| Previous changeset 6:a6fe04d64b6d (2015-12-16) Next changeset 8:c8cc033c5fe3 (2015-12-16) |
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Commit message:
Deleted selected files |
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removed:
vcfs2fasta/test-data/2_short.vcf |
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| diff -r a6fe04d64b6d -r 5529e558e3b2 vcfs2fasta/test-data/2_short.vcf --- a/vcfs2fasta/test-data/2_short.vcf Wed Dec 16 07:23:57 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,50000 +0,0 @@\n-##fileformat=VCFv4.1\n-##FILTER=<ID=LowQual,Description="Low quality">\n-##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n-##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n-##GATKCommandLine=<ID=SelectVariants,Version=2.6-5-gba531bd,Date="Thu May 22 09:15:54 BST 2014",Epoch=1400746554393,CommandLineOptions="analysis_type=SelectVariants input_file=[] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/phengs/galaxy/database/tmp/tmp-gatk-4mpB9s/gatk_input.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=2 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/phengs/galaxy/database/tmp/tmp-gatk-4mpB9s/input_variant.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] select_expressions=[] excludeNonVariants=false excludeFiltered=false restrictAllelesTo=ALL keepOriginalAC=false mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[SNP] keepIDs=null fullyDecode=false forceGenotypesDecode=false justRead=false maxIndelSize=2147483647 ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">\n-##GATKCommandLine=<ID=UnifiedGenotyper,Version=2.6-5-gba531bd,Date="Thu May 22 09:06:54 BST 2014",Epoch=1400746014908,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/phengs/galaxy/database/tmp/tmp-gatk-Gz3f1A/gatk_input_0.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[BadCigar] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/phengs/galaxy/database/tmp/tmp-gatk-Gz3f1A/gatk_input.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOrigina'..b'AN=2;DP=48;MQ=60.00;MQ0=0\tGT:DP\t0/0:48\n-gi|15829254|ref|NC_002695.1|\t49921\t.\tT\t.\t157.23\t.\tAN=2;DP=49;MQ=60.00;MQ0=0\tGT:DP\t0/0:49\n-gi|15829254|ref|NC_002695.1|\t49922\t.\tT\t.\t157.23\t.\tAN=2;DP=48;MQ=60.00;MQ0=0\tGT:DP\t0/0:48\n-gi|15829254|ref|NC_002695.1|\t49923\t.\tC\t.\t154.23\t.\tAN=2;DP=47;MQ=60.00;MQ0=0\tGT:DP\t0/0:47\n-gi|15829254|ref|NC_002695.1|\t49924\t.\tA\t.\t151.23\t.\tAN=2;DP=45;MQ=60.00;MQ0=0\tGT:DP\t0/0:45\n-gi|15829254|ref|NC_002695.1|\t49925\t.\tA\t.\t163.23\t.\tAN=2;DP=50;MQ=60.00;MQ0=0\tGT:DP\t0/0:50\n-gi|15829254|ref|NC_002695.1|\t49926\t.\tT\t.\t160.23\t.\tAN=2;DP=50;MQ=60.00;MQ0=0\tGT:DP\t0/0:50\n-gi|15829254|ref|NC_002695.1|\t49927\t.\tG\t.\t160.23\t.\tAN=2;DP=51;MQ=60.00;MQ0=0\tGT:DP\t0/0:51\n-gi|15829254|ref|NC_002695.1|\t49928\t.\tT\t.\t160.23\t.\tAN=2;DP=52;MQ=60.00;MQ0=0\tGT:DP\t0/0:51\n-gi|15829254|ref|NC_002695.1|\t49929\t.\tC\t.\t160.23\t.\tAN=2;DP=51;MQ=60.00;MQ0=0\tGT:DP\t0/0:51\n-gi|15829254|ref|NC_002695.1|\t49930\t.\tG\t.\t163.23\t.\tAN=2;DP=53;MQ=60.00;MQ0=0\tGT:DP\t0/0:53\n-gi|15829254|ref|NC_002695.1|\t49931\t.\tA\t.\t166.23\t.\tAN=2;DP=54;MQ=60.00;MQ0=0\tGT:DP\t0/0:54\n-gi|15829254|ref|NC_002695.1|\t49932\t.\tT\t.\t169.23\t.\tAN=2;DP=55;MQ=60.00;MQ0=0\tGT:DP\t0/0:55\n-gi|15829254|ref|NC_002695.1|\t49933\t.\tG\t.\t163.23\t.\tAN=2;DP=51;MQ=60.00;MQ0=0\tGT:DP\t0/0:50\n-gi|15829254|ref|NC_002695.1|\t49934\t.\tA\t.\t166.23\t.\tAN=2;DP=51;MQ=60.00;MQ0=0\tGT:DP\t0/0:51\n-gi|15829254|ref|NC_002695.1|\t49935\t.\tA\t.\t169.23\t.\tAN=2;DP=51;MQ=60.00;MQ0=0\tGT:DP\t0/0:51\n-gi|15829254|ref|NC_002695.1|\t49936\t.\tG\t.\t169.23\t.\tAN=2;DP=51;MQ=60.00;MQ0=0\tGT:DP\t0/0:51\n-gi|15829254|ref|NC_002695.1|\t49937\t.\tA\t.\t163.23\t.\tAN=2;DP=50;MQ=60.00;MQ0=0\tGT:DP\t0/0:50\n-gi|15829254|ref|NC_002695.1|\t49938\t.\tG\t.\t160.23\t.\tAN=2;DP=50;MQ=60.00;MQ0=0\tGT:DP\t0/0:50\n-gi|15829254|ref|NC_002695.1|\t49939\t.\tC\t.\t154.23\t.\tAN=2;DP=47;MQ=60.00;MQ0=0\tGT:DP\t0/0:47\n-gi|15829254|ref|NC_002695.1|\t49940\t.\tA\t.\t151.23\t.\tAN=2;DP=48;MQ=60.00;MQ0=0\tGT:DP\t0/0:48\n-gi|15829254|ref|NC_002695.1|\t49941\t.\tT\t.\t157.23\t.\tAN=2;DP=49;MQ=60.00;MQ0=0\tGT:DP\t0/0:49\n-gi|15829254|ref|NC_002695.1|\t49942\t.\tC\t.\t160.23\t.\tAN=2;DP=50;MQ=60.00;MQ0=0\tGT:DP\t0/0:50\n-gi|15829254|ref|NC_002695.1|\t49943\t.\tC\t.\t157.23\t.\tAN=2;DP=47;MQ=60.00;MQ0=0\tGT:DP\t0/0:47\n-gi|15829254|ref|NC_002695.1|\t49944\t.\tG\t.\t157.23\t.\tAN=2;DP=48;MQ=60.00;MQ0=0\tGT:DP\t0/0:48\n-gi|15829254|ref|NC_002695.1|\t49945\t.\tC\t.\t154.23\t.\tAN=2;DP=47;MQ=60.00;MQ0=0\tGT:DP\t0/0:47\n-gi|15829254|ref|NC_002695.1|\t49946\t.\tA\t.\t154.23\t.\tAN=2;DP=48;MQ=60.00;MQ0=0\tGT:DP\t0/0:48\n-gi|15829254|ref|NC_002695.1|\t49947\t.\tC\t.\t154.23\t.\tAN=2;DP=48;MQ=60.00;MQ0=0\tGT:DP\t0/0:48\n-gi|15829254|ref|NC_002695.1|\t49948\t.\tA\t.\t151.23\t.\tAN=2;DP=46;MQ=60.00;MQ0=0\tGT:DP\t0/0:46\n-gi|15829254|ref|NC_002695.1|\t49949\t.\tT\t.\t151.23\t.\tAN=2;DP=46;MQ=60.00;MQ0=0\tGT:DP\t0/0:46\n-gi|15829254|ref|NC_002695.1|\t49950\t.\tT\t.\t148.23\t.\tAN=2;DP=46;MQ=60.00;MQ0=0\tGT:DP\t0/0:46\n-gi|15829254|ref|NC_002695.1|\t49951\t.\tG\t.\t154.23\t.\tAN=2;DP=49;MQ=60.00;MQ0=0\tGT:DP\t0/0:49\n-gi|15829254|ref|NC_002695.1|\t49952\t.\tT\t.\t157.23\t.\tAN=2;DP=49;MQ=60.00;MQ0=0\tGT:DP\t0/0:49\n-gi|15829254|ref|NC_002695.1|\t49953\t.\tT\t.\t154.23\t.\tAN=2;DP=49;MQ=60.00;MQ0=0\tGT:DP\t0/0:49\n-gi|15829254|ref|NC_002695.1|\t49954\t.\tG\t.\t157.23\t.\tAN=2;DP=48;MQ=60.00;MQ0=0\tGT:DP\t0/0:48\n-gi|15829254|ref|NC_002695.1|\t49955\t.\tT\t.\t151.23\t.\tAN=2;DP=48;MQ=60.00;MQ0=0\tGT:DP\t0/0:48\n-gi|15829254|ref|NC_002695.1|\t49956\t.\tG\t.\t154.23\t.\tAN=2;DP=47;MQ=60.00;MQ0=0\tGT:DP\t0/0:47\n-gi|15829254|ref|NC_002695.1|\t49957\t.\tA\t.\t151.23\t.\tAN=2;DP=47;MQ=60.00;MQ0=0\tGT:DP\t0/0:47\n-gi|15829254|ref|NC_002695.1|\t49958\t.\tA\t.\t148.23\t.\tAN=2;DP=47;MQ=60.00;MQ0=0\tGT:DP\t0/0:47\n-gi|15829254|ref|NC_002695.1|\t49959\t.\tA\t.\t148.23\t.\tAN=2;DP=47;MQ=60.00;MQ0=0\tGT:DP\t0/0:47\n-gi|15829254|ref|NC_002695.1|\t49960\t.\tG\t.\t145.23\t.\tAN=2;DP=46;MQ=60.00;MQ0=0\tGT:DP\t0/0:46\n-gi|15829254|ref|NC_002695.1|\t49961\t.\tC\t.\t145.23\t.\tAN=2;DP=46;MQ=60.00;MQ0=0\tGT:DP\t0/0:46\n-gi|15829254|ref|NC_002695.1|\t49962\t.\tC\t.\t148.23\t.\tAN=2;DP=46;MQ=60.00;MQ0=0\tGT:DP\t0/0:46\n-gi|15829254|ref|NC_002695.1|\t49963\t.\tG\t.\t145.23\t.\tAN=2;DP=46;MQ=60.00;MQ0=0\tGT:DP\t0/0:46\n-gi|15829254|ref|NC_002695.1|\t49964\t.\tA\t.\t145.23\t.\tAN=2;DP=46;MQ=60.00;MQ0=0\tGT:DP\t0/0:46\n' 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