## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[S23M.sorted.bam] OUTPUT=../output/11-RNAseq-snps/S23M.dedup.bam METRICS_FILE=../output/11-RNAseq-snps/S23M.dup_metrics.txt REMOVE_DUPLICATES=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 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=2 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: Wed Mar 09 11:38:57 PST 2022

## 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	4628799	17527616	21917004	29868193	608335	837454	79924	0.057536	195071641

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.004378	15895768	0	15969271
2.0	1.922446	759426	78976	691947
3.0	2.761621	32046	471	26342
4.0	3.528683	1838	2	1550
5.0	4.229828	366	0	340
6.0	4.870721	203	0	206
7.0	5.45654	126	0	119
8.0	5.992017	73	0	76
9.0	6.481479	58	0	53
10.0	6.92888	52	0	54
11.0	7.337833	36	0	38
12.0	7.711644	22	0	21
13.0	8.053332	23	0	21
14.0	8.365657	15	0	15
15.0	8.651143	13	0	13
16.0	8.912096	8	0	7
17.0	9.150625	13	0	14
18.0	9.368655	7	0	6
19.0	9.56795	6	0	6
20.0	9.750119	3	0	3
21.0	9.916633	7	0	8
22.0	10.068837	8	0	9
23.0	10.207963	7	0	5
24.0	10.335133	3	0	3
25.0	10.451374	1	0	2
26.0	10.557627	2	0	1
27.0	10.654749	1	0	1
28.0	10.743525	5	0	5
29.0	10.824672	1	0	2
30.0	10.898845	1	0	1
31.0	10.966645	3	0	2
32.0	11.028618	2	0	3
33.0	11.085266	1	0	0
34.0	11.137046	2	0	2
35.0	11.184376	1	0	1
36.0	11.227639	1	0	1
37.0	11.267184	1	0	2
38.0	11.303331	3	0	2
39.0	11.336372	1	0	1
40.0	11.366573	0	0	0
41.0	11.39418	0	0	0
42.0	11.419413	0	0	0
43.0	11.442479	0	0	0
44.0	11.463562	2	0	2
45.0	11.482833	0	0	0
46.0	11.500449	0	0	0
47.0	11.516551	0	0	0
48.0	11.531269	0	0	1
49.0	11.544722	1	0	0
50.0	11.557019	0	0	0
51.0	11.568259	0	0	0
52.0	11.578534	0	0	0
53.0	11.587925	0	0	0
54.0	11.59651	0	0	0
55.0	11.604357	0	0	0
56.0	11.611529	0	0	0
57.0	11.618085	0	0	0
58.0	11.624078	0	0	0
59.0	11.629556	1	0	1
60.0	11.634563	1	0	1
61.0	11.639139	0	0	0
62.0	11.643323	0	0	0
63.0	11.647147	1	0	1
64.0	11.650642	0	0	0
65.0	11.653837	0	0	0
66.0	11.656758	0	0	0
67.0	11.659427	0	0	0
68.0	11.661867	0	0	0
69.0	11.664098	0	0	0
70.0	11.666136	0	0	0
71.0	11.668	0	0	0
72.0	11.669703	0	0	0
73.0	11.67126	0	0	1
74.0	11.672683	1	0	0
75.0	11.673984	0	0	0
76.0	11.675173	0	0	0
77.0	11.67626	0	0	0
78.0	11.677254	0	0	0
79.0	11.678162	1	0	1
80.0	11.678992	0	0	0
81.0	11.679751	0	0	0
82.0	11.680444	0	0	0
83.0	11.681078	0	0	0
84.0	11.681658	0	0	0
85.0	11.682188	0	0	0
86.0	11.682672	0	0	0
87.0	11.683114	1	0	1
88.0	11.683519	0	0	0
89.0	11.683889	0	0	0
90.0	11.684227	0	0	0
91.0	11.684536	0	0	0
92.0	11.684818	0	0	0
93.0	11.685076	0	0	0
94.0	11.685312	0	0	0
95.0	11.685528	0	0	0
96.0	11.685725	0	0	0
97.0	11.685905	0	0	0
98.0	11.68607	0	0	0
99.0	11.68622	0	0	0
100.0	11.686358	0	0	0