Mercurial > repos > jpruab > jpr_picard
diff test-data/picard_output_collect_AS_sorted_pair.txt @ 4:f4d018471628 draft default tip
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| author | jpruab |
|---|---|
| date | Tue, 13 Aug 2013 12:09:14 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_output_collect_AS_sorted_pair.txt Tue Aug 13 12:09:14 2013 -0400 @@ -0,0 +1,12 @@ +## net.sf.picard.metrics.StringHeader +# net.sf.picard.analysis.CollectAlignmentSummaryMetrics INPUT=testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam OUTPUT=output_test_as/test_as_sorted-pair.txt REFERENCE_SEQUENCE=testdata/picard/reference/Homo_sapiens_assembly18.trimmed.fasta ASSUME_SORTED=true MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] IS_BISULFITE_SEQUENCED=false TMP_DIR=/tmp/raphael VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +## net.sf.picard.metrics.StringHeader +# Started on: Tue Oct 26 14:06:32 EDT 2010 + +## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics +CATEGORY TOTAL_READS PF_READS PCT_PF_READS PF_NOISE_READS PF_READS_ALIGNED PCT_PF_READS_ALIGNED PF_HQ_ALIGNED_READS PF_HQ_ALIGNED_BASES PF_HQ_ALIGNED_Q20_BASES PF_HQ_MEDIAN_MISMATCHES PF_HQ_ERROR_RATE MEAN_READ_LENGTH READS_ALIGNED_IN_PAIRS PCT_READS_ALIGNED_IN_PAIRS BAD_CYCLES STRAND_BALANCE PCT_CHIMERAS PCT_ADAPTER +FIRST_OF_PAIR 5 5 1 0 0 0 0 0 0 0 ? 13 0 ? 0 ? ? 0 +SECOND_OF_PAIR 5 5 1 0 0 0 0 0 0 0 ? 13 0 ? 0 ? ? 0 +PAIR 10 10 1 0 0 0 0 0 0 0 ? 13 0 ? 0 ? ? 0 + +