annotate test-data/picard_MD_output1.txt @ 3:bf1c3f9f8282

Fix for FastqToSam MAX_Q usage detection.
author Daniel Blankenberg <dan@bx.psu.edu>
date Fri, 03 May 2013 17:13:01 -0400
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1 ## net.sf.picard.metrics.StringHeader
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2 # net.sf.picard.sam.MarkDuplicates INPUT=picard_input_tiny_coord.bam OUTPUT=picard_MD_output2.bam METRICS_FILE=picard_MD_output1.txt REMOVE_DUPLICATES=false ASSUME_SORTED=true READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 TMP_DIR=/tmp/kpvincent VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
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3 ## net.sf.picard.metrics.StringHeader
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4 # Started on: Tue Apr 19 15:28:21 EDT 2011
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5
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6 ## METRICS CLASS net.sf.picard.sam.DuplicationMetrics
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7 LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE
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8 1 3 1 1 1 0 0.428571 3
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10 ## HISTOGRAM java.lang.Double
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11 BIN VALUE
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12 1.0 0.948181
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13 2.0 1.296997
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14 3.0 1.425319
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15 4.0 1.472527
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16 5.0 1.489893
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17 6.0 1.496282
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18 7.0 1.498632
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19 8.0 1.499497
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20 9.0 1.499815
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21 10.0 1.499932
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22 11.0 1.499975
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23 12.0 1.499991
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24 13.0 1.499997
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25 14.0 1.499999
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