## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT /dreamworld/ngs_data/NIPT/N29/IRs/N29.primary.bam --OUTPUT /dev/stdout --METRICS_FILE /dreamworld/ngs_data/NIPT/N29/N29.md_metrics.txt --REMOVE_DUPLICATES true --ASSUME_SORT_ORDER queryname --TMP_DIR /tmp/tmp3foemyg_ --VERBOSITY ERROR --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 --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 --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Sep 09 19:58:39 KRAT 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
LIB-N29-001	2613	691114	9596	9383	606	114333	11408	0.165558	2011552

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.014068	478048	0	486359
2.0	1.733277	85227	10860	79460
3.0	2.243363	11774	262	9681
4.0	2.605132	1474	8	1108
5.0	2.861711	212	0	139
6.0	3.043685	28	0	18
7.0	3.172746	11	0	9
8.0	3.264281	0	0	0
9.0	3.3292	3	0	4
10.0	3.375243	1	0	0
11.0	3.407898	0	0	1
12.0	3.431058	1	0	0
13.0	3.447484	0	0	0
14.0	3.459133	0	0	0
15.0	3.467396	0	0	0
16.0	3.473256	0	0	0
17.0	3.477412	0	0	0
18.0	3.480359	1	0	1
19.0	3.48245	0	0	0
20.0	3.483933	0	0	0
21.0	3.484984	0	0	1
22.0	3.48573	1	0	0
23.0	3.486259	0	0	0
24.0	3.486634	0	0	0
25.0	3.4869	0	0	0
26.0	3.487089	0	0	0
27.0	3.487223	0	0	0
28.0	3.487317	0	0	0
29.0	3.487385	0	0	0
30.0	3.487433	0	0	0
31.0	3.487466	0	0	0
32.0	3.48749	0	0	0
33.0	3.487507	0	0	0
34.0	3.48752	0	0	0
35.0	3.487528	0	0	0
36.0	3.487534	0	0	0
37.0	3.487538	0	0	0
38.0	3.487542	0	0	0
39.0	3.487544	0	0	0
40.0	3.487545	0	0	0
41.0	3.487546	0	0	0
42.0	3.487547	0	0	0
43.0	3.487548	0	0	0
44.0	3.487548	0	0	0
45.0	3.487548	0	0	0
46.0	3.487549	0	0	0
47.0	3.487549	0	0	0
48.0	3.487549	0	0	0
49.0	3.487549	0	0	0
50.0	3.487549	0	0	0
51.0	3.487549	0	0	0
52.0	3.487549	0	0	0
53.0	3.487549	0	0	0
54.0	3.487549	0	0	0
55.0	3.487549	0	0	0
56.0	3.487549	0	0	0
57.0	3.487549	0	0	0
58.0	3.487549	0	0	0
59.0	3.487549	0	0	0
60.0	3.487549	0	0	0
61.0	3.487549	0	0	0
62.0	3.487549	0	0	0
63.0	3.487549	0	0	0
64.0	3.487549	0	0	0
65.0	3.487549	0	0	0
66.0	3.487549	0	0	0
67.0	3.487549	0	0	0
68.0	3.487549	0	0	0
69.0	3.487549	0	0	0
70.0	3.487549	0	0	0
71.0	3.487549	0	0	0
72.0	3.487549	0	0	0
73.0	3.487549	0	0	0
74.0	3.487549	0	0	0
75.0	3.487549	0	0	0
76.0	3.487549	0	0	0
77.0	3.487549	0	0	0
78.0	3.487549	0	0	0
79.0	3.487549	0	0	0
80.0	3.487549	0	0	0
81.0	3.487549	0	0	0
82.0	3.487549	0	0	0
83.0	3.487549	0	0	0
84.0	3.487549	0	0	0
85.0	3.487549	0	0	0
86.0	3.487549	0	0	0
87.0	3.487549	0	0	0
88.0	3.487549	0	0	0
89.0	3.487549	0	0	0
90.0	3.487549	0	0	0
91.0	3.487549	0	0	0
92.0	3.487549	0	0	0
93.0	3.487549	0	0	0
94.0	3.487549	0	0	0
95.0	3.487549	0	0	0
96.0	3.487549	0	0	0
97.0	3.487549	0	0	0
98.0	3.487549	0	0	0
99.0	3.487549	0	0	0
100.0	3.487549	0	0	0