## htsjdk.samtools.metrics.StringHeader
# CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, METRIC_ACCUMULATION_LEVEL=ALL_READS] IS_BISULFITE_SEQUENCED=false INPUT=picard_CASM_bam OUTPUT=/tmp/tmpjhdz2g17/job_working_directory/000/3/outputs/dataset_4d6599a2-4dca-4fa0-8d6b-b676800fb9a8.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa    EXPECTED_PAIR_ORIENTATIONS=[FR] METRIC_ACCUMULATION_LEVEL=[ALL_READS] COLLECT_ALIGNMENT_INFORMATION=true STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Sat Mar 02 17:42:27 GMT 2024

## 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	SD_READ_LENGTH	MEDIAN_READ_LENGTH	MAD_READ_LENGTH	MIN_READ_LENGTH	MAX_READ_LENGTH	MEAN_ALIGNED_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	100	100	1	0	100	1	17831	100	17831	16865	1	0.008188	0.008188	0	251	0	251	0	251	251	178.31	99	0.99	1	0.01	0	0.46	0.74	0	0.289602	0	57.985294			
SECOND_OF_PAIR	100	100	1	0	99	0.99	17907	99	17907	16887	1	0.008879	0.008879	0	251	0	251	0	251	251	179.07	99	1	0	0	0	0.545455	0.676768	0	0.276574	0	48.307692			
PAIR	200	200	1	0	199	0.995	35738	199	35738	33752	1	0.008534	0.008534	0	251	0	251	0	251	251	178.69	198	0.994975	1	0.005025	0	0.502513	0.708543	0	0.283088	0	53.255639			

## HISTOGRAM	java.lang.Integer
READ_LENGTH	PAIRED_TOTAL_LENGTH_COUNT	PAIRED_ALIGNED_LENGTH_COUNT
0	0	1
112	0	1
113	0	1
120	0	2
124	0	1
127	0	1
130	0	2
131	0	1
132	0	5
133	0	2
134	0	3
137	0	2
138	0	12
139	0	1
140	0	3
141	0	3
143	0	3
144	0	1
146	0	4
147	0	1
151	0	4
152	0	1
155	0	1
156	0	9
157	0	4
158	0	1
159	0	2
161	0	4
162	0	1
167	0	2
169	0	1
170	0	1
171	0	10
172	0	1
173	0	3
176	0	2
177	0	3
179	0	5
180	0	1
181	0	1
182	0	5
184	0	9
185	0	2
186	0	2
187	0	4
192	0	2
193	0	1
194	0	3
200	0	2
201	0	6
203	0	8
205	0	1
206	0	1
208	0	3
213	0	7
216	0	3
222	0	1
228	0	6
229	0	2
230	0	1
231	0	5
232	0	1
233	0	1
236	0	2
238	0	2
241	0	5
242	0	3
250	0	2
251	200	3