## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[S9M.sorted.bam] OUTPUT=../output/11-RNAseq-snps/S9M.dedup.bam METRICS_FILE=../output/11-RNAseq-snps/S9M.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 13:29:17 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	3824089	16057966	18220830	26077187	512502	635340	60717	0.049615	217313185

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.003657	14818067	0	14874788
2.0	1.935824	581424	60185	528457
3.0	2.801594	20690	266	17117
4.0	3.605696	1337	0	1172
5.0	4.352523	366	0	356
6.0	5.046153	208	0	204
7.0	5.690377	120	0	122
8.0	6.288714	93	0	92
9.0	6.844431	55	0	55
10.0	7.360565	55	0	56
11.0	7.839936	40	0	39
12.0	8.285161	29	0	26
13.0	8.698673	18	0	20
14.0	9.082731	17	0	18
15.0	9.439433	22	0	21
16.0	9.770728	12	0	11
17.0	10.078425	9	0	8
18.0	10.364204	7	0	8
19.0	10.629628	4	0	5
20.0	10.876146	7	0	5
21.0	11.105105	3	0	3
22.0	11.317755	2	0	3
23.0	11.515258	3	0	3
24.0	11.698694	5	0	4
25.0	11.869063	3	0	3
26.0	12.027297	2	0	2
27.0	12.17426	1	0	1
28.0	12.310755	1	0	2
29.0	12.437528	1	0	0
30.0	12.555271	3	0	3
31.0	12.664627	2	0	2
32.0	12.766194	1	0	1
33.0	12.860526	2	0	2
34.0	12.948139	1	0	1
35.0	13.029512	0	0	0
36.0	13.105088	0	0	1
37.0	13.175281	3	0	2
38.0	13.240475	0	0	0
39.0	13.301024	1	0	2
40.0	13.357261	2	0	1
41.0	13.409492	1	0	1
42.0	13.458003	1	0	1
43.0	13.503058	0	0	0
44.0	13.544904	0	0	0
45.0	13.58377	0	0	0
46.0	13.619867	1	0	1
47.0	13.653393	0	0	0
48.0	13.68453	0	0	0
49.0	13.71345	1	0	1
50.0	13.74031	0	0	0
51.0	13.765257	0	0	0
52.0	13.788427	0	0	0
53.0	13.809947	0	0	0
54.0	13.829933	0	0	0
55.0	13.848496	0	0	0
56.0	13.865737	0	0	0
57.0	13.88175	0	0	0
58.0	13.896622	0	0	0
59.0	13.910435	1	0	1
60.0	13.923264	1	0	1
61.0	13.935179	0	0	0
62.0	13.946246	0	0	0
63.0	13.956524	0	0	0
64.0	13.96607	0	0	0
65.0	13.974936	0	0	0
66.0	13.983171	0	0	0
67.0	13.990819	0	0	0
68.0	13.997922	0	0	0
69.0	14.004519	0	0	0
70.0	14.010647	0	0	0
71.0	14.016338	0	0	0
72.0	14.021623	0	0	0
73.0	14.026533	0	0	0
74.0	14.031092	0	0	0
75.0	14.035327	0	0	0
76.0	14.03926	0	0	0
77.0	14.042913	0	0	1
78.0	14.046305	1	0	1
79.0	14.049456	1	0	0
80.0	14.052383	0	0	1
81.0	14.055101	1	0	0
82.0	14.057626	0	0	0
83.0	14.05997	0	0	0
84.0	14.062148	0	0	0
85.0	14.064171	0	0	0
86.0	14.066049	0	0	0
87.0	14.067794	0	0	0
88.0	14.069414	0	0	0
89.0	14.070919	0	0	0
90.0	14.072317	0	0	0
91.0	14.073616	0	0	0
92.0	14.074821	0	0	1
93.0	14.075941	1	0	0
94.0	14.076981	0	0	0
95.0	14.077947	0	0	0
96.0	14.078845	0	0	0
97.0	14.079678	0	0	0
98.0	14.080452	0	0	0
99.0	14.081171	0	0	0
100.0	14.081838	0	0	0