## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[./pipeline_output_destplus/US_Tex_Sto_1_2013-09-15/US_Tex_Sto_1_2013-09-15.sorted_merged.bam] OUTPUT=./pipeline_output_destplus/US_Tex_Sto_1_2013-09-15/US_Tex_Sto_1_2013-09-15.dedup.bam METRICS_FILE=./pipeline_output_destplus/US_Tex_Sto_1_2013-09-15/US_Tex_Sto_1_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: Sat Jan 14 00:20:52 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	386295	9172101	0	0	54219	90639	0	0.012573	461017253

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	8882382	8882382
2.0	1.980301	85144	85144
3.0	2.941292	1922	1922
4.0	3.883352	316	316
5.0	4.806855	82	82
6.0	5.712166	30	30
7.0	6.599643	12	12
8.0	7.469639	6	6
9.0	8.322496	4	4
10.0	9.158553	1	1
11.0	9.978141	7	7
12.0	10.781584	0	0
13.0	11.569201	0	0
14.0	12.341302	0	0
15.0	13.098194	0	0
16.0	13.840176	0	0
17.0	14.567542	0	0
18.0	15.280579	0	0
19.0	15.979571	0	0
20.0	16.664794	0	0
21.0	17.336518	0	0
22.0	17.99501	0	0
23.0	18.640531	0	0
24.0	19.273336	0	0
25.0	19.893676	0	0
26.0	20.501795	0	0
27.0	21.097935	0	0
28.0	21.682333	0	0
29.0	22.255218	0	0
30.0	22.816818	0	0
31.0	23.367355	0	0
32.0	23.907048	0	0
33.0	24.436109	0	0
34.0	24.954748	0	0
35.0	25.463171	0	0
36.0	25.961578	0	0
37.0	26.450168	0	0
38.0	26.929133	0	0
39.0	27.398662	0	0
40.0	27.858943	0	0
41.0	28.310157	0	0
42.0	28.752482	0	0
43.0	29.186094	0	0
44.0	29.611165	0	0
45.0	30.027862	0	0
46.0	30.436351	0	0
47.0	30.836793	0	0
48.0	31.229347	0	0
49.0	31.614168	0	0
50.0	31.991408	0	0
51.0	32.361218	0	0
52.0	32.723742	0	0
53.0	33.079125	0	0
54.0	33.427508	0	0
55.0	33.769028	0	0
56.0	34.103821	0	0
57.0	34.432018	0	0
58.0	34.753751	0	0
59.0	35.069145	0	0
60.0	35.378327	0	0
61.0	35.681418	0	0
62.0	35.978539	0	0
63.0	36.269807	0	0
64.0	36.555337	0	0
65.0	36.835243	0	0
66.0	37.109635	0	0
67.0	37.378621	0	0
68.0	37.64231	0	0
69.0	37.900803	0	0
70.0	38.154205	0	0
71.0	38.402615	0	0
72.0	38.646131	0	0
73.0	38.884851	0	0
74.0	39.118868	0	0
75.0	39.348276	0	0
76.0	39.573164	0	0
77.0	39.793622	0	0
78.0	40.009738	0	0
79.0	40.221596	0	0
80.0	40.429281	0	0
81.0	40.632875	0	0
82.0	40.832458	0	0
83.0	41.02811	0	0
84.0	41.219908	0	0
85.0	41.407927	0	0
86.0	41.592243	0	0
87.0	41.772928	0	0
88.0	41.950053	0	0
89.0	42.12369	0	0
90.0	42.293906	0	0
91.0	42.460769	0	0
92.0	42.624345	0	0
93.0	42.784699	0	0
94.0	42.941894	0	0
95.0	43.095993	0	0
96.0	43.247056	0	0
97.0	43.395143	0	0
98.0	43.540313	0	0
99.0	43.682623	0	0
100.0	43.82213	0	0