## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[./pipeline_output_destplus/CA_Nov_Gas_7_2013-10-15/CA_Nov_Gas_7_2013-10-15.sorted_merged.bam] OUTPUT=./pipeline_output_destplus/CA_Nov_Gas_7_2013-10-15/CA_Nov_Gas_7_2013-10-15.dedup.bam METRICS_FILE=./pipeline_output_destplus/CA_Nov_Gas_7_2013-10-15/CA_Nov_Gas_7_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 21:20:10 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	546550	9790594	0	0	103298	102280	0	0.015295	465325449

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	9505654	9505654
2.0	1.979179	100904	100904
3.0	2.937972	554	554
4.0	3.876802	49	49
5.0	4.796085	18	18
6.0	5.696228	2	2
7.0	6.57763	2	2
8.0	7.44068	1	1
9.0	8.285761	0	0
10.0	9.113247	0	0
11.0	9.923505	2	2
12.0	10.716892	0	0
13.0	11.493761	0	0
14.0	12.254455	0	0
15.0	12.999311	0	0
16.0	13.728659	0	0
17.0	14.442821	0	0
18.0	15.142114	0	0
19.0	15.826848	0	0
20.0	16.497325	0	0
21.0	17.153842	0	0
22.0	17.79669	0	0
23.0	18.426154	0	0
24.0	19.042512	0	0
25.0	19.646037	0	0
26.0	20.236997	0	0
27.0	20.815652	0	0
28.0	21.382259	0	0
29.0	21.93707	0	0
30.0	22.480329	0	0
31.0	23.012277	0	0
32.0	23.53315	0	0
33.0	24.043177	0	0
34.0	24.542586	0	0
35.0	25.031597	0	0
36.0	25.510426	0	0
37.0	25.979286	0	0
38.0	26.438384	0	0
39.0	26.887923	0	0
40.0	27.328103	0	0
41.0	27.759118	0	0
42.0	28.181159	0	0
43.0	28.594413	0	0
44.0	28.999062	0	0
45.0	29.395287	0	0
46.0	29.783262	0	0
47.0	30.163159	0	0
48.0	30.535147	0	0
49.0	30.89939	0	0
50.0	31.256049	0	0
51.0	31.605282	0	0
52.0	31.947243	0	0
53.0	32.282085	0	0
54.0	32.609956	0	0
55.0	32.931	0	0
56.0	33.24536	0	0
57.0	33.553174	0	0
58.0	33.85458	0	0
59.0	34.14971	0	0
60.0	34.438696	0	0
61.0	34.721665	0	0
62.0	34.998742	0	0
63.0	35.27005	0	0
64.0	35.53571	0	0
65.0	35.795838	0	0
66.0	36.05055	0	0
67.0	36.299959	0	0
68.0	36.544176	0	0
69.0	36.783307	0	0
70.0	37.01746	0	0
71.0	37.246737	0	0
72.0	37.471241	0	0
73.0	37.691071	0	0
74.0	37.906323	0	0
75.0	38.117094	0	0
76.0	38.323477	0	0
77.0	38.525563	0	0
78.0	38.723441	0	0
79.0	38.917199	0	0
80.0	39.106923	0	0
81.0	39.292697	0	0
82.0	39.474603	0	0
83.0	39.652721	0	0
84.0	39.827131	0	0
85.0	39.99791	0	0
86.0	40.165133	0	0
87.0	40.328874	0	0
88.0	40.489207	0	0
89.0	40.646201	0	0
90.0	40.799926	0	0
91.0	40.950451	0	0
92.0	41.097841	0	0
93.0	41.242163	0	0
94.0	41.38348	0	0
95.0	41.521855	0	0
96.0	41.657349	0	0
97.0	41.790021	0	0
98.0	41.919932	0	0
99.0	42.047137	0	0
100.0	42.171694	0	0