## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[./pipeline_output_destplus/US_Tex_Lub_9_2013-09-15/US_Tex_Lub_9_2013-09-15.sorted_merged.bam] OUTPUT=./pipeline_output_destplus/US_Tex_Lub_9_2013-09-15/US_Tex_Lub_9_2013-09-15.dedup.bam METRICS_FILE=./pipeline_output_destplus/US_Tex_Lub_9_2013-09-15/US_Tex_Lub_9_2013-09-15.mark_duplicates_report.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT    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: Fri Jan 13 23:55:29 UTC 2023

## 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
lib1	383175	7765828	0	0	42292	58339	0	0.009989	514284364

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	7568801	7568801
2.0	1.985013	51550	51550
3.0	2.955264	1230	1230
4.0	3.910974	298	298
5.0	4.852361	143	143
6.0	5.77964	77	77
7.0	6.693021	52	52
8.0	7.592714	37	37
9.0	8.478923	27	27
10.0	9.351851	24	24
11.0	10.211697	3	3
12.0	11.058656	11	11
13.0	11.892922	10	10
14.0	12.714685	9	9
15.0	13.524132	2	2
16.0	14.321448	7	7
17.0	15.106815	4	4
18.0	15.880412	3	3
19.0	16.642415	1	1
20.0	17.392998	2	2
21.0	18.132332	3	3
22.0	18.860586	3	3
23.0	19.577926	2	2
24.0	20.284515	2	2
25.0	20.980514	2	2
26.0	21.666083	2	2
27.0	22.341377	0	0
28.0	23.006551	2	2
29.0	23.661756	0	0
30.0	24.307141	1	1
31.0	24.942855	1	1
32.0	25.56904	0	0
33.0	26.185842	1	1
34.0	26.793399	1	1
35.0	27.391851	0	0
36.0	27.981334	1	1
37.0	28.561983	0	0
38.0	29.13393	0	0
39.0	29.697305	1	1
40.0	30.252236	0	0
41.0	30.798851	0	0
42.0	31.337274	0	0
43.0	31.867628	0	0
44.0	32.390034	0	0
45.0	32.90461	0	0
46.0	33.411474	0	0
47.0	33.910743	0	0
48.0	34.402528	0	0
49.0	34.886944	0	0
50.0	35.364099	2	2
51.0	35.834104	0	0
52.0	36.297064	0	0
53.0	36.753087	0	0
54.0	37.202275	0	0
55.0	37.644731	0	0
56.0	38.080556	0	0
57.0	38.509849	0	0
58.0	38.932709	0	0
59.0	39.349231	0	0
60.0	39.759511	0	0
61.0	40.163642	1	1
62.0	40.561717	0	0
63.0	40.953826	0	0
64.0	41.340058	1	1
65.0	41.720502	0	0
66.0	42.095244	0	0
67.0	42.46437	0	0
68.0	42.827964	0	0
69.0	43.186109	0	0
70.0	43.538886	0	0
71.0	43.886377	0	0
72.0	44.228659	0	0
73.0	44.565812	0	0
74.0	44.897912	0	0
75.0	45.225035	0	0
76.0	45.547255	0	0
77.0	45.864647	0	0
78.0	46.177281	0	0
79.0	46.485231	0	0
80.0	46.788565	0	0
81.0	47.087353	0	0
82.0	47.381663	0	0
83.0	47.671562	0	0
84.0	47.957117	0	0
85.0	48.238392	0	0
86.0	48.515452	0	0
87.0	48.788359	0	0
88.0	49.057177	0	0
89.0	49.321966	0	0
90.0	49.582786	0	0
91.0	49.839698	0	0
92.0	50.092759	0	0
93.0	50.342027	0	0
94.0	50.58756	0	0
95.0	50.829414	0	0
96.0	51.067642	0	0
97.0	51.3023	0	0
98.0	51.533442	0	0
99.0	51.761119	0	0
100.0	51.985384	0	0