## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[S31M.sorted.bam] OUTPUT=../output/11-RNAseq-snps/S31M.dedup.bam METRICS_FILE=../output/11-RNAseq-snps/S31M.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 11:50:59 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	2349657	10934543	13615835	15403793	275213	504106	40844	0.052993	124426189

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.003587	9951767	0	9989224
2.0	1.922743	457036	40404	422726
3.0	2.764572	19801	217	16873
4.0	3.535578	1241	2	1030
5.0	4.24172	242	0	240
6.0	4.888456	130	0	126
7.0	5.480782	75	0	73
8.0	6.023276	34	0	34
9.0	6.520131	35	0	35
10.0	6.975186	9	0	9
11.0	7.391957	14	0	14
12.0	7.773666	11	0	11
13.0	8.123263	9	0	10
14.0	8.443448	7	0	6
15.0	8.736696	0	0	0
16.0	9.005273	3	0	3
17.0	9.251256	2	0	3
18.0	9.476544	4	0	3
19.0	9.682879	4	0	4
20.0	9.871855	1	0	1
21.0	10.044932	1	0	1
22.0	10.203449	3	0	3
23.0	10.34863	0	0	0
24.0	10.481597	0	0	0
25.0	10.603378	2	0	2
26.0	10.714913	0	0	0
27.0	10.817066	0	0	1
28.0	10.910624	3	0	2
29.0	10.996311	1	0	1
30.0	11.074789	0	0	0
31.0	11.146665	0	0	0
32.0	11.212494	0	0	0
33.0	11.272785	0	0	0
34.0	11.328004	0	0	0
35.0	11.378578	0	0	0
36.0	11.424896	0	0	0
37.0	11.467318	0	0	0
38.0	11.506171	0	0	0
39.0	11.541755	0	0	0
40.0	11.574346	0	0	0
41.0	11.604195	0	0	0
42.0	11.631533	0	0	0
43.0	11.65657	0	0	0
44.0	11.679502	0	0	0
45.0	11.700504	0	0	0
46.0	11.719739	0	0	0
47.0	11.737356	0	0	0
48.0	11.753491	0	0	0
49.0	11.768269	0	0	0
50.0	11.781803	0	0	0
51.0	11.794199	0	0	0
52.0	11.805552	0	0	0
53.0	11.815949	0	0	0
54.0	11.825472	0	0	0
55.0	11.834194	0	0	0
56.0	11.842182	0	0	0
57.0	11.849498	0	0	0
58.0	11.856199	0	0	0
59.0	11.862336	0	0	0
60.0	11.867956	0	0	0
61.0	11.873104	0	0	0
62.0	11.877819	0	0	0
63.0	11.882137	0	0	0
64.0	11.886091	0	0	0
65.0	11.889713	0	0	0
66.0	11.893031	0	0	0
67.0	11.896069	0	0	1
68.0	11.898851	1	0	0
69.0	11.9014	0	0	0
70.0	11.903734	0	0	0
71.0	11.905872	0	0	0
72.0	11.90783	0	0	0
73.0	11.909623	0	0	0
74.0	11.911265	0	0	0
75.0	11.912769	0	0	1
76.0	11.914147	1	0	0
77.0	11.915409	0	0	0
78.0	11.916564	0	0	0
79.0	11.917623	0	0	0
80.0	11.918592	0	0	0
81.0	11.91948	0	0	0
82.0	11.920293	0	0	0
83.0	11.921037	0	0	0
84.0	11.921719	0	0	0
85.0	11.922344	0	0	0
86.0	11.922916	0	0	0
87.0	11.92344	0	0	0
88.0	11.92392	0	0	0
89.0	11.92436	0	0	0
90.0	11.924762	0	0	0
91.0	11.925131	0	0	0
92.0	11.925468	0	0	0
93.0	11.925778	0	0	0
94.0	11.926061	0	0	0
95.0	11.92632	0	0	0
96.0	11.926558	0	0	0
97.0	11.926776	0	0	0
98.0	11.926975	0	0	0
99.0	11.927157	0	0	0
100.0	11.927325	0	0	0