## htsjdk.samtools.metrics.StringHeader
# CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=2000 ADAPTER_SEQUENCE=[] INPUT=/mnt/nfsscratch/npacalin/data/032818_cfdna/cfdnapipeline-output/mapped/NaomicfDNA2_S2_R1.bam OUTPUT=/mnt/nfsscratch/npacalin/data/032818_cfdna/cfdnapipeline-output/alignment-metrics/NaomicfDNA2_S2_R1.alignment_summary_metrics.txt REFERENCE_SEQUENCE=/mnt/data/pipeline_genome_data/hg19/male.hg19.fa    EXPECTED_PAIR_ORIENTATIONS=[FR] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT 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: Tue Apr 03 01:03:33 PDT 2018

## 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	85674936	85674936	1	0	70648929	0.824616	4060760565	62978241	3663982299	3516765022	0	0.006252	0.004184	0.000206	59	69936630	0.989918	2674973	0.037863	0	0.50006	0.020871	0			
SECOND_OF_PAIR	85674936	85674936	1	0	70354723	0.821182	4036325718	62652141	3640457386	3447650496	0	0.006958	0.004905	0.000201	59	69936630	0.994057	2380767	0.033839	0	0.50045	0.020958	0			
PAIR	171349872	171349872	1	0	141003652	0.822899	8097086283	125630382	7304439685	6964415518	0	0.006604	0.004544	0.000203	59	139873260	0.991983	5055740	0.035855	0	0.500254	0.020914	0