## htsjdk.samtools.metrics.StringHeader
# picard.sam.markduplicates.MarkDuplicates INPUT=[~/myExpt/2_alignedData/bams/Sample1.bam] OUTPUT=~/myExpt/3_markedDuplicates/bam/Sample1.bam METRICS_FILE=~/myExpt/3_markedDuplicates/logs/Sample1_Dedup_metrics.log REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag 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 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
## htsjdk.samtools.metrics.StringHeader
# Started on: Tue Nov 06 06:07:05 UTC 2018

## 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
Unknown Library	93	43490914	5366030	0	79	11494386	642648	0.264295	69609522

## HISTOGRAM	java.lang.Double
BIN	VALUE
1.0	1.010803
2.0	1.551963
3.0	1.841688
4.0	1.996801
5.0	2.079844
6.0	2.124304
7.0	2.148106
8.0	2.16085
9.0	2.167672
10.0	2.171325
11.0	2.17328
12.0	2.174327
13.0	2.174888
14.0	2.175188
15.0	2.175348
16.0	2.175434
17.0	2.175481
18.0	2.175505
19.0	2.175518
20.0	2.175525
21.0	2.175529
22.0	2.175531
23.0	2.175532
24.0	2.175533
25.0	2.175533
26.0	2.175533
27.0	2.175534
28.0	2.175534
29.0	2.175534
30.0	2.175534
31.0	2.175534
32.0	2.175534
33.0	2.175534
34.0	2.175534
35.0	2.175534
36.0	2.175534
37.0	2.175534
38.0	2.175534
39.0	2.175534
40.0	2.175534
41.0	2.175534
42.0	2.175534
43.0	2.175534
44.0	2.175534
45.0	2.175534
46.0	2.175534
47.0	2.175534
48.0	2.175534
49.0	2.175534
50.0	2.175534
51.0	2.175534
52.0	2.175534
53.0	2.175534
54.0	2.175534
55.0	2.175534
56.0	2.175534
57.0	2.175534
58.0	2.175534
59.0	2.175534
60.0	2.175534
61.0	2.175534
62.0	2.175534
63.0	2.175534
64.0	2.175534
65.0	2.175534
66.0	2.175534
67.0	2.175534
68.0	2.175534
69.0	2.175534
70.0	2.175534
71.0	2.175534
72.0	2.175534
73.0	2.175534
74.0	2.175534
75.0	2.175534
76.0	2.175534
77.0	2.175534
78.0	2.175534
79.0	2.175534
80.0	2.175534
81.0	2.175534
82.0	2.175534
83.0	2.175534
84.0	2.175534
85.0	2.175534
86.0	2.175534
87.0	2.175534
88.0	2.175534
89.0	2.175534
90.0	2.175534
91.0	2.175534
92.0	2.175534
93.0	2.175534
94.0	2.175534
95.0	2.175534
96.0	2.175534
97.0	2.175534
98.0	2.175534
99.0	2.175534
100.0	2.175534

