.0	1.729994	7	0	6
69.0	1.729994	5	0	7
70.0	1.729994	6	0	2
71.0	1.729994	2	0	6
72.0	1.729994	7	0	2
73.0	1.729994	9	0	0
74.0	1.729994	2	0	6
75.0	1.729994	1	0	3
76.0	1.729994	2	0	2
77.0	1.729994	3	0	6
78.0	1.729994	4	0	1
79.0	1.729994	2	0	0
80.0	1.729994	3	0	2
81.0	1.729994	1	0	6
82.0	1.729994	7	0	4
83.0	1.729994	3	0	2
84.0	1.729994	1	1	2
85.0	1.729994	2	0	5
86.0	1.729994	4	0	2
87.0	1.729994	2	0	2
88.0	1.729994	4	0	2
89.0	1.729994	5	0	0
90.0	1.729994	4	0	2
91.0	1.729994	3	0	5
92.0	1.729994	4	0	0
93.0	1.729994	1	0	2
94.0	1.729994	3	0	6
95.0	1.729994	3	0	0
96.0	1.729994	3	0	0
97.0	1.729994	1	0	0
98.0	1.729994	1	0	0
99.0	1.729994	1	0	2
100.0	1.729994	1	0	0
101.0	0	1	0	3
102.0	0	1	0	1
103.0	0	2	0	2
104.0	0	1	0	0
105.0	0	2	0	2
106.0	0	0	0	1
107.0	0	2	0	2
108.0	0	1	0	0
109.0	0	0	0	1
110.0	0	1	0	1
112.0	0	0	0	2
113.0	0	0	0	3
114.0	0	1	1	3
115.0	0	1	0	2
116.0	0	2	0	0
117.0	0	1	0	2
118.0	0	1	0	1
119.0	0	2	0	1
120.0	0	1	0	1
121.0	0	3	0	0
122.0	0	3	0	0
123.0	0	1	0	1
124.0	0	1	0	0
125.0	0	1	0	1
126.0	0	0	0	2
127.0	0	1	0	1
128.0	0	2	0	0
129.0	0	0	0	2
130.0	0	1	0	1
131.0	0	0	0	3
133.0	0	1	0	1
134.0	0	1	0	1
136.0	0	2	0	0
137.0	0	2	0	2
138.0	0	1	0	2
139.0	0	2	0	0
140.0	0	0	0	1
141.0	0	1	0	3
142.0	0	2	0	1
143.0	0	1	0	0
144.0	0	1	0	1
146.0	0	1	0	1
147.0	0	0	0	1
149.0	0	0	0	1
150.0	0	1	0	0
151.0	0	4	0	2
152.0	0	0	0	1
153.0	0	2	0	0
156.0	0	1	0	0
157.0	0	2	0	2
158.0	0	0	0	1
159.0	0	1	0	0
160.0	0	1	0	2
161.0	0	1	0	0
162.0	0	1	0	2
163.0	0	0	0	1
164.0	0	1	0	0
165.0	0	1	0	2
166.0	0	1	0	0
167.0	0	0	0	1
168.0	0	1	0	1
170.0	0	1	0	2
174.0	0	2	0	0
175.0	0	1	0	1
176.0	0	1	0	0
177.0	0	0	0	1
178.0	0	2	0	0
179.0	0	0	0	1
180.0	0	0	0	1
182.0	0	2	0	1
183.0	0	2	0	1
184.0	0	1	0	1
185.0	0	0	0	1
188.0	0	2	0	0
192.0	0	0	0	1
193.0	0	1	0	1
196.0	0	1	0	0
197.0	0	1	0	1
198.0	0	0	0	1
200.0	0	0	0	1
202.0	0	1	0	0
203.0	0	0	0	1
209.0	0	0	0	1
210.0	0	1	0	0
211.0	0	0	0	1
212.0	0	1	0	1
215.0	0	1	0	1
217.0	0	2	0	1
218.0	0	1	0	0
220.0	0	1	0	0
221.0	0	0	0	1
222.0	0	1	0	1
223.0	0	0	0	1
226.0	0	0	0	1
228.0	0	0	0	2
229.0	0	0	0	1
231.0	0	1	0	1
232.0	0	0	0	1
233.0	0	3	0	1
235.0	0	2	0	0
236.0	0	0	0	1
237.0	0	1	0	0
241.0	0	1	0	0
242.0	0	0	0	1
243.0	0	0	0	1
245.0	0	1	0	2
247.0	0	1	0	0
250.0	0	1	0	1
252.0	0	3	0	0
253.0	0	1	0	0
255.0	0	1	0	0
260.0	0	0	0	1
263.0	0	1	0	1
265.0	0	1	0	0
273.0	0	0	0	1
274.0	0	1	0	1
277.0	0	2	0	1
294.0	0	0	0	1
296.0	0	1	0	0
298.0	0	1	0	0
303.0	0	0	0	1
311.0	0	1	0	0
312.0	0	1	0	0
315.0	0	1	0	0
319.0	0	0	0	2
320.0	0	0	0	1
326.0	0	1	0	0
327.0	0	0	0	1
328.0	0	0	0	1
329.0	0	0	0	1
331.0	0	1	0	0
336.0	0	1	0	0
342.0	0	1	0	0
344.0	0	0	0	1
349.0	0	1	0	0
355.0	0	0	0	1
365.0	0	0	0	1
367.0	0	1	0	0
370.0	0	1	0	1
382.0	0	0	0	1
394.0	0	1	0	0
402.0	0	1	0	0
419.0	0	1	0	0
430.0	0	1	0	0
448.0	0	0	0	1
455.0	0	1	0	0
473.0	0	0	0	1
479.0	0	0	0	1
484.0	0	1	0	0
502.0	0	0	0	1
507.0	0	1	0	1
510.0	0	1	0	0
540.0	0	1	0	1
546.0	0	0	0	1
594.0	0	1	0	0
600.0	0	1	0	0
657.0	0	0	0	1
740.0	0	1	0	0
897.0	0	0	0	1
1010.0	0	1	0	0