## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT /mounts/lovelace/temporary/porter/full-MT-compared/05_sam_sort_coord/2_3_S6.bam --OUTPUT /mounts/lovelace/temporary/porter/full-MT-compared/06_picard_dedupe/2_3_S6.bam --METRICS_FILE /mounts/lovelace/temporary/porter/full-MT-compared/06_picard_dedupe/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: Fri Jun 13 16:29:15 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	40566	20646	0	0	17985	2244	254	0.274536	97566

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.011184	16434	0	16632
2.0	1.829515	1727	242	1574
3.0	2.491774	207	6	172
4.0	3.027726	33	0	24
5.0	3.461462	1	0	0
6.0	3.812475	0	0	0
7.0	4.096543	0	0	0
8.0	4.326433	0	0	0
9.0	4.512479	0	0	0
10.0	4.663042	0	0	0
11.0	4.78489	0	0	0
12.0	4.883499	0	0	0
13.0	4.963301	0	0	0
14.0	5.027883	0	0	0
15.0	5.080148	0	0	0
16.0	5.122445	0	0	0
17.0	5.156675	0	0	0
18.0	5.184377	0	0	0
19.0	5.206796	0	0	0
20.0	5.224939	0	0	0
21.0	5.239621	0	0	0
22.0	5.251504	0	0	0
23.0	5.26112	0	0	0
24.0	5.268902	0	0	0
25.0	5.2752	0	0	0
26.0	5.280297	0	0	0
27.0	5.284421	0	0	0
28.0	5.287759	0	0	0
29.0	5.290461	0	0	0
30.0	5.292647	0	0	0
31.0	5.294416	0	0	0
32.0	5.295848	0	0	0
33.0	5.297007	0	0	0
34.0	5.297945	0	0	0
35.0	5.298703	0	0	0
36.0	5.299318	0	0	0
37.0	5.299815	0	0	0
38.0	5.300217	0	0	0
39.0	5.300542	0	0	0
40.0	5.300806	0	0	0
41.0	5.301019	0	0	0
42.0	5.301192	0	0	0
43.0	5.301331	0	0	0
44.0	5.301444	0	0	0
45.0	5.301536	0	0	0
46.0	5.30161	0	0	0
47.0	5.30167	0	0	0
48.0	5.301718	0	0	0
49.0	5.301757	0	0	0
50.0	5.301789	0	0	0
51.0	5.301815	0	0	0
52.0	5.301835	0	0	0
53.0	5.301852	0	0	0
54.0	5.301866	0	0	0
55.0	5.301877	0	0	0
56.0	5.301886	0	0	0
57.0	5.301893	0	0	0
58.0	5.301899	0	0	0
59.0	5.301904	0	0	0
60.0	5.301907	0	0	0
61.0	5.301911	0	0	0
62.0	5.301913	0	0	0
63.0	5.301915	0	0	0
64.0	5.301917	0	0	0
65.0	5.301918	0	0	0
66.0	5.301919	0	0	0
67.0	5.30192	0	0	0
68.0	5.301921	0	0	0
69.0	5.301921	0	0	0
70.0	5.301922	0	0	0
71.0	5.301922	0	0	0
72.0	5.301922	0	0	0
73.0	5.301923	0	0	0
74.0	5.301923	0	0	0
75.0	5.301923	0	0	0
76.0	5.301923	0	0	0
77.0	5.301923	0	0	0
78.0	5.301923	0	0	0
79.0	5.301923	0	0	0
80.0	5.301923	0	0	0
81.0	5.301924	0	0	0
82.0	5.301924	0	0	0
83.0	5.301924	0	0	0
84.0	5.301924	0	0	0
85.0	5.301924	0	0	0
86.0	5.301924	0	0	0
87.0	5.301924	0	0	0
88.0	5.301924	0	0	0
89.0	5.301924	0	0	0
90.0	5.301924	0	0	0
91.0	5.301924	0	0	0
92.0	5.301924	0	0	0
93.0	5.301924	0	0	0
94.0	5.301924	0	0	0
95.0	5.301924	0	0	0
96.0	5.301924	0	0	0
97.0	5.301924	0	0	0
98.0	5.301924	0	0	0
99.0	5.301924	0	0	0
100.0	5.301924	0	0	0