## htsjdk.samtools.metrics.StringHeader
# CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=2000 ADAPTER_SEQUENCE=[] INPUT=/mnt/nfsscratch/npacalin/data/032818_cfdna/cfdnapipeline-output/mapped/NaomicfDNA4_S3_R1.dedup.bam OUTPUT=/mnt/nfsscratch/npacalin/data/032818_cfdna/cfdnapipeline-output/alignment-metrics/NaomicfDNA4_S3_R1.dedup.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 03:43:40 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	126651937	126651937	1	0	71218484	0.562317	3978585749	63081618	3591342165	3443299384	0	0.0065	0.004653	0.000228	59	69982143	0.98264	2587210	0.036328	0	0.500098	0.018029	0			
SECOND_OF_PAIR	126608213	126608213	1	0	70835810	0.559488	3948212635	62590081	3558266854	3345778344	0	0.007413	0.005575	0.000226	59	69982143	0.987949	2204536	0.031122	0	0.50109	0.018139	0			
PAIR	253260150	253260150	1	0	142054294	0.560903	7926798384	125671699	7149609019	6789077728	0	0.006955	0.005112	0.000227	59	139964286	0.985287	4791746	0.033732	0	0.500593	0.018084	0