Mercurial > repos > gbcs-embl-heidelberg > je_clip
view test-data/markdupes_metrics.txt @ 2:b61628ae2371 draft
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 62411561ae3bc65ea8762d27ec79a7d912503e5b
| author | gbcs-embl-heidelberg |
|---|---|
| date | Wed, 07 Dec 2016 11:57:50 -0500 |
| parents | 101525093ba1 |
| children |
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## htsjdk.samtools.metrics.StringHeader # org.embl.gbcs.je.jeduplicates.MarkDuplicatesWithMolecularCode MISMATCHES=2 MAX_NUMBER_OF_N=1 BARCODE_FILE=/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp2n_ITx/files/000/dataset_5.dat SLOTS=[-1, -2] INPUT=[/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp2n_ITx/files/000/dataset_4.dat] OUTPUT=/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp2n_ITx/files/000/dataset_6.dat METRICS_FILE=/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp2n_ITx/files/000/dataset_7.dat COMMENT=[test-run] REMOVE_DUPLICATES=true ASSUME_SORTED=true DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT SPLIT_CHAR=: TRIM_HEADERS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMolecularCode COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json ## htsjdk.samtools.metrics.StringHeader # Started on: Tue Nov 10 17:01:18 CET 2015 ## METRICS CLASS picard.sam.DuplicationMetrics LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE Unknown Library 196 674 196 186 467 0 0.725389 216 ## HISTOGRAM java.lang.Double BIN VALUE 1.0 0.997418 2.0 1.041445 3.0 1.043389 4.0 1.043474 5.0 1.043478 6.0 1.043478 7.0 1.043478 8.0 1.043478 9.0 1.043478 10.0 1.043478 11.0 1.043478 12.0 1.043478 13.0 1.043478 14.0 1.043478 15.0 1.043478 16.0 1.043478 17.0 1.043478 18.0 1.043478 19.0 1.043478 20.0 1.043478 21.0 1.043478 22.0 1.043478 23.0 1.043478 24.0 1.043478 25.0 1.043478 26.0 1.043478 27.0 1.043478 28.0 1.043478 29.0 1.043478 30.0 1.043478 31.0 1.043478 32.0 1.043478 33.0 1.043478 34.0 1.043478 35.0 1.043478 36.0 1.043478 37.0 1.043478 38.0 1.043478 39.0 1.043478 40.0 1.043478 41.0 1.043478 42.0 1.043478 43.0 1.043478 44.0 1.043478 45.0 1.043478 46.0 1.043478 47.0 1.043478 48.0 1.043478 49.0 1.043478 50.0 1.043478 51.0 1.043478 52.0 1.043478 53.0 1.043478 54.0 1.043478 55.0 1.043478 56.0 1.043478 57.0 1.043478 58.0 1.043478 59.0 1.043478 60.0 1.043478 61.0 1.043478 62.0 1.043478 63.0 1.043478 64.0 1.043478 65.0 1.043478 66.0 1.043478 67.0 1.043478 68.0 1.043478 69.0 1.043478 70.0 1.043478 71.0 1.043478 72.0 1.043478 73.0 1.043478 74.0 1.043478 75.0 1.043478 76.0 1.043478 77.0 1.043478 78.0 1.043478 79.0 1.043478 80.0 1.043478 81.0 1.043478 82.0 1.043478 83.0 1.043478 84.0 1.043478 85.0 1.043478 86.0 1.043478 87.0 1.043478 88.0 1.043478 89.0 1.043478 90.0 1.043478 91.0 1.043478 92.0 1.043478 93.0 1.043478 94.0 1.043478 95.0 1.043478 96.0 1.043478 97.0 1.043478 98.0 1.043478 99.0 1.043478 100.0 1.043478