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annotate test-data/err_summary @ 29:1aac2a13842a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 1ef1c65fa4d78e1332411af1999862d5a8f28125"
author iuc
date Sun, 20 Mar 2022 14:06:40 +0000
parents 1cd1cf786389
children 3f254c5ced1d
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1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
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1 ## htsjdk.samtools.metrics.StringHeader
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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2 # 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
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
3 ## htsjdk.samtools.metrics.StringHeader
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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4 # Started on: Fri May 03 21:58:49 EDT 2019
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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6 ## METRICS CLASS picard.analysis.artifacts.ErrorSummaryMetrics
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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7 REF_BASE ALT_BASE SUBSTITUTION REF_COUNT ALT_COUNT SUBSTITUTION_RATE
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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8 A C A>C 3877 0 0
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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9 A G A>G 3877 2 0.000516
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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10 A T A>T 3877 0 0
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
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