## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[./pipeline_output_destplus/CA_Nov_Gas_10_2013-10-15/CA_Nov_Gas_10_2013-10-15.sorted_merged.bam] OUTPUT=./pipeline_output_destplus/CA_Nov_Gas_10_2013-10-15/CA_Nov_Gas_10_2013-10-15.dedup.bam METRICS_FILE=./pipeline_output_destplus/CA_Nov_Gas_10_2013-10-15/CA_Nov_Gas_10_2013-10-15.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 21:13:05 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	136088	4201934	0	0	6326	9280	0	0.002914	949905376

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	4140172	4140172
2.0	1.995586	8055	8055
3.0	2.986778	311	311
4.0	3.973595	67	67
5.0	4.956057	25	25
6.0	5.934182	9	9
7.0	6.90799	11	11
8.0	7.8775	2	2
9.0	8.84273	5	5
10.0	9.803701	2	2
11.0	10.760429	0	0
12.0	11.712935	3	3
13.0	12.661237	2	2
14.0	13.605354	1	1
15.0	14.545303	0	0
16.0	15.481104	1	1
17.0	16.412774	1	1
18.0	17.340332	0	0
19.0	18.263796	1	1
20.0	19.183184	0	0
21.0	20.098514	0	0
22.0	21.009804	0	0
23.0	21.917071	0	0
24.0	22.820335	0	0
25.0	23.719611	0	0
26.0	24.614919	0	0
27.0	25.506274	0	0
28.0	26.393696	0	0
29.0	27.2772	0	0
30.0	28.156805	0	0
31.0	29.032528	0	0
32.0	29.904385	0	0
33.0	30.772394	0	0
34.0	31.636573	0	0
35.0	32.496936	0	0
36.0	33.353503	0	0
37.0	34.206288	0	0
38.0	35.05531	0	0
39.0	35.900584	0	0
40.0	36.742128	0	0
41.0	37.579957	0	0
42.0	38.414088	0	0
43.0	39.244537	0	0
44.0	40.071321	0	0
45.0	40.894456	0	0
46.0	41.713958	0	0
47.0	42.529842	0	0
48.0	43.342126	0	0
49.0	44.150824	0	0
50.0	44.955953	0	0
51.0	45.757528	0	0
52.0	46.555566	0	0
53.0	47.350081	0	0
54.0	48.141089	0	0
55.0	48.928605	0	0
56.0	49.712646	0	0
57.0	50.493227	0	0
58.0	51.270362	0	0
59.0	52.044067	0	0
60.0	52.814357	0	0
61.0	53.581247	0	0
62.0	54.344752	0	0
63.0	55.104887	0	0
64.0	55.861668	0	0
65.0	56.615108	0	0
66.0	57.365222	0	0
67.0	58.112026	0	0
68.0	58.855533	0	0
69.0	59.595759	0	0
70.0	60.332718	0	0
71.0	61.066424	0	0
72.0	61.796891	0	0
73.0	62.524135	0	0
74.0	63.248168	0	0
75.0	63.969006	0	0
76.0	64.686662	0	0
77.0	65.401151	0	0
78.0	66.112486	0	0
79.0	66.820681	0	0
80.0	67.525751	0	0
81.0	68.227708	0	0
82.0	68.926568	0	0
83.0	69.622342	0	0
84.0	70.315046	0	0
85.0	71.004692	0	0
86.0	71.691295	0	0
87.0	72.374866	0	0
88.0	73.055421	0	0
89.0	73.732972	0	0
90.0	74.407533	0	0
91.0	75.079116	0	0
92.0	75.747734	0	0
93.0	76.413402	0	0
94.0	77.076132	0	0
95.0	77.735936	0	0
96.0	78.392828	0	0
97.0	79.046821	0	0
98.0	79.697928	0	0
99.0	80.34616	0	0
100.0	80.991532	0	0