view test-data/pos_details @ 18:f8748e3fd865 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582

## htsjdk.samtools.metrics.StringHeader
# CollectSequencingArtifactMetrics MINIMUM_QUALITY_SCORE=30 MINIMUM_MAPPING_QUALITY=20 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true CONTEXT_SIZE=1 CONTEXTS_TO_PRINT=[AAA, CAA, AAC, AAT, AAG] INPUT=test-data/picard_ARRG_test1.bam OUTPUT=OutPut ASSUME_SORTED=false 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 REFERENCE_SEQUENCE=test-data/picard_BedToIntervalList_ref.fa GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false   
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri May 03 21:58:49 EDT 2019

## METRICS CLASS	picard.analysis.artifacts.SequencingArtifactMetrics$BaitBiasDetailMetrics
SAMPLE_ALIAS	LIBRARY	REF_BASE	ALT_BASE	CONTEXT	FWD_CXT_REF_BASES	FWD_CXT_ALT_BASES	REV_CXT_REF_BASES	REV_CXT_ALT_BASES	FWD_ERROR_RATE	REV_ERROR_RATE	ERROR_RATE	QSCORE
sample-a	tumor-a	A	C	AAA	58	0	857	0	0	0	0	100
sample-a	tumor-a	A	C	AAC	234	0	139	0	0	0	0	100
sample-a	tumor-a	A	C	AAG	52	0	265	0	0	0	0	100
sample-a	tumor-a	A	C	AAT	240	0	1358	0	0	0	0	100
sample-a	tumor-a	A	C	CAA	101	0	573	0	0	0	0	100
sample-a	tumor-a	A	G	AAA	58	0	857	1	0	0.001166	0	100
sample-a	tumor-a	A	G	AAC	234	1	139	0	0.004255	0	0.004255	24
sample-a	tumor-a	A	G	AAG	52	0	265	0	0	0	0	100
sample-a	tumor-a	A	G	AAT	240	0	1358	0	0	0	0	100
sample-a	tumor-a	A	G	CAA	101	0	573	0	0	0	0	100
sample-a	tumor-a	A	T	AAA	58	0	857	0	0	0	0	100
sample-a	tumor-a	A	T	AAC	234	0	139	0	0	0	0	100
sample-a	tumor-a	A	T	AAG	52	0	265	0	0	0	0	100
sample-a	tumor-a	A	T	AAT	240	0	1358	0	0	0	0	100
sample-a	tumor-a	A	T	CAA	101	0	573	0	0	0	0	100