Mercurial > repos > jpruab > jpr_picard

annotate test-data/picard_output_collect_AS_sorted_pair.txt @ 4:f4d018471628 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jpruab
date Tue, 13 Aug 2013 12:09:14 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
f4d018471628 Uploaded
jpruab
parents:
diff changeset
1 ## net.sf.picard.metrics.StringHeader
f4d018471628 Uploaded
jpruab
parents:
diff changeset
2 # 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
f4d018471628 Uploaded
jpruab
parents:
diff changeset
3 ## net.sf.picard.metrics.StringHeader
f4d018471628 Uploaded
jpruab
parents:
diff changeset
4 # Started on: Tue Oct 26 14:06:32 EDT 2010
f4d018471628 Uploaded
jpruab
parents:
diff changeset
5
f4d018471628 Uploaded
jpruab
parents:
diff changeset
6 ## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics
f4d018471628 Uploaded
jpruab
parents:
diff changeset
7 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
f4d018471628 Uploaded
jpruab
parents:
diff changeset
8 FIRST_OF_PAIR 5 5 1 0 0 0 0 0 0 0 ? 13 0 ? 0 ? ? 0
f4d018471628 Uploaded
jpruab
parents:
diff changeset
9 SECOND_OF_PAIR 5 5 1 0 0 0 0 0 0 0 ? 13 0 ? 0 ? ? 0
f4d018471628 Uploaded
jpruab
parents:
diff changeset
10 PAIR 10 10 1 0 0 0 0 0 0 0 ? 13 0 ? 0 ? ? 0
f4d018471628 Uploaded
jpruab
parents:
diff changeset
11
f4d018471628 Uploaded
jpruab
parents:
diff changeset
12