## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[test.sorted.bam] OUTPUT=test.markdup.bam METRICS_FILE=test.markdup_metrics.txt REMOVE_DUPLICATES=false READ_NAME_REGEX=^(?:[^:]*:){4}([^:]+):([^:]+):([^:]+)(?::[^:]*) OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 TMP_DIR=[/tmp/nxf.TTWv5IRBtJ] VALIDATION_STRINGENCY=SILENT MAX_RECORDS_IN_RAM=250000 CREATE_INDEX=true    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false 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 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Thu May 14 22:40:35 UTC 2026

## 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
test	16	244701	1339	130	0	15622	14589	0.063839	25553215

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.063097	214429	0	228063
2.0	2.116061	13753	12936	1006
3.0	3.158991	832	735	6
4.0	4.191981	57	53	2
5.0	5.215126	6	6	1
6.0	6.22852	2	0	1
7.0	7.232256	0	0	0
8.0	8.226426	0	0	0
9.0	9.211121	0	0	0
10.0	10.186432	0	0	0
11.0	11.152447	0	0	0
12.0	12.109256	0	0	0
13.0	13.056946	0	0	0
14.0	13.995605	0	0	0
15.0	14.925317	0	0	0
16.0	15.846169	0	0	0
17.0	16.758245	0	0	0
18.0	17.661628	0	0	0
19.0	18.556401	0	0	0
20.0	19.442647	0	0	0
21.0	20.320447	0	0	0
22.0	21.189881	0	0	0
23.0	22.051029	0	0	0
24.0	22.90397	0	0	0
25.0	23.748782	0	0	0
26.0	24.585542	0	0	0
27.0	25.414328	0	0	0
28.0	26.235215	0	0	0
29.0	27.048279	0	0	0
30.0	27.853593	0	0	0
31.0	28.651233	0	0	0
32.0	29.441271	0	0	0
33.0	30.22378	0	0	0
34.0	30.998831	0	0	0
35.0	31.766495	0	0	0
36.0	32.526843	0	0	0
37.0	33.279945	0	0	0
38.0	34.02587	0	0	0
39.0	34.764685	0	0	0
40.0	35.496459	0	0	0
41.0	36.221259	0	0	0
42.0	36.939152	0	0	0
43.0	37.650202	0	0	0
44.0	38.354476	0	0	0
45.0	39.052038	0	0	0
46.0	39.742952	0	0	0
47.0	40.427281	0	0	0
48.0	41.105088	0	0	0
49.0	41.776436	0	0	0
50.0	42.441385	0	0	0
51.0	43.099997	0	0	0
52.0	43.752332	0	0	0
53.0	44.39845	0	0	0
54.0	45.03841	0	0	0
55.0	45.672271	0	0	0
56.0	46.300092	0	0	0
57.0	46.921928	0	0	0
58.0	47.537839	0	0	0
59.0	48.147879	0	0	0
60.0	48.752106	0	0	0
61.0	49.350574	0	0	0
62.0	49.943338	0	0	0
63.0	50.530453	0	0	0
64.0	51.111973	0	0	0
65.0	51.687951	0	0	0
66.0	52.258439	0	0	0
67.0	52.82349	0	0	0
68.0	53.383156	0	0	0
69.0	53.937488	0	0	0
70.0	54.486537	0	0	0
71.0	55.030354	0	0	0
72.0	55.568988	0	0	0
73.0	56.102488	0	0	0
74.0	56.630904	0	0	0
75.0	57.154283	0	0	0
76.0	57.672675	0	0	0
77.0	58.186126	0	0	0
78.0	58.694684	0	0	0
79.0	59.198395	0	0	0
80.0	59.697305	0	0	0
81.0	60.191461	0	0	0
82.0	60.680907	0	0	0
83.0	61.165689	0	0	0
84.0	61.64585	0	0	0
85.0	62.121435	0	0	0
86.0	62.592488	0	0	0
87.0	63.059051	0	0	0
88.0	63.521168	0	0	0
89.0	63.97888	0	0	0
90.0	64.432231	0	0	0
91.0	64.88126	0	0	0
92.0	65.326011	0	0	0
93.0	65.766522	0	0	0
94.0	66.202836	0	0	0
95.0	66.634991	0	0	0
96.0	67.063027	0	0	0
97.0	67.486985	0	0	0
98.0	67.906901	0	0	0
99.0	68.322816	0	0	0
100.0	68.734767	0	0	0