## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT 2_3_sorted.bam --OUTPUT 2_3_sorted_deduped.bam --METRICS_FILE input-dedupe-stats.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 --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 --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 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: Mon Jun 16 15:30:40 EDT 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	43857	21573	267577	0	20667	1967	225	0.28276	123591

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.009647	17866	0	18040
2.0	1.857582	1538	213	1408
3.0	2.569706	177	6	140
4.0	3.167772	25	0	18
5.0	3.670048	0	0	0
6.0	4.091876	0	0	0
7.0	4.446141	0	0	0
8.0	4.743665	0	0	0
9.0	4.993536	0	0	0
10.0	5.203385	0	0	0
11.0	5.379624	0	0	0
12.0	5.527636	0	0	0
13.0	5.65194	0	0	0
14.0	5.756336	0	0	0
15.0	5.844011	0	0	0
16.0	5.917643	0	0	0
17.0	5.979482	0	0	0
18.0	6.031416	0	0	0
19.0	6.075032	0	0	0
20.0	6.111662	0	0	0
21.0	6.142426	0	0	0
22.0	6.168262	0	0	0
23.0	6.18996	0	0	0
24.0	6.208183	0	0	0
25.0	6.223487	0	0	0
26.0	6.236339	0	0	0
27.0	6.247134	0	0	0
28.0	6.256199	0	0	0
29.0	6.263813	0	0	0
30.0	6.270207	0	0	0
31.0	6.275576	0	0	0
32.0	6.280086	0	0	0
33.0	6.283874	0	0	0
34.0	6.287055	0	0	0
35.0	6.289726	0	0	0
36.0	6.29197	0	0	0
37.0	6.293854	0	0	0
38.0	6.295436	0	0	0
39.0	6.296765	0	0	0
40.0	6.297881	0	0	0
41.0	6.298819	0	0	0
42.0	6.299606	0	0	0
43.0	6.300267	0	0	0
44.0	6.300822	0	0	0
45.0	6.301288	0	0	0
46.0	6.30168	0	0	0
47.0	6.302009	0	0	0
48.0	6.302285	0	0	0
49.0	6.302517	0	0	0
50.0	6.302712	0	0	0
51.0	6.302876	0	0	0
52.0	6.303013	0	0	0
53.0	6.303128	0	0	0
54.0	6.303225	0	0	0
55.0	6.303307	0	0	0
56.0	6.303375	0	0	0
57.0	6.303433	0	0	0
58.0	6.303481	0	0	0
59.0	6.303521	0	0	0
60.0	6.303555	0	0	0
61.0	6.303584	0	0	0
62.0	6.303608	0	0	0
63.0	6.303628	0	0	0
64.0	6.303645	0	0	0
65.0	6.303659	0	0	0
66.0	6.303671	0	0	0
67.0	6.303681	0	0	0
68.0	6.303689	0	0	0
69.0	6.303696	0	0	0
70.0	6.303702	0	0	0
71.0	6.303707	0	0	0
72.0	6.303712	0	0	0
73.0	6.303715	0	0	0
74.0	6.303718	0	0	0
75.0	6.303721	0	0	0
76.0	6.303723	0	0	0
77.0	6.303724	0	0	0
78.0	6.303726	0	0	0
79.0	6.303727	0	0	0
80.0	6.303728	0	0	0
81.0	6.303729	0	0	0
82.0	6.30373	0	0	0
83.0	6.30373	0	0	0
84.0	6.303731	0	0	0
85.0	6.303731	0	0	0
86.0	6.303732	0	0	0
87.0	6.303732	0	0	0
88.0	6.303732	0	0	0
89.0	6.303732	0	0	0
90.0	6.303733	0	0	0
91.0	6.303733	0	0	0
92.0	6.303733	0	0	0
93.0	6.303733	0	0	0
94.0	6.303733	0	0	0
95.0	6.303733	0	0	0
96.0	6.303733	0	0	0
97.0	6.303733	0	0	0
98.0	6.303733	0	0	0
99.0	6.303733	0	0	0
100.0	6.303733	0	0	0