## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[./pipeline_output_destplus/US_Tex_Lub_3_2013-09-15/US_Tex_Lub_3_2013-09-15.sorted_merged.bam] OUTPUT=./pipeline_output_destplus/US_Tex_Lub_3_2013-09-15/US_Tex_Lub_3_2013-09-15.dedup.bam METRICS_FILE=./pipeline_output_destplus/US_Tex_Lub_3_2013-09-15/US_Tex_Lub_3_2013-09-15.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 23:32:38 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	233606	6926618	0	0	30662	52568	0	0.00964	454030807

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	6746406	6746406
2.0	1.98486	49467	49467
3.0	2.954809	888	888
4.0	3.910073	161	161
5.0	4.850874	55	55
6.0	5.777432	30	30
7.0	6.689961	23	23
8.0	7.588675	8	8
9.0	8.473782	7	7
10.0	9.345488	7	7
11.0	10.203997	3	3
12.0	11.049508	0	0
13.0	11.882218	5	5
14.0	12.702321	0	0
15.0	13.510007	0	0
16.0	14.305465	0	0
17.0	15.088879	1	1
18.0	15.860433	0	0
19.0	16.620305	0	0
20.0	17.368673	0	0
21.0	18.10571	0	0
22.0	18.831589	0	0
23.0	19.546478	0	0
24.0	20.250543	0	0
25.0	20.943949	0	0
26.0	21.626856	1	1
27.0	22.299424	0	0
28.0	22.96181	0	0
29.0	23.614167	1	1
30.0	24.256647	0	0
31.0	24.8894	0	0
32.0	25.512574	0	0
33.0	26.126312	0	0
34.0	26.730758	0	0
35.0	27.326053	0	0
36.0	27.912335	0	0
37.0	28.489741	0	0
38.0	29.058405	0	0
39.0	29.618459	0	0
40.0	30.170034	0	0
41.0	30.713258	0	0
42.0	31.248258	0	0
43.0	31.775158	0	0
44.0	32.29408	0	0
45.0	32.805146	0	0
46.0	33.308474	0	0
47.0	33.804182	0	0
48.0	34.292385	0	0
49.0	34.773197	0	0
50.0	35.246729	0	0
51.0	35.713091	0	0
52.0	36.172393	0	0
53.0	36.624742	0	0
54.0	37.070241	0	0
55.0	37.508996	0	0
56.0	37.941108	0	0
57.0	38.366677	0	0
58.0	38.785804	0	0
59.0	39.198585	0	0
60.0	39.605116	0	0
61.0	40.005492	0	0
62.0	40.399807	0	0
63.0	40.788152	0	0
64.0	41.170617	0	0
65.0	41.547292	0	0
66.0	41.918264	0	0
67.0	42.283619	0	0
68.0	42.643443	0	0
69.0	42.997819	0	0
70.0	43.34683	0	0
71.0	43.690557	0	0
72.0	44.029079	0	0
73.0	44.362477	0	0
74.0	44.690827	0	0
75.0	45.014205	0	0
76.0	45.332688	0	0
77.0	45.646348	0	0
78.0	45.95526	0	0
79.0	46.259495	0	0
80.0	46.559124	0	0
81.0	46.854217	0	0
82.0	47.144841	0	0
83.0	47.431066	0	0
84.0	47.712957	0	0
85.0	47.990581	0	0
86.0	48.264001	0	0
87.0	48.533281	0	0
88.0	48.798485	0	0
89.0	49.059673	0	0
90.0	49.316907	0	0
91.0	49.570247	0	0
92.0	49.819751	0	0
93.0	50.065477	0	0
94.0	50.307483	0	0
95.0	50.545825	0	0
96.0	50.780559	0	0
97.0	51.011738	0	0
98.0	51.239418	0	0
99.0	51.463651	0	0
100.0	51.684488	0	0