Mercurial > repos > devteam > picard

diff test-data/picard_CASM_test1.tab @ 3:52fdfc45590a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Thu, 16 Jul 2015 15:32:31 -0400
parents
children 08f69add4d06
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_CASM_test1.tab	Thu Jul 16 15:32:31 2015 -0400
@@ -0,0 +1,12 @@
+## htsjdk.samtools.metrics.StringHeader
+# picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, METRIC_ACCUMULATION_LEVEL=None] IS_BISULFITE_SEQUENCED=false INPUT=/Users/anton/galaxy-central/database/files/000/dataset_616.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_639.dat REFERENCE_SEQUENCE=localref.fa ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT    METRIC_ACCUMULATION_LEVEL=[ALL_READS] STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
+## htsjdk.samtools.metrics.StringHeader
+# Started on: Thu Oct 02 13:35:09 EDT 2014
+
+## METRICS CLASS	picard.analysis.AlignmentSummaryMetrics
+CATEGORY	TOTAL_READS	PF_READS	PCT_PF_READS	PF_NOISE_READS	PF_READS_ALIGNED	PCT_PF_READS_ALIGNED	PF_ALIGNED_BASES	PF_HQ_ALIGNED_READS	PF_HQ_ALIGNED_BASES	PF_HQ_ALIGNED_Q20_BASES	PF_HQ_MEDIAN_MISMATCHES	PF_MISMATCH_RATE	PF_HQ_ERROR_RATE	PF_INDEL_RATE	MEAN_READ_LENGTH	READS_ALIGNED_IN_PAIRS	PCT_READS_ALIGNED_IN_PAIRS	BAD_CYCLES	STRAND_BALANCE	PCT_CHIMERAS	PCT_ADAPTER	SAMPLE	LIBRARY	READ_GROUP
+FIRST_OF_PAIR	100	100	1	0	100	1	17831	100	17831	16865	1	0.008188	0.008188	0	251	99	0.99	0	0.46	0	0			
+SECOND_OF_PAIR	100	100	1	0	99	0.99	17907	99	17907	16887	1	0.008879	0.008879	0	251	99	1	0	0.545455	0	0			
+PAIR	200	200	1	0	199	0.995	35738	199	35738	33752	1	0.008534	0.008534	0	251	198	0.994975	0	0.502513	0	0			
+
+