## htsjdk.samtools.metrics.StringHeader
# CollectAlignmentSummaryMetrics  --MAX_INSERT_SIZE 100000   --IS_BISULFITE_SEQUENCED true --INPUT data/3A_WT_WGBS_chr2_17k R1_sorted.bam --OUTPUT data/3A_WT_WGBS_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 04 21:37:49 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
UNPAIRED	1397	1397	1	0	1397	1	78841	1397	78841	77340	14	0.262287	0.262287	0	56.435934	0	0	0	0	0	0.526843	0	0			


