## htsjdk.samtools.metrics.StringHeader
# CollectAlignmentSummaryMetrics --MAX_INSERT_SIZE 100000  --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE ['AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT', 'CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT', 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT', 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT', 'CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT', 'AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG', 'TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC', 'TTTTTTTTTTCAAGCAGAAGACGGCATACGA', 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG', 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG', 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG', 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTG', 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG', 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTG', 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTG', 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCCGTCTTCTGCTTG', 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTG', 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTG', 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTG', 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTG', 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAACAATCTCGTATGCCGTCTTCTGCTTG', 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTTCCGTATCTCGTATGCCGTCTTCTGCTTG', 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACATGTCAGAATCTCGTATGCCGTCTTCTGCTTG', 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCCCGATCTCGTATGCCGTCTTCTGCTTG', 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCGCACATCTCGTATGCCGTCTTCTGCTTG', 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTATGCCGTCTTCTGCTTG', 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGGCCTTATCTCGTATGCCGTCTTCTGCTTG', 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTTTCGGAATCTCGTATGCCGTCTTCTGCTTG', 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGTACGTAATCTCGTATGCCGTCTTCTGCTTG', 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGTGGATATCTCGTATGCCGTCTTCTGCTTG', 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTGATATATCTCGTATGCCGTCTTCTGCTTG', 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACATTCCTTTATCTCGTATGCCGTCTTCTGCTTG'] --IS_BISULFITE_SEQUENCED false --INPUT /data_local/1/TP53.primerclipped.bam --OUTPUT TP53.primerclipped_alignment_metrics.txt --ASSUME_SORTED false --VALIDATION_STRINGENCY STRICT --REFERENCE_SEQUENCE /data_local/2/hs_b37_chr17_upto_TP53.fasta --METRIC_ACCUMULATION_LEVEL ALL_READS --COLLECT_ALIGNMENT_INFORMATION true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
## htsjdk.samtools.metrics.StringHeader
# Started on: Thu Feb 10 10:34:23 UTC 2022

## METRICS CLASS	picard.analysis.AlignmentSummaryMetrics
CATEGORY	TOTAL_READS	PF_READS	PCT_PF_READS	PF_NOISE_READS	PF_READS_ALIGNED	PCT_PF_READS_ALIGNED	PF_ALIGNED_BASES	PF_HQ_ALIGNED_READS	PF_HQ_ALIGNED_BASES	PF_HQ_ALIGNED_Q20_BASES	PF_HQ_MEDIAN_MISMATCHES	PF_MISMATCH_RATE	PF_HQ_ERROR_RATE	PF_INDEL_RATE	MEAN_READ_LENGTH	READS_ALIGNED_IN_PAIRS	PCT_READS_ALIGNED_IN_PAIRS	PF_READS_IMPROPER_PAIRS	PCT_PF_READS_IMPROPER_PAIRS	BAD_CYCLES	STRAND_BALANCE	PCT_CHIMERAS	PCT_ADAPTER	PCT_SOFTCLIP	PCT_HARDCLIP	AVG_POS_3PRIME_SOFTCLIP_LENGTH	SAMPLE	LIBRARY	READ_GROUP
FIRST_OF_PAIR	667	667	1	0	661	0.991004	63496	661	63496	60832	0	0.005591	0.005591	0.000283	150.563718	643	0.972769	309	0.467474	0	0.567322	0.972769	0	0.358772	0	7.066667			
SECOND_OF_PAIR	667	667	1	0	649	0.973013	60647	649	60647	57020	0	0.006101	0.006101	0.000264	149.82009	643	0.990755	297	0.457627	0	0.440678	0.990755	0	0.366697	0	30.503864			
PAIR	1334	1334	1	0	1310	0.982009	124143	1310	124143	117852	0	0.00584	0.00584	0.000274	150.191904	1286	0.981679	606	0.462595	0	0.50458	0.981679	0	0.362724	0	21.90411			

## HISTOGRAM	java.lang.Integer
READ_LENGTH	PAIRED_TOTAL_LENGTH_COUNT	PAIRED_ALIGNED_LENGTH_COUNT
0	0	24
43	0	1
47	0	1
60	0	3
62	0	2
63	0	2
64	0	4
65	0	274
66	0	1
67	0	1
68	0	2
69	0	7
70	0	240
71	0	30
72	0	1
73	0	1
74	0	2
113	0	1
114	0	3
115	0	17
116	0	709
117	0	8
135	1	0
138	1	0
139	1	0
140	2	0
141	1	0
143	1	0
144	1	0
145	3	0
146	1	0
147	3	0
148	24	0
149	47	0
150	789	0
151	459	0

