## htsjdk.samtools.metrics.StringHeader
# CollectAlignmentSummaryMetrics  --MAX_INSERT_SIZE 100000   --IS_BISULFITE_SEQUENCED true --INPUT data/3A_WT_WGBS_chr2_17k_R1_sorted.bam --OUTPUT 3A_WT_WGBS_paired_alignment_metrics.txt --ASSUME_SORTED true --VALIDATION_STRINGENCY STRICT --REFERENCE_SEQUENCE data/hg19_chr2_17k.fasta  --METRIC_ACCUMULATION_LEVEL ALL_READS --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: Tue Feb 25 07:42:56 UTC 2020

## 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	SAMPLE	LIBRARY	READ_GROUP
FIRST_OF_PAIR	1095	1095	1	0	1095	1	60083	1095	60083	59110	14	0.266531	0.266531	0	54.87032	1095	1	0	0	0	0.516895	1	0			
SECOND_OF_PAIR	1095	1095	1	0	1095	1	60124	1095	60124	57359	14	0.269077	0.269077	0	54.907763	1095	1	0	0	0	0.483105	1	0			
PAIR	2190	2190	1	0	2190	1	120207	2190	120207	116469	14	0.267805	0.267805	0	54.889041	2190	1	0	0	0	0.5	1	0			


