# HG changeset patch
# User iuc
# Date 1547247055 18000
# Node ID 3123ce7acd0eda8baf1dc32503420596db7ad08e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
diff -r 000000000000 -r 3123ce7acd0e gemini_inheritance.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_inheritance.xml Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,486 @@
+
+ based identification of candidate genes
+
+ gemini_macros.xml
+
+
+
+
+
+
+
+
+ 0:
+ --min-kindreds ${family_wise.min_kindreds}
+ #end if
+
+ #if str($family_wise.families).strip():
+ #set $families = ','.join([f.strip() for f in $family_wise.families.split(',')])
+ --families "$families"
+ #end if
+
+ #if int($family_wise.per_variant_selection.min_dp) > 0:
+ -d ${family_wise.per_variant_selection.min_dp}
+ #end if
+
+ #if int($family_wise.per_variant_selection.min_gq) > 0:
+ --min-gq ${family_wise.per_variant_selection.min_gq}
+ #end if
+
+ #if int($family_wise.per_variant_selection.max_pl) > -1:
+ --gt-pl-max ${family_wise.per_variant_selection.max_pl}
+ #end if
+
+ #set $report = $oformat.report
+ @COLUMN_SELECT@
+
+ "${ infile }"
+ > "${ outfile }"
+]]>
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diff -r 000000000000 -r 3123ce7acd0e gemini_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_macros.xml Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,254 @@
+
+
+ 0.20.1
+
+ 200
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+
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+ gemini
+
+
+
+
+
+ gemini --version
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+ 10.1371/journal.pcbi.1003153
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+ value.strip()
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+ value.strip()
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+ value.strip()
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+ not value or value.isdigit()
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+ not value or value.isdigit()
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+
+ #set $sql_expr = str($multiline_sql_expr).strip()
+ #if str($sql_expr):
+ #set $sql_expr = $sql_expr.replace('\r\n', '\n')
+ #set $sql_expr = $sql_expr.replace('\r', '\n')
+ #set $sql_expr = $sql_expr.replace('\\\n', ' ')
+ $cmdln_param '$sql_expr'
+ #end if
+
+
+
+ #if str($report.report_selector) == 'full':
+ #set cols = "*"
+ #else:
+ #if $report.columns and str($report.columns) != '':
+ #set $cols = str($report.columns)
+ #else
+ #set $cols = ''
+ #end if
+ #if str($report.extra_cols).strip():
+ #if $cols:
+ #set $cols = $cols + ', ' + str($report.extra_cols)
+ #else:
+ #set $cols = str($report.extra_cols)
+ #end if
+ #end if
+ #if not $cols:
+ #set $cols = "variant_id, gene"
+ #end if
+ #end if
+
+
+
+ @SET_COLS@
+ #if $cols != "*"
+ --columns '$cols'
+ #end if
+
+
+ = %d" % int($r.start))
+ #end if
+ #if str($r.stop).strip():
+ #silent $r_elements.append("end <= %d" % int($r.stop))
+ #end if
+ #silent $region_elements.append("(%s)" % " AND ".join($r_elements))
+ #end for
+ ]]>
+
+
diff -r 000000000000 -r 3123ce7acd0e readme.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,65 @@
+=========================
+Galaxy wrapper for GEMINI
+=========================
+
+
+GEMINI: a flexible framework for exploring genome variation
+
+GEMINI (GEnome MINIng) is designed to be a flexible framework for exploring genetic variation in the context of
+the wealth of genome annotations available for the human genome. By placing genetic variants, sample genotypes,
+and useful genome annotations into an integrated database framework, GEMINI provides a simple, flexible, yet very
+powerful system for exploring genetic variation for for disease and population genetics.
+
+Using the GEMINI framework begins by loading a VCF file into a database. Each variant is automatically
+annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks,
+OMIM, dbSNP, KEGG, and HPRD. All of this information is stored in portable SQLite database that allows
+one to explore and interpret both coding and non-coding variation using “off-the-shelf” tools or an
+enhanced SQL engine.
+
+Please also see the original [manuscript](http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003153).
+
+
+============
+Installation
+============
+
+It is recommended to install this wrapper via the `Galaxy Tool Shed`.
+
+.. _`Galaxy Tool Shed`: https://testtoolshed.g2.bx.psu.edu/view/iuc/gemini
+
+
+=======
+History
+=======
+- 0.9.1: Initial public release
+
+
+====================
+Detailed description
+====================
+
+View the original GEMINI documentation: http://gemini.readthedocs.org/en/latest/index.html
+
+
+===============================
+Wrapper Licence (MIT/BSD style)
+===============================
+
+Permission to use, copy, modify, and distribute this software and its
+documentation with or without modifications and for any purpose and
+without fee is hereby granted, provided that any copyright notices
+appear in all copies and that both those copyright notices and this
+permission notice appear in supporting documentation, and that the
+names of the contributors or copyright holders not be used in
+advertising or publicity pertaining to distribution of the software
+without specific prior permission.
+
+THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
+WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
+CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
+OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
+OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
+OR PERFORMANCE OF THIS SOFTWARE.
+
diff -r 000000000000 -r 3123ce7acd0e repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,4 @@
+
+
+
+
\ No newline at end of file
diff -r 000000000000 -r 3123ce7acd0e static/images/gemini_mendel_errors.png
Binary file static/images/gemini_mendel_errors.png has changed
diff -r 000000000000 -r 3123ce7acd0e test-data/anno.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/anno.bed Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,3 @@
+chr3 187000000 187150000
+chr3 187150000 187300000
+chr3 187300000 187450000
diff -r 000000000000 -r 3123ce7acd0e test-data/gemini_actionable_mutations_result.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gemini_actionable_mutations_result.tabular Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,1 @@
+tum_name chrom start end ref alt gene impact is_somatic in_cosmic_census dgidb_info
diff -r 000000000000 -r 3123ce7acd0e test-data/gemini_amend.ped
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gemini_amend.ped Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,10 @@
+#family_id sample_id paternal_id maternal_id sex phenotype
+1 1_dad 0 0 -1 1
+1 1_mom 0 0 -1 1
+1 1_kid 1_dad 1_mom -1 2
+2 2_dad 0 0 -1 1
+2 2_mom 0 0 -1 1
+2 2_kid 2_dad 2_mom -1 2
+3 3_dad 0 0 -1 1
+3 3_mom 0 0 -1 1
+3 3_kid 3_dad 3_mom -1 2
diff -r 000000000000 -r 3123ce7acd0e test-data/gemini_amend.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gemini_amend.vcf Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,127 @@
+##fileformat=VCFv4.1
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[bam/M10478.conc.on.pos.realigned.bam, bam/M10475.conc.on.pos.realigned.bam, bam/M10500.conc.on.pos.realigned.bam, bam/M128215.conc.on.pos.realigned.bam] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/m/cphg-quinlan/cphg-quinlan/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=10 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 multiallelic=false max_alternate_alleles=5 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 bandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
+##contig=
+##contig=
+##contig=
+##contig=
+##contig=
+##contig=
+##contig=
+##contig=
+##contig=
+##contig=
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+##contig=
+##contig=
+##contig=
+##contig=
+##contig=
+##reference=file:///m/cphg-quinlan/cphg-quinlan/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa
+##INFO=
+##SnpEffVersion="SnpEff 3.0g (build 2012-08-31), by Pablo Cingolani"
+##SnpEffCmd="SnpEff -i vcf -o vcf GRCh37.66 test4.vep.vcf "
+##INFO=
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1_dad 1_mom 1_kid 2_dad 2_mom 2_kid 3_dad 3_mom 3_kid
+chr10 1142208 . T C 3404.3 . AC=8;AF=1.00;AN=8;DP=122;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=2.6747;MQ=36.00;MQ0=0;QD=27.90;CSQ=intron_variant|||ENSG00000047056|WDR37|ENST00000263150|||,downstream_gene_variant|||ENSG00000047056|WDR37|ENST00000436154|||,intron_variant|||ENSG00000047056|WDR37|ENST00000358220|||,stop_lost|Tga/Cga|*/R|ENSG00000047056|WDR37|ENST00000381329|9/9||;EFF=DOWNSTREAM(MODIFIER||||208|WDR37|protein_coding|CODING|ENST00000436154|),INTRON(MODIFIER||||494|WDR37|protein_coding|CODING|ENST00000263150|),INTRON(MODIFIER||||494|WDR37|protein_coding|CODING|ENST00000358220|),STOP_LOST(HIGH|MISSENSE|Tga/Cga|*250R|249|WDR37|protein_coding|CODING|ENST00000381329|exon_10_1142110_1142566) GT:AD:DP:GQ:PL 0/1:1,37:39:87.16:940,87,0 0/1:0,29:29:78.20:899,78,0 1/1:0,24:24:66.14:729,66,0 0/1:1,37:59:87.16:940,87,0 0/1:0,29:49:78.20:899,78,0 1/1:0,24:64:66.14:729,66,0 0/1:1,37:39:87.16:940,87,0 0/1:0,29:29:78.20:899,78,0 0/1:0,24:24:66.14:729,66,0
+chr10 48003992 . C T 1047.87 . AC=4;AF=0.50;AN=8;BaseQRankSum=-0.053;DP=165;Dels=0.00;FS=6.377;HRun=0;HaplotypeScore=4.3830;MQ=20.94;MQ0=0;MQRankSum=-0.368;QD=9.53;ReadPosRankSum=1.346;CSQ=missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000420079|16/17|benign(0)|tolerated(1),missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000426610|17/18|benign(0)|tolerated(1);EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C540Y|610|ASAH2C|protein_coding|CODING|ENST00000420079|exon_10_48003968_48004056),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C552Y|622|ASAH2C|protein_coding|CODING|ENST00000426610|exon_10_48003968_48004056) GT:AD:DP:GQ:PL 0/1:1,37:39:87.16:940,87,0 0/1:0,29:29:78.20:899,78,0 1/1:0,24:24:66.14:729,66,0 0/1:1,37:39:87.16:940,87,0 0/1:0,29:29:78.20:899,78,0 0/1:0,24:24:66.14:729,66,0 0/1:1,37:39:87.16:940,87,0 0/1:0,29:29:78.20:899,78,0 0/1:0,24:24:66.14:729,66,0
+chr10 48004992 . C T 1047.87 . AC=4;AF=0.50;AN=8;BaseQRankSum=-0.053;DP=165;Dels=0.00;FS=6.377;HRun=0;HaplotypeScore=4.3830;MQ=20.94;MQ0=0;MQRankSum=-0.368;QD=9.53;ReadPosRankSum=1.346;CSQ=missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000420079|16/17|benign(0)|tolerated(1),missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000426610|17/18|benign(0)|tolerated(1);EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C540Y|610|ASAH2C|protein_coding|CODING|ENST00000420079|exon_10_48003968_48004056),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C552Y|622|ASAH2C|protein_coding|CODING|ENST00000426610|exon_10_48003968_48004056) GT:AD:DP:GQ:PL 0/1:1,37:39:87.16:940,87,0 0/1:0,29:29:78.20:899,78,0 0/1:0,24:24:66.14:729,66,0 0/1:1,37:39:87.16:940,87,0 0/1:0,29:29:78.20:899,78,0 1/1:0,24:24:66.14:729,66,0 0/1:1,37:39:87.16:940,87,0 0/1:0,29:29:78.20:899,78,0 0/1:0,24:24:66.14:729,66,0
+chr10 135336656 . G A 38.34 . AC=4;AF=1.00;AN=4;DP=2;Dels=0.00;FS=0.000;HRun=4;HaplotypeScore=0.0000;MQ=37.00;MQ0=0;QD=19.17;CSQ=upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000418356|||,intron_variant&nc_transcript_variant|||ENSG00000214279||ENST00000488261|||,intron_variant|||ENSG00000203772|SPRN|ENST00000541506|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000541261|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000421586|||,intron_variant|||ENSG00000130649|CYP2E1|ENST00000463117|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000252945|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000541080|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000477500|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000480558|||,intron_variant|||ENSG00000214279||ENST00000356567|||;EFF=INTRON(MODIFIER||||151|SPRN|protein_coding|CODING|ENST00000541506|),INTRON(MODIFIER||||493|CYP2E1|protein_coding|CODING|ENST00000463117|),INTRON(MODIFIER||||693|RP11-108K14.4.1|protein_coding|CODING|ENST00000356567|),INTRON(MODIFIER|||||RP11-108K14.4.1|retained_intron|CODING|ENST00000488261|),UPSTREAM(MODIFIER||||305|CYP2E1|protein_coding|CODING|ENST00000418356|),UPSTREAM(MODIFIER||||355|CYP2E1|protein_coding|CODING|ENST00000421586|),UPSTREAM(MODIFIER||||493|CYP2E1|protein_coding|CODING|ENST00000252945|),UPSTREAM(MODIFIER||||85|CYP2E1|protein_coding|CODING|ENST00000541261|),UPSTREAM(MODIFIER|||||CYP2E1|processed_transcript|CODING|ENST00000477500|),UPSTREAM(MODIFIER|||||CYP2E1|processed_transcript|CODING|ENST00000480558|) GT:AD:DP:GQ:PL 0/1:1,37:39:87.16:940,87,0 0/1:0,29:29:78.20:899,78,0 0/1:0,24:24:66.14:729,66,0 0/1:1,37:39:87.16:940,87,0 0/1:0,29:29:78.20:899,78,0 0/1:0,24:24:66.14:729,66,0 0/1:1,37:39:87.16:940,87,0 0/1:0,29:29:78.20:899,78,0 0/1:0,24:24:66.14:729,66,0
+chr10 135369532 . T C 122.62 . AC=2;AF=0.25;AN=8;BaseQRankSum=2.118;DP=239;Dels=0.00;FS=5.194;HRun=2;HaplotypeScore=5.7141;MQ=36.02;MQ0=0;MQRankSum=0.082;QD=2.31;ReadPosRankSum=-0.695;CSQ=missense_variant|aAg/aGg|K/R|ENSG00000171772|SYCE1|ENST00000303903|9/13|benign(0.001)|tolerated(1),missense_variant|aAg/aGg|K/R|ENSG00000171772|SYCE1|ENST00000432597|10/14|benign(0)|tolerated(1),downstream_gene_variant|||ENSG00000171772|SYCE1|ENST00000460441|||,missense_variant|aAg/aGg|K/R|ENSG00000171772|SYCE1|ENST00000343131|9/13|benign(0.001)|tolerated(1),intron_variant|||ENSG00000203772|SPRN|ENST00000541506|||,non_coding_exon_variant&nc_transcript_variant|||ENSG00000171772|SYCE1|ENST00000479535|6/10||,downstream_gene_variant|||ENSG00000171772|SYCE1|ENST00000482127|||,non_coding_exon_variant&nc_transcript_variant|||ENSG00000130649|CYP2E1|ENST00000368520|6/6||,missense_variant|aAg/aGg|K/R|ENSG00000171772|SYCE1|ENST00000368517|9/13|benign(0)|tolerated(1);EFF=DOWNSTREAM(MODIFIER|||||SYCE1|processed_transcript|CODING|ENST00000460441|),DOWNSTREAM(MODIFIER|||||SYCE1|processed_transcript|CODING|ENST00000482127|),EXON(MODIFIER|||||CYP2E1|retained_intron|CODING|ENST00000368520|),EXON(MODIFIER|||||SYCE1|processed_transcript|CODING|ENST00000479535|),INTRON(MODIFIER||||151|SPRN|protein_coding|CODING|ENST00000541506|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K147R|282|SYCE1|protein_coding|CODING|ENST00000368517|exon_10_135369485_135369551),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K147R|282|SYCE1|protein_coding|CODING|ENST00000432597|exon_10_135369485_135369551),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K183R|318|SYCE1|protein_coding|CODING|ENST00000303903|exon_10_135369485_135369551),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K183R|351|SYCE1|protein_coding|CODING|ENST00000343131|exon_10_135369485_135369551) GT:AD:DP:GQ:PL 0/1:1,37:39:87.16:940,87,0 0/1:0,29:29:78.20:899,78,0 0/1:0,24:24:66.14:729,66,0 0/1:1,37:39:87.16:940,87,0 0/1:0,29:29:78.20:899,78,0 0/1:0,24:24:66.14:729,66,0 0/1:1,37:39:87.16:940,87,0 0/1:0,29:29:78.20:899,78,0 1/1:0,24:24:66.14:729,66,0
\ No newline at end of file
diff -r 000000000000 -r 3123ce7acd0e test-data/gemini_amend_input.db
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diff -r 000000000000 -r 3123ce7acd0e test-data/gemini_annotate_result.db
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diff -r 000000000000 -r 3123ce7acd0e test-data/gemini_auto_dom_input.db
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diff -r 000000000000 -r 3123ce7acd0e test-data/gemini_auto_rec_input.db
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diff -r 000000000000 -r 3123ce7acd0e test-data/gemini_burden_calpha_template.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gemini_burden_calpha_template.tabular Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,4 @@
+gene T c Z p_value
+SYCE1 .+ .+ .+ .+
+WDR37 .+ .+ .+ .+
+ASAH2C .+ .+ .+ .+
diff -r 000000000000 -r 3123ce7acd0e test-data/gemini_burden_count_highimpact_result.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gemini_burden_count_highimpact_result.tabular Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,2 @@
+gene 1_kid 3_kid
+WDR37 1 2
diff -r 000000000000 -r 3123ce7acd0e test-data/gemini_burden_count_nonsynonymous_result.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gemini_burden_count_nonsynonymous_result.tabular Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,5 @@
+gene 1_dad 1_kid 1_mom 2_dad 2_kid 2_mom 3_dad 3_kid 3_mom
+SYCE1 0 1 0 0 1 0 0 1 0
+SPRN 0 1 0 0 1 0 1 1 1
+WDR37 0 1 0 0 0 0 0 2 0
+ASAH2C 2 3 2 1 3 1 1 2 1
diff -r 000000000000 -r 3123ce7acd0e test-data/gemini_comphets_input.db
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diff -r 000000000000 -r 3123ce7acd0e test-data/gemini_de_novo_input.db
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diff -r 000000000000 -r 3123ce7acd0e test-data/gemini_fusions_result.tabular
diff -r 000000000000 -r 3123ce7acd0e test-data/gemini_is_somatic_result.db
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diff -r 000000000000 -r 3123ce7acd0e test-data/gemini_load_input.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gemini_load_input.vcf Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,70 @@
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+##INFO=
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+##INFO=
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+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##reference=GRCh37
+##SnpEffVersion="SnpEff 3.0f (build 2012-08-23), by Pablo Cingolani"
+##SnpEffCmd="SnpEff GRCh37.66 -i vcf -o vcf -c /Users/arq5x/src/other/snpEff_3_0/snpEff.config ALL.wgs.integrated_phase1_v3.20101123.snps_indels_sv.sites.vcf.gz "
+##INFO=
+#CHROM POS ID REF ALT QUAL FILTER INFO
+1 10583 rs58108140 G A 100.0 PASS AVGPOST=0.7707;RSQ=0.4319;LDAF=0.2327;ERATE=0.0161;AN=2184;VT=SNP;AA=.;THETA=0.0046;AC=314;SNPSOURCE=LOWCOV;AF=0.14;ASN_AF=0.13;AMR_AF=0.17;AFR_AF=0.04;EUR_AF=0.21;EFF=DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),UPSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|)
+1 10611 rs189107123 C G 100.0 PASS AN=2184;THETA=0.0077;VT=SNP;AA=.;AC=41;ERATE=0.0048;SNPSOURCE=LOWCOV;AVGPOST=0.9330;LDAF=0.0479;RSQ=0.3475;AF=0.02;ASN_AF=0.01;AMR_AF=0.03;AFR_AF=0.01;EUR_AF=0.02;EFF=DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),UPSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|)
+1 13302 rs180734498 C T 100.0 PASS THETA=0.0048;AN=2184;AC=249;VT=SNP;AA=.;RSQ=0.6281;LDAF=0.1573;SNPSOURCE=LOWCOV;AVGPOST=0.8895;ERATE=0.0058;AF=0.11;ASN_AF=0.02;AMR_AF=0.08;AFR_AF=0.21;EUR_AF=0.14;EFF=DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),EXON(MODIFIER||||209|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),EXON(MODIFIER||||550|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),EXON(MODIFIER||||551|DDX11L1|processed_transcript|NON_CODING|ENST00000456328|),INTRON(MODIFIER||||493|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|)
+1 13327 rs144762171 G C 100.0 PASS AVGPOST=0.9698;AN=2184;VT=SNP;AA=.;RSQ=0.6482;AC=59;SNPSOURCE=LOWCOV;ERATE=0.0012;LDAF=0.0359;THETA=0.0204;AF=0.03;ASN_AF=0.02;AMR_AF=0.03;AFR_AF=0.02;EUR_AF=0.04;EFF=DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),EXON(MODIFIER||||209|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),EXON(MODIFIER||||550|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),EXON(MODIFIER||||551|DDX11L1|processed_transcript|NON_CODING|ENST00000456328|),INTRON(MODIFIER||||493|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|)
+1 13957 . TC T 28.0 PASS AA=TC;AC=35;AN=2184;VT=INDEL;AVGPOST=0.8711;RSQ=0.2501;LDAF=0.0788;THETA=0.0100;ERATE=0.0065;AF=0.02;ASN_AF=0.01;AMR_AF=0.02;AFR_AF=0.02;EUR_AF=0.02;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),EXON(MODIFIER||||493|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|),EXON(MODIFIER||||550|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),EXON(MODIFIER||||551|DDX11L1|processed_transcript|NON_CODING|ENST00000456328|)
+1 13980 rs151276478 T C 100.0 PASS AN=2184;AC=45;ERATE=0.0034;THETA=0.0139;RSQ=0.3603;LDAF=0.0525;VT=SNP;AA=.;AVGPOST=0.9221;SNPSOURCE=LOWCOV;AF=0.02;ASN_AF=0.02;AMR_AF=0.02;AFR_AF=0.01;EUR_AF=0.02;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),EXON(MODIFIER||||493|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|),EXON(MODIFIER||||550|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),EXON(MODIFIER||||551|DDX11L1|processed_transcript|NON_CODING|ENST00000456328|)
+1 30923 rs140337953 G T 100.0 PASS AC=1584;AA=T;AN=2184;RSQ=0.5481;VT=SNP;THETA=0.0162;SNPSOURCE=LOWCOV;ERATE=0.0183;LDAF=0.6576;AVGPOST=0.7335;AF=0.73;ASN_AF=0.89;AMR_AF=0.80;AFR_AF=0.48;EUR_AF=0.73;EFF=DOWNSTREAM(MODIFIER|||||FAM138A|processed_transcript|CODING|ENST00000461467|),DOWNSTREAM(MODIFIER|||||FAM138A|protein_coding|CODING|ENST00000417324|),DOWNSTREAM(MODIFIER|||||MIR1302-10|miRNA|NON_CODING|ENST00000408384|),INTRON(MODIFIER||||177|MIR1302-10|antisense|NON_CODING|ENST00000469289|),INTRON(MODIFIER||||236|MIR1302-10|antisense|NON_CODING|ENST00000473358|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|)
+1 46402 . C CTGT 31.0 PASS AA=.;RSQ=0.0960;AN=2184;AC=8;VT=INDEL;AVGPOST=0.8325;THETA=0.0121;ERATE=0.0072;LDAF=0.0903;AF=0.0037;ASN_AF=0.0017;AFR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
+1 47190 . G GA 192.0 PASS AA=G;AVGPOST=0.9041;AN=2184;AC=29;VT=INDEL;LDAF=0.0628;THETA=0.0153;RSQ=0.2883;ERATE=0.0041;AF=0.01;AMR_AF=0.0028;AFR_AF=0.06;EFF=INTERGENIC(MODIFIER|||||||||)
+1 51476 rs187298206 T C 100.0 PASS ERATE=0.0021;AA=C;AC=18;AN=2184;VT=SNP;THETA=0.0103;LDAF=0.0157;SNPSOURCE=LOWCOV;AVGPOST=0.9819;RSQ=0.5258;AF=0.01;ASN_AF=0.01;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
+1 51479 rs116400033 T A 100.0 PASS RSQ=0.7414;AVGPOST=0.9085;AA=T;AN=2184;THETA=0.0131;AC=235;VT=SNP;LDAF=0.1404;SNPSOURCE=LOWCOV;ERATE=0.0012;AF=0.11;ASN_AF=0.0035;AMR_AF=0.16;AFR_AF=0.03;EUR_AF=0.22;EFF=INTERGENIC(MODIFIER|||||||||)
+1 51914 rs190452223 T G 100.0 PASS ERATE=0.0004;AVGPOST=0.9985;THETA=0.0159;AA=T;AN=2184;VT=SNP;SNPSOURCE=LOWCOV;AC=1;RSQ=0.4089;LDAF=0.0012;AF=0.0005;ASN_AF=0.0017;EFF=INTERGENIC(MODIFIER|||||||||)
+1 51935 rs181754315 C T 100.0 PASS THETA=0.0126;AA=C;AN=2184;RSQ=0.1888;AVGPOST=0.9972;LDAF=0.0015;VT=SNP;AC=0;SNPSOURCE=LOWCOV;ERATE=0.0006;AF=0;EFF=INTERGENIC(MODIFIER|||||||||)
+1 51954 rs185832753 G C 100.0 PASS LDAF=0.0021;AA=G;AN=2184;RSQ=0.4692;AVGPOST=0.9975;VT=SNP;SNPSOURCE=LOWCOV;THETA=0.0029;ERATE=0.0006;AC=2;AF=0.0009;AMR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
+1 52058 rs62637813 G C 100.0 PASS AA=C;ERATE=0.0057;AN=2184;AVGPOST=0.9264;VT=SNP;RSQ=0.4882;AC=64;SNPSOURCE=LOWCOV;LDAF=0.0620;THETA=0.0069;AF=0.03;ASN_AF=0.0017;AMR_AF=0.04;AFR_AF=0.02;EUR_AF=0.05;EFF=INTERGENIC(MODIFIER|||||||||)
+1 52144 rs190291950 T A 100.0 PASS THETA=0.0093;ERATE=0.0013;LDAF=0.0156;AA=T;AN=2184;VT=SNP;RSQ=0.5220;AVGPOST=0.9811;SNPSOURCE=LOWCOV;AC=21;AF=0.01;ASN_AF=0.0035;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
+1 52185 . TTAA T 244.0 PASS AA=.;AN=2184;LDAF=0.0124;VT=INDEL;AC=10;THETA=0.0232;RSQ=0.4271;AVGPOST=0.9840;ERATE=0.0037;AF=0.0046;ASN_AF=0.0035;AMR_AF=0.02;AFR_AF=0.0020;EFF=INTERGENIC(MODIFIER|||||||||)
+1 52238 rs150021059 T G 100.0 PASS THETA=0.0132;AA=G;AN=2184;RSQ=0.6256;VT=SNP;ERATE=0.0026;AVGPOST=0.8617;SNPSOURCE=LOWCOV;AC=1941;LDAF=0.8423;AF=0.89;ASN_AF=0.99;AMR_AF=0.93;AFR_AF=0.64;EUR_AF=0.95;EFF=INTERGENIC(MODIFIER|||||||||)
+1 53234 . CAT C 227.0 PASS AA=CAT;AVGPOST=0.9936;AN=2184;VT=INDEL;THETA=0.0119;AC=10;LDAF=0.0074;RSQ=0.6237;ERATE=0.0007;AF=0.0046;AMR_AF=0.0028;AFR_AF=0.02;EFF=INTERGENIC(MODIFIER|||||||||)
+1 54353 rs140052487 C A 100.0 PASS THETA=0.0026;AA=C;AN=2184;AC=16;VT=SNP;RSQ=0.5074;SNPSOURCE=LOWCOV;AVGPOST=0.9844;LDAF=0.0146;ERATE=0.0058;AF=0.01;ASN_AF=0.01;AMR_AF=0.0028;AFR_AF=0.02;EUR_AF=0.0013;EFF=INTERGENIC(MODIFIER|||||||||)
+1 54421 rs146477069 A G 100.0 PASS ERATE=0.0013;AN=2184;AC=220;VT=SNP;RSQ=0.7869;AVGPOST=0.9461;AA=A;THETA=0.0025;SNPSOURCE=LOWCOV;LDAF=0.1190;AF=0.10;ASN_AF=0.25;AMR_AF=0.12;AFR_AF=0.03;EUR_AF=0.02;EFF=INTERGENIC(MODIFIER|||||||||)
+1 54490 rs141149254 G A 100.0 PASS ERATE=0.0004;THETA=0.0074;AA=G;AN=2184;VT=SNP;RSQ=0.8366;AVGPOST=0.9646;AC=175;SNPSOURCE=LOWCOV;LDAF=0.0929;AF=0.08;ASN_AF=0.0035;AMR_AF=0.12;AFR_AF=0.03;EUR_AF=0.15;EFF=INTERGENIC(MODIFIER|||||||||)
+1 54676 rs2462492 C T 100.0 PASS LDAF=0.1528;RSQ=0.6989;AA=T;AN=2184;AC=267;VT=SNP;AVGPOST=0.8998;SNPSOURCE=LOWCOV;THETA=0.0110;ERATE=0.0037;AF=0.12;ASN_AF=0.02;AMR_AF=0.20;AFR_AF=0.09;EUR_AF=0.18;EFF=INTERGENIC(MODIFIER|||||||||)
+1 54753 rs143174675 T G 100.0 PASS AA=T;AN=2184;RSQ=0.6820;AC=65;VT=SNP;THETA=0.0080;ERATE=0.0016;SNPSOURCE=LOWCOV;AVGPOST=0.9697;LDAF=0.0399;AF=0.03;AMR_AF=0.04;AFR_AF=0.07;EUR_AF=0.03;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55164 rs3091274 C A 100.0 PASS AN=2184;VT=SNP;ERATE=0.0045;AA=A;THETA=0.0162;SNPSOURCE=LOWCOV;AC=1955;RSQ=0.6373;AVGPOST=0.8686;LDAF=0.8489;AF=0.90;ASN_AF=0.99;AMR_AF=0.94;AFR_AF=0.65;EUR_AF=0.96;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55249 . C CTATGG 443.0 PASS AA=C;AVGPOST=0.9073;ERATE=0.0063;RSQ=0.5891;AN=2184;THETA=0.0038;VT=INDEL;AC=151;LDAF=0.0968;AF=0.07;ASN_AF=0.16;AMR_AF=0.08;AFR_AF=0.03;EUR_AF=0.02;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55299 rs10399749 C T 100.0 PASS RSQ=0.7602;LDAF=0.2954;AN=2184;VT=SNP;ERATE=0.0051;AA=c;AC=554;SNPSOURCE=LOWCOV;AVGPOST=0.8845;THETA=0.0070;AF=0.25;ASN_AF=0.33;AMR_AF=0.21;AFR_AF=0.39;EUR_AF=0.13;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55313 rs182462964 A T 100.0 PASS ERATE=0.0004;RSQ=0.6112;AVGPOST=0.9994;AN=2184;VT=SNP;THETA=0.0057;AA=A;SNPSOURCE=LOWCOV;AC=1;LDAF=0.0008;AF=0.0005;AFR_AF=0.0020;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55326 rs3107975 T C 100.0 PASS AA=C;ERATE=0.0074;AN=2184;THETA=0.0085;VT=SNP;SNPSOURCE=LOWCOV;AVGPOST=0.9622;AC=90;RSQ=0.6901;LDAF=0.0562;AF=0.04;ASN_AF=0.07;AMR_AF=0.02;AFR_AF=0.07;EUR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55330 rs185215913 G A 100.0 PASS ERATE=0.0005;AA=G;AN=2184;VT=SNP;THETA=0.0086;AVGPOST=0.9988;LDAF=0.0011;SNPSOURCE=LOWCOV;AC=1;RSQ=0.4701;AF=0.0005;AFR_AF=0.0020;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55367 rs190850374 G A 100.0 PASS ERATE=0.0004;THETA=0.0044;AA=G;AN=2184;VT=SNP;LDAF=0.0029;RSQ=0.3860;SNPSOURCE=LOWCOV;AVGPOST=0.9961;AC=2;AF=0.0009;AMR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55388 rs182711216 C T 100.0 PASS THETA=0.0102;ERATE=0.0005;AA=C;AVGPOST=0.9983;AN=2184;LDAF=0.0010;VT=SNP;RSQ=0.2348;SNPSOURCE=LOWCOV;AC=1;AF=0.0005;ASN_AF=0.0017;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55394 rs2949420 T A 100.0 PASS AC=18;AN=2184;VT=SNP;AA=A;RSQ=0.4995;AVGPOST=0.9784;LDAF=0.0171;SNPSOURCE=LOWCOV;ERATE=0.0012;THETA=0.0063;AF=0.01;AMR_AF=0.01;AFR_AF=0.0041;EUR_AF=0.02;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55416 rs193242050 G A 100.0 PASS AA=G;AN=2184;AVGPOST=0.9944;VT=SNP;LDAF=0.0064;AC=9;THETA=0.0019;RSQ=0.6553;SNPSOURCE=LOWCOV;ERATE=0.0006;AF=0.0041;AFR_AF=0.02;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55427 rs183189405 T C 100.0 PASS THETA=0.0054;AA=T;AN=2184;VT=SNP;AVGPOST=0.9969;LDAF=0.0020;SNPSOURCE=LOWCOV;AC=1;RSQ=0.2759;ERATE=0.0007;AF=0.0005;AFR_AF=0.0020;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55816 rs187434873 G A 100.0 PASS AN=2184;THETA=0.0119;VT=SNP;AC=10;RSQ=0.4578;AA=A;SNPSOURCE=LOWCOV;AVGPOST=0.9844;LDAF=0.0108;ERATE=0.0007;AF=0.0046;AMR_AF=0.01;EUR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55850 rs191890754 C G 100.0 PASS AVGPOST=0.9921;AA=G;AN=2184;VT=SNP;RSQ=0.4083;THETA=0.0045;LDAF=0.0056;AC=5;SNPSOURCE=LOWCOV;ERATE=0.0006;AF=0.0023;EUR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55852 rs184233019 G C 100.0 PASS THETA=0.0137;AA=G;AN=2184;RSQ=0.5433;ERATE=0.0009;LDAF=0.0046;VT=SNP;AVGPOST=0.9953;AC=5;SNPSOURCE=LOWCOV;AF=0.0023;AMR_AF=0.01;EUR_AF=0.0013;EFF=INTERGENIC(MODIFIER|||||||||)
diff -r 000000000000 -r 3123ce7acd0e test-data/gemini_load_result1.db
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diff -r 000000000000 -r 3123ce7acd0e test-data/gemini_load_result2.db
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diff -r 000000000000 -r 3123ce7acd0e test-data/gemini_versioned_databases.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gemini_versioned_databases.loc Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,3 @@
+## GEMINI versioned databases
+#DownloadDate dbkey DBversion Description Path
+1999-01-01 hg19 200 GEMINI annotations (test snapshot) ${__HERE__}/test-cache
diff -r 000000000000 -r 3123ce7acd0e test-data/gemini_windower_template.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gemini_windower_template.tabular Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,142 @@
+chr1 0 50000 .
+chr1 50000000 50050000 .
+chr1 100000000 100050000 .
+chr1 150000000 150050000 .
+chr1 200000000 200050000 .
+chr10 0 50000 .
+chr10 50000000 50050000 .
+chr10 100000000 100050000 .
+chr11 0 50000 .
+chr11 50000000 50050000 .
+chr11 100000000 100050000 .
+chr11_gl000202_random 0 40103 .
+chr12 0 50000 .
+chr12 50000000 50050000 .
+chr12 100000000 100050000 .
+chr13 0 50000 .
+chr13 50000000 50050000 .
+chr13 100000000 100050000 .
+chr14 0 50000 .
+chr14 50000000 50050000 .
+chr14 100000000 100050000 .
+chr15 0 50000 .
+chr15 50000000 50050000 .
+chr15 100000000 100050000 .
+chr16 0 50000 .
+chr16 50000000 50050000 .
+chr17 0 50000 .
+chr17 50000000 50050000 .
+chr17_ctg5_hap1 0 50000 .
+chr17_gl000203_random 0 37498 .
+chr17_gl000204_random 0 50000 .
+chr17_gl000205_random 0 50000 .
+chr17_gl000206_random 0 41001 .
+chr18 0 50000 .
+chr18 50000000 50050000 .
+chr18_gl000207_random 0 4262 .
+chr19 0 50000 .
+chr19 50000000 50050000 .
+chr19_gl000208_random 0 50000 .
+chr19_gl000209_random 0 50000 .
+chr1_gl000191_random 0 50000 .
+chr1_gl000192_random 0 50000 .
+chr2 0 50000 .
+chr2 50000000 50050000 .
+chr2 100000000 100050000 .
+chr2 150000000 150050000 .
+chr2 200000000 200050000 .
+chr20 0 50000 .
+chr20 50000000 50050000 .
+chr21 0 50000 .
+chr21_gl000210_random 0 27682 .
+chr22 0 50000 .
+chr22 50000000 50050000 .
+chr3 0 50000 .
+chr3 50000000 50050000 .
+chr3 100000000 100050000 .
+chr3 150000000 150050000 .
+chr4 0 50000 .
+chr4 50000000 50050000 .
+chr4 100000000 100050000 .
+chr4 150000000 150050000 .
+chr4_ctg9_hap1 0 50000 .
+chr4_gl000193_random 0 50000 .
+chr4_gl000194_random 0 50000 .
+chr5 0 50000 .
+chr5 50000000 50050000 .
+chr5 100000000 100050000 .
+chr5 150000000 150050000 .
+chr6 0 50000 .
+chr6 50000000 50050000 .
+chr6 100000000 100050000 .
+chr6 150000000 150050000 .
+chr6_apd_hap1 0 50000 .
+chr6_cox_hap2 0 50000 .
+chr6_dbb_hap3 0 50000 .
+chr6_mann_hap4 0 50000 .
+chr6_mcf_hap5 0 50000 .
+chr6_qbl_hap6 0 50000 .
+chr6_ssto_hap7 0 50000 .
+chr7 0 50000 .
+chr7 50000000 50050000 .
+chr7 100000000 100050000 .
+chr7 150000000 150050000 .
+chr7_gl000195_random 0 50000 .
+chr8 0 50000 .
+chr8 50000000 50050000 .
+chr8 100000000 100050000 .
+chr8_gl000196_random 0 38914 .
+chr8_gl000197_random 0 37175 .
+chr9 0 50000 .
+chr9 50000000 50050000 .
+chr9 100000000 100050000 .
+chr9_gl000198_random 0 50000 .
+chr9_gl000199_random 0 50000 .
+chr9_gl000200_random 0 50000 .
+chr9_gl000201_random 0 36148 .
+chrM 0 16571 .
+chrUn_gl000211 0 50000 .
+chrUn_gl000212 0 50000 .
+chrUn_gl000213 0 50000 .
+chrUn_gl000214 0 50000 .
+chrUn_gl000215 0 50000 .
+chrUn_gl000216 0 50000 .
+chrUn_gl000217 0 50000 .
+chrUn_gl000218 0 50000 .
+chrUn_gl000219 0 50000 .
+chrUn_gl000220 0 50000 .
+chrUn_gl000221 0 50000 .
+chrUn_gl000222 0 50000 .
+chrUn_gl000223 0 50000 .
+chrUn_gl000224 0 50000 .
+chrUn_gl000225 0 50000 .
+chrUn_gl000226 0 15008 .
+chrUn_gl000227 0 50000 .
+chrUn_gl000228 0 50000 .
+chrUn_gl000229 0 19913 .
+chrUn_gl000230 0 43691 .
+chrUn_gl000231 0 27386 .
+chrUn_gl000232 0 40652 .
+chrUn_gl000233 0 45941 .
+chrUn_gl000234 0 40531 .
+chrUn_gl000235 0 34474 .
+chrUn_gl000236 0 41934 .
+chrUn_gl000237 0 45867 .
+chrUn_gl000238 0 39939 .
+chrUn_gl000239 0 33824 .
+chrUn_gl000240 0 41933 .
+chrUn_gl000241 0 42152 .
+chrUn_gl000242 0 43523 .
+chrUn_gl000243 0 43341 .
+chrUn_gl000244 0 39929 .
+chrUn_gl000245 0 36651 .
+chrUn_gl000246 0 38154 .
+chrUn_gl000247 0 36422 .
+chrUn_gl000248 0 39786 .
+chrUn_gl000249 0 38502 .
+chrX 0 50000 .
+chrX 50000000 50050000 .
+chrX 100000000 100050000 .
+chrX 150000000 150050000 .
+chrY 0 50000 .
+chrY 50000000 50050000 .
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini-config.yaml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-cache/gemini-config.yaml Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,15 @@
+annotation_dir: gemini/data
+versions:
+ ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.tidy.vcf.gz: 4
+ ESP6500SI.all.snps_indels.tidy.v2.vcf.gz: 2
+ ExAC.r0.3.sites.vep.tidy.vcf.gz: 4
+ GRCh37-gms-mappability.vcf.gz: 2
+ clinvar_20170130.tidy.vcf.gz: 5
+ cosmic-v68-GRCh37.tidy.vcf.gz: 3
+ dbsnp.b147.20160601.tidy.vcf.gz: 1
+ detailed_gene_table_v75: 2
+ geno2mp.variants.tidy.vcf.gz: 1
+ gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz: 2
+ hg19.rmsk.bed.gz: 2
+ summary_gene_table_v75: 2
+ whole_genome_SNVs.tsv.compressed.gz: 2
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/29way_pi_lods_elements_12mers.chr_specific.fdr_0.1_with_scores.txt.hg19.merged.bed.gz
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.tidy.vcf.gz
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/ESP6500SI.all.snps_indels.tidy.v2.vcf.gz
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/ESP6500SI.all.snps_indels.tidy.v2.vcf.gz.tbi
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/ExAC.r0.3.sites.vep.tidy.vcf.gz
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/GRC_patch_regions.bed.gz
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/GRCh37-gms-mappability.vcf.gz
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/GRCh37-gms-mappability.vcf.gz.tbi
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/cancer_gene_census.20140120.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-cache/gemini/data/cancer_gene_census.20140120.tsv Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,19 @@
+ARHH "RAS homolog gene family, member H (TTF)" 399 4 4p13 yes NHL L Dom T BCL6
+BCL5 B-cell CLL/lymphoma 5 603 17 17q22 yes CLL L Dom T MYC
+BCL6 B-cell CLL/lymphoma 6 604 3 3q27 yes "NHL, CLL" L Dom "T, Mis" "IG loci, ZNFN1A1, LCP1, PIM1, TFRC, CIITA, NACA, HSPCB, HSPCA, HIST1H4I, IL21R, POU2AF1, ARHH, EIF4A2, SFRS3"
+BCOR BCL6 corepressor 54880 X Xp11.4 yes "retinoblastoma, AML, APL (translocation)" Rec "F, N, S, T" RARA yes oculo-facio-cardio-dental genetic
+CIITA "class II, major histocompatibility complex, transactivator" 4261 16 16p13 yes "PMBL, Hodgkin lymphoma" L Dom T "FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"
+EIF4A2 "eukaryotic translation initiation factor 4A, isoform 2" 1974 3 3q27.3 yes NHL L Dom T BCL6
+HIST1H4I "histone 1, H4i (H4FM)" 8294 6 6p21.3 yes NHL L Dom T BCL6
+HSPCA "heat shock 90kDa protein 1, alpha" 3320 14 14q32.31 yes NHL L Dom T BCL6
+HSPCB "heat shock 90kDa protein 1, beta" 3326 6 6p12 yes NHL L Dom T BCL6
+IGH@ immunoglobulin heavy locus 3492 14 14q32.33 yes "MM, Burkitt lymphoma, NHL, CLL, B-ALL, MALT, MLCLS" L Dom T "MYC, FGFR3,PAX5, IRTA1, IRF4, CCND1, BCL9, BCL8, BCL6, BCL2, BCL3, BCL10, BCL11A. LHX4, DDX6, NFKB2, PAFAH1B2, PCSK7, CRLF2"
+IKZF1 IKAROS family zinc finger 1 10320 7 7p12.2 yes "ALL, DLBCL" L "Rec,Dom" "D,T" BCL6
+IL21R interleukin 21 receptor 50615 16 16p11 yes NHL L Dom T BCL6
+LCP1 lymphocyte cytosolic protein 1 (L-plastin) 3936 13 13q14.1-q14.3 yes NHL L Dom T BCL6
+MYC v-myc myelocytomatosis viral oncogene homolog (avian) 4609 8 8q24.12-q24.13 yes "Burkitt lymphoma, amplified in other cancers, B-CLL" "L, E" Dom "A, T" "IGK@, BCL5, BCL7A , BTG1, TRA@, IGH@"
+NACA nascent-polypeptide-associated complex alpha polypeptide 4666 12 12q23-q24.1 yes NHL L Dom T BCL6
+PIM1 pim-1 oncogene 5292 6 6p21.2 yes NHL L Dom T BCL6
+POU2AF1 "POU domain, class 2, associating factor 1 (OBF1)" 5450 11 11q23.1 yes NHL L Dom T BCL6
+SFRS3 "splicing factor, arginine/serine-rich 3" 6428 6 6p21 yes follicular lymphoma L Dom T BCL6
+TFRC "transferrin receptor (p90, CD71)" 7037 3 3q29 yes NHL L Dom T BCL6
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/cosmic-v68-GRCh37.tidy.vcf.gz
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/detailed_gene_table_v75
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-cache/gemini/data/detailed_gene_table_v75 Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,114 @@
+Chromosome Gene_name Is_hgnc Ensembl_gene_id Ensembl_transcript_id Biotype Transcript_status CCDS_id HGNC_id CDS_length Protein_length Transcript_start Transcript_end strand Synonyms Rvis_pct entrez_gene_id mammalian_phenotype_id
+chr3 None 0 ENSG00000239093 ENST00000459452 snoRNA KNOWN None None None None 187141103 187141207 1 None None None None
+chr3 None 0 ENSG00000228952 ENST00000440726 lincRNA KNOWN None None None None 187166633 187167238 1 None None None None
+chr3 None 0 ENSG00000223401 ENST00000450760 lincRNA KNOWN None None None None 187461474 187463208 1 None None None None
+chr3 MASP 0 ENSG00000127241 ENST00000337774 protein_coding KNOWN CCDS33907 None 2100 699 186935942 187009810 -1 PRSS5,MASP1,CRARF 16.8141071 5648 None
+chr3 PRSS5 0 ENSG00000127241 ENST00000337774 protein_coding KNOWN CCDS33907 None 2100 699 186935942 187009810 -1 MASP1,CRARF,MASP 16.8141071 5648 None
+chr3 MASP1 1 ENSG00000127241 ENST00000337774 protein_coding KNOWN CCDS33907 6901 2100 699 186935942 187009810 -1 PRSS5,CRARF,MASP 16.8141071 5648 None
+chr3 CRARF 0 ENSG00000127241 ENST00000337774 protein_coding KNOWN CCDS33907 None 2100 699 186935942 187009810 -1 PRSS5,MASP1,MASP 16.8141071 5648 None
+chr3 MASP 0 ENSG00000127241 ENST00000296280 protein_coding KNOWN CCDS33908 None 2187 728 186951870 187009646 -1 PRSS5,MASP1,CRARF 16.8141071 5648 None
+chr3 PRSS5 0 ENSG00000127241 ENST00000296280 protein_coding KNOWN CCDS33908 None 2187 728 186951870 187009646 -1 MASP1,CRARF,MASP 16.8141071 5648 None
+chr3 MASP1 1 ENSG00000127241 ENST00000296280 protein_coding KNOWN CCDS33908 6901 2187 728 186951870 187009646 -1 PRSS5,CRARF,MASP 16.8141071 5648 None
+chr3 CRARF 0 ENSG00000127241 ENST00000296280 protein_coding KNOWN CCDS33908 None 2187 728 186951870 187009646 -1 PRSS5,MASP1,MASP 16.8141071 5648 None
+chr3 MASP 0 ENSG00000127241 ENST00000392472 protein_coding PUTATIVE None None 1848 615 186951872 187009765 -1 PRSS5,MASP1,CRARF 16.8141071 5648 None
+chr3 PRSS5 0 ENSG00000127241 ENST00000392472 protein_coding PUTATIVE None None 1848 615 186951872 187009765 -1 MASP1,CRARF,MASP 16.8141071 5648 None
+chr3 MASP1 1 ENSG00000127241 ENST00000392472 protein_coding PUTATIVE None 6901 1848 615 186951872 187009765 -1 PRSS5,CRARF,MASP 16.8141071 5648 None
+chr3 CRARF 0 ENSG00000127241 ENST00000392472 protein_coding PUTATIVE None None 1848 615 186951872 187009765 -1 PRSS5,MASP1,MASP 16.8141071 5648 None
+chr3 MASP 0 ENSG00000127241 ENST00000495249 processed_transcript PUTATIVE None None None None 186953655 187009542 -1 PRSS5,MASP1,CRARF 16.8141071 5648 None
+chr3 PRSS5 0 ENSG00000127241 ENST00000495249 processed_transcript PUTATIVE None None None None 186953655 187009542 -1 MASP1,CRARF,MASP 16.8141071 5648 None
+chr3 MASP1 1 ENSG00000127241 ENST00000495249 processed_transcript PUTATIVE None 6901 None None 186953655 187009542 -1 PRSS5,CRARF,MASP 16.8141071 5648 None
+chr3 CRARF 0 ENSG00000127241 ENST00000495249 processed_transcript PUTATIVE None None None None 186953655 187009542 -1 PRSS5,MASP1,MASP 16.8141071 5648 None
+chr3 MASP 0 ENSG00000127241 ENST00000169293 protein_coding KNOWN CCDS33909 None 1143 380 186964149 187009745 -1 PRSS5,MASP1,CRARF 16.8141071 5648 None
+chr3 PRSS5 0 ENSG00000127241 ENST00000169293 protein_coding KNOWN CCDS33909 None 1143 380 186964149 187009745 -1 MASP1,CRARF,MASP 16.8141071 5648 None
+chr3 MASP1 1 ENSG00000127241 ENST00000169293 protein_coding KNOWN CCDS33909 6901 1143 380 186964149 187009745 -1 PRSS5,CRARF,MASP 16.8141071 5648 None
+chr3 CRARF 0 ENSG00000127241 ENST00000169293 protein_coding KNOWN CCDS33909 None 1143 380 186964149 187009745 -1 PRSS5,MASP1,MASP 16.8141071 5648 None
+chr3 MASP 0 ENSG00000127241 ENST00000392470 protein_coding PUTATIVE None None 1065 354 186964947 187009670 -1 PRSS5,MASP1,CRARF 16.8141071 5648 None
+chr3 PRSS5 0 ENSG00000127241 ENST00000392470 protein_coding PUTATIVE None None 1065 354 186964947 187009670 -1 MASP1,CRARF,MASP 16.8141071 5648 None
+chr3 MASP1 1 ENSG00000127241 ENST00000392470 protein_coding PUTATIVE None 6901 1065 354 186964947 187009670 -1 PRSS5,CRARF,MASP 16.8141071 5648 None
+chr3 CRARF 0 ENSG00000127241 ENST00000392470 protein_coding PUTATIVE None None 1065 354 186964947 187009670 -1 PRSS5,MASP1,MASP 16.8141071 5648 None
+chr3 MASP 0 ENSG00000127241 ENST00000460839 retained_intron KNOWN None None None None 186974373 187003796 -1 PRSS5,MASP1,CRARF 16.8141071 5648 None
+chr3 PRSS5 0 ENSG00000127241 ENST00000460839 retained_intron KNOWN None None None None 186974373 187003796 -1 MASP1,CRARF,MASP 16.8141071 5648 None
+chr3 MASP1 1 ENSG00000127241 ENST00000460839 retained_intron KNOWN None 6901 None None 186974373 187003796 -1 PRSS5,CRARF,MASP 16.8141071 5648 None
+chr3 CRARF 0 ENSG00000127241 ENST00000460839 retained_intron KNOWN None None None None 186974373 187003796 -1 PRSS5,MASP1,MASP 16.8141071 5648 None
+chr3 MASP 0 ENSG00000127241 ENST00000392475 protein_coding NOVEL None None 614 203 186974603 187009768 -1 PRSS5,MASP1,CRARF 16.8141071 5648 None
+chr3 PRSS5 0 ENSG00000127241 ENST00000392475 protein_coding NOVEL None None 614 203 186974603 187009768 -1 MASP1,CRARF,MASP 16.8141071 5648 None
+chr3 MASP1 1 ENSG00000127241 ENST00000392475 protein_coding NOVEL None 6901 614 203 186974603 187009768 -1 PRSS5,CRARF,MASP 16.8141071 5648 None
+chr3 CRARF 0 ENSG00000127241 ENST00000392475 protein_coding NOVEL None None 614 203 186974603 187009768 -1 PRSS5,MASP1,MASP 16.8141071 5648 None
+chr3 MASP 0 ENSG00000127241 ENST00000439271 protein_coding PUTATIVE None None 355 117 186980469 187009746 -1 PRSS5,MASP1,CRARF 16.8141071 5648 None
+chr3 PRSS5 0 ENSG00000127241 ENST00000439271 protein_coding PUTATIVE None None 355 117 186980469 187009746 -1 MASP1,CRARF,MASP 16.8141071 5648 None
+chr3 MASP1 1 ENSG00000127241 ENST00000439271 protein_coding PUTATIVE None 6901 355 117 186980469 187009746 -1 PRSS5,CRARF,MASP 16.8141071 5648 None
+chr3 CRARF 0 ENSG00000127241 ENST00000439271 protein_coding PUTATIVE None None 355 117 186980469 187009746 -1 PRSS5,MASP1,MASP 16.8141071 5648 None
+chr3 MASP 0 ENSG00000127241 ENST00000425937 protein_coding PUTATIVE None None 166 54 186980502 187009485 -1 PRSS5,MASP1,CRARF 16.8141071 5648 None
+chr3 PRSS5 0 ENSG00000127241 ENST00000425937 protein_coding PUTATIVE None None 166 54 186980502 187009485 -1 MASP1,CRARF,MASP 16.8141071 5648 None
+chr3 MASP1 1 ENSG00000127241 ENST00000425937 protein_coding PUTATIVE None 6901 166 54 186980502 187009485 -1 PRSS5,CRARF,MASP 16.8141071 5648 None
+chr3 CRARF 0 ENSG00000127241 ENST00000425937 protein_coding PUTATIVE None None 166 54 186980502 187009485 -1 PRSS5,MASP1,MASP 16.8141071 5648 None
+chr3 IFRG28 0 ENSG00000136514 ENST00000259030 protein_coding KNOWN CCDS33910 None 741 246 187086120 187089864 1 RTP4,Z3CXXC4 94.35008257 64108 None
+chr3 RTP4 1 ENSG00000136514 ENST00000259030 protein_coding KNOWN CCDS33910 23992 741 246 187086120 187089864 1 IFRG28,Z3CXXC4 94.35008257 64108 None
+chr3 Z3CXXC4 0 ENSG00000136514 ENST00000259030 protein_coding KNOWN CCDS33910 None 741 246 187086120 187089864 1 IFRG28,RTP4 94.35008257 64108 None
+chr3 SST 1 ENSG00000157005 ENST00000287641 protein_coding KNOWN CCDS3288 11329 351 116 187386694 187388187 -1 SMST 78.16112291 6750 MP:0002873,MP:0005386,MP:0005376,MP:0005381,MP:0003631,MP:0005378
+chr3 SMST 0 ENSG00000157005 ENST00000287641 protein_coding KNOWN CCDS3288 None 351 116 187386694 187388187 -1 SST 78.16112291 6750 MP:0002873,MP:0005386,MP:0005376,MP:0005381,MP:0003631,MP:0005378
+chr3 Z3CXXC2 0 ENSG00000198471 ENST00000358241 protein_coding KNOWN CCDS33911 None 678 225 187416047 187420345 -1 RTP2,MGC78665 69.20853975 344892 MP:0005389
+chr3 RTP2 1 ENSG00000198471 ENST00000358241 protein_coding KNOWN CCDS33911 32486 678 225 187416047 187420345 -1 Z3CXXC2,MGC78665 69.20853975 344892 MP:0005389
+chr3 MGC78665 0 ENSG00000198471 ENST00000358241 protein_coding KNOWN CCDS33911 None 678 225 187416047 187420345 -1 Z3CXXC2,RTP2 69.20853975 344892 MP:0005389
+chr3 None 0 ENSG00000228804 ENST00000449623 protein_coding PUTATIVE None None 390 129 187420101 187451637 1 None None None None
+chr3 None 0 ENSG00000228804 ENST00000437407 protein_coding PUTATIVE None None 153 50 187420154 187450203 1 None None None None
+chr3 ZNF51 0 ENSG00000113916 ENST00000406870 protein_coding KNOWN CCDS3289 None 2121 706 187439165 187463515 -1 LAZ3,BCL5,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 LAZ3 0 ENSG00000113916 ENST00000406870 protein_coding KNOWN CCDS3289 None 2121 706 187439165 187463515 -1 BCL5,ZNF51,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL5 0 ENSG00000113916 ENST00000406870 protein_coding KNOWN CCDS3289 None 2121 706 187439165 187463515 -1 LAZ3,ZNF51,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL6A 0 ENSG00000113916 ENST00000406870 protein_coding KNOWN CCDS3289 None 2121 706 187439165 187463515 -1 LAZ3,ZNF51,BCL6,BCL5,ZBTB27 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL6 1 ENSG00000113916 ENST00000406870 protein_coding KNOWN CCDS3289 1001 2121 706 187439165 187463515 -1 LAZ3,ZNF51,ZBTB27,BCL5,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 ZBTB27 0 ENSG00000113916 ENST00000406870 protein_coding KNOWN CCDS3289 None 2121 706 187439165 187463515 -1 LAZ3,ZNF51,BCL6,BCL5,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 ZNF51 0 ENSG00000113916 ENST00000419510 nonsense_mediated_decay KNOWN None None 168 55 187439175 187454876 -1 LAZ3,BCL5,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 LAZ3 0 ENSG00000113916 ENST00000419510 nonsense_mediated_decay KNOWN None None 168 55 187439175 187454876 -1 BCL5,ZNF51,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL5 0 ENSG00000113916 ENST00000419510 nonsense_mediated_decay KNOWN None None 168 55 187439175 187454876 -1 LAZ3,ZNF51,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL6A 0 ENSG00000113916 ENST00000419510 nonsense_mediated_decay KNOWN None None 168 55 187439175 187454876 -1 LAZ3,ZNF51,BCL6,BCL5,ZBTB27 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL6 1 ENSG00000113916 ENST00000419510 nonsense_mediated_decay KNOWN None 1001 168 55 187439175 187454876 -1 LAZ3,ZNF51,ZBTB27,BCL5,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 ZBTB27 0 ENSG00000113916 ENST00000419510 nonsense_mediated_decay KNOWN None None 168 55 187439175 187454876 -1 LAZ3,ZNF51,BCL6,BCL5,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 ZNF51 0 ENSG00000113916 ENST00000232014 protein_coding KNOWN CCDS3289 None 2121 706 187440186 187454357 -1 LAZ3,BCL5,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 LAZ3 0 ENSG00000113916 ENST00000232014 protein_coding KNOWN CCDS3289 None 2121 706 187440186 187454357 -1 BCL5,ZNF51,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL5 0 ENSG00000113916 ENST00000232014 protein_coding KNOWN CCDS3289 None 2121 706 187440186 187454357 -1 LAZ3,ZNF51,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL6A 0 ENSG00000113916 ENST00000232014 protein_coding KNOWN CCDS3289 None 2121 706 187440186 187454357 -1 LAZ3,ZNF51,BCL6,BCL5,ZBTB27 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL6 1 ENSG00000113916 ENST00000232014 protein_coding KNOWN CCDS3289 1001 2121 706 187440186 187454357 -1 LAZ3,ZNF51,ZBTB27,BCL5,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 ZBTB27 0 ENSG00000113916 ENST00000232014 protein_coding KNOWN CCDS3289 None 2121 706 187440186 187454357 -1 LAZ3,ZNF51,BCL6,BCL5,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 ZNF51 0 ENSG00000113916 ENST00000450123 protein_coding NOVEL CCDS46975 None 1953 650 187440220 187452670 -1 LAZ3,BCL5,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 LAZ3 0 ENSG00000113916 ENST00000450123 protein_coding NOVEL CCDS46975 None 1953 650 187440220 187452670 -1 BCL5,ZNF51,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL5 0 ENSG00000113916 ENST00000450123 protein_coding NOVEL CCDS46975 None 1953 650 187440220 187452670 -1 LAZ3,ZNF51,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL6A 0 ENSG00000113916 ENST00000450123 protein_coding NOVEL CCDS46975 None 1953 650 187440220 187452670 -1 LAZ3,ZNF51,BCL6,BCL5,ZBTB27 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL6 1 ENSG00000113916 ENST00000450123 protein_coding NOVEL CCDS46975 1001 1953 650 187440220 187452670 -1 LAZ3,ZNF51,ZBTB27,BCL5,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 ZBTB27 0 ENSG00000113916 ENST00000450123 protein_coding NOVEL CCDS46975 None 1953 650 187440220 187452670 -1 LAZ3,ZNF51,BCL6,BCL5,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 ZNF51 0 ENSG00000113916 ENST00000479110 retained_intron KNOWN None None None None 187442357 187443411 -1 LAZ3,BCL5,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 LAZ3 0 ENSG00000113916 ENST00000479110 retained_intron KNOWN None None None None 187442357 187443411 -1 BCL5,ZNF51,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL5 0 ENSG00000113916 ENST00000479110 retained_intron KNOWN None None None None 187442357 187443411 -1 LAZ3,ZNF51,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL6A 0 ENSG00000113916 ENST00000479110 retained_intron KNOWN None None None None 187442357 187443411 -1 LAZ3,ZNF51,BCL6,BCL5,ZBTB27 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL6 1 ENSG00000113916 ENST00000479110 retained_intron KNOWN None 1001 None None 187442357 187443411 -1 LAZ3,ZNF51,ZBTB27,BCL5,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 ZBTB27 0 ENSG00000113916 ENST00000479110 retained_intron KNOWN None None None None 187442357 187443411 -1 LAZ3,ZNF51,BCL6,BCL5,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 ZNF51 0 ENSG00000113916 ENST00000430339 protein_coding KNOWN None None 365 120 187449515 187452735 -1 LAZ3,BCL5,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 LAZ3 0 ENSG00000113916 ENST00000430339 protein_coding KNOWN None None 365 120 187449515 187452735 -1 BCL5,ZNF51,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL5 0 ENSG00000113916 ENST00000430339 protein_coding KNOWN None None 365 120 187449515 187452735 -1 LAZ3,ZNF51,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL6A 0 ENSG00000113916 ENST00000430339 protein_coding KNOWN None None 365 120 187449515 187452735 -1 LAZ3,ZNF51,BCL6,BCL5,ZBTB27 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL6 1 ENSG00000113916 ENST00000430339 protein_coding KNOWN None 1001 365 120 187449515 187452735 -1 LAZ3,ZNF51,ZBTB27,BCL5,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 ZBTB27 0 ENSG00000113916 ENST00000430339 protein_coding KNOWN None None 365 120 187449515 187452735 -1 LAZ3,ZNF51,BCL6,BCL5,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 ZNF51 0 ENSG00000113916 ENST00000480458 processed_transcript KNOWN None None None None 187449553 187463225 -1 LAZ3,BCL5,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 LAZ3 0 ENSG00000113916 ENST00000480458 processed_transcript KNOWN None None None None 187449553 187463225 -1 BCL5,ZNF51,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL5 0 ENSG00000113916 ENST00000480458 processed_transcript KNOWN None None None None 187449553 187463225 -1 LAZ3,ZNF51,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL6A 0 ENSG00000113916 ENST00000480458 processed_transcript KNOWN None None None None 187449553 187463225 -1 LAZ3,ZNF51,BCL6,BCL5,ZBTB27 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL6 1 ENSG00000113916 ENST00000480458 processed_transcript KNOWN None 1001 None None 187449553 187463225 -1 LAZ3,ZNF51,ZBTB27,BCL5,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 ZBTB27 0 ENSG00000113916 ENST00000480458 processed_transcript KNOWN None None None None 187449553 187463225 -1 LAZ3,ZNF51,BCL6,BCL5,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 ZNF51 0 ENSG00000113916 ENST00000438077 protein_coding KNOWN None None 312 103 187449568 187455732 -1 LAZ3,BCL5,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 LAZ3 0 ENSG00000113916 ENST00000438077 protein_coding KNOWN None None 312 103 187449568 187455732 -1 BCL5,ZNF51,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL5 0 ENSG00000113916 ENST00000438077 protein_coding KNOWN None None 312 103 187449568 187455732 -1 LAZ3,ZNF51,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL6A 0 ENSG00000113916 ENST00000438077 protein_coding KNOWN None None 312 103 187449568 187455732 -1 LAZ3,ZNF51,BCL6,BCL5,ZBTB27 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL6 1 ENSG00000113916 ENST00000438077 protein_coding KNOWN None 1001 312 103 187449568 187455732 -1 LAZ3,ZNF51,ZBTB27,BCL5,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 ZBTB27 0 ENSG00000113916 ENST00000438077 protein_coding KNOWN None None 312 103 187449568 187455732 -1 LAZ3,ZNF51,BCL6,BCL5,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 ZNF51 0 ENSG00000113916 ENST00000470319 retained_intron KNOWN None None None None 187452233 187463260 -1 LAZ3,BCL5,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 LAZ3 0 ENSG00000113916 ENST00000470319 retained_intron KNOWN None None None None 187452233 187463260 -1 BCL5,ZNF51,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL5 0 ENSG00000113916 ENST00000470319 retained_intron KNOWN None None None None 187452233 187463260 -1 LAZ3,ZNF51,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL6A 0 ENSG00000113916 ENST00000470319 retained_intron KNOWN None None None None 187452233 187463260 -1 LAZ3,ZNF51,BCL6,BCL5,ZBTB27 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL6 1 ENSG00000113916 ENST00000470319 retained_intron KNOWN None 1001 None None 187452233 187463260 -1 LAZ3,ZNF51,ZBTB27,BCL5,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 ZBTB27 0 ENSG00000113916 ENST00000470319 retained_intron KNOWN None None None None 187452233 187463260 -1 LAZ3,ZNF51,BCL6,BCL5,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 ZNF51 0 ENSG00000113916 ENST00000496823 processed_transcript PUTATIVE None None None None 187453975 187463247 -1 LAZ3,BCL5,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 LAZ3 0 ENSG00000113916 ENST00000496823 processed_transcript PUTATIVE None None None None 187453975 187463247 -1 BCL5,ZNF51,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL5 0 ENSG00000113916 ENST00000496823 processed_transcript PUTATIVE None None None None 187453975 187463247 -1 LAZ3,ZNF51,BCL6,ZBTB27,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL6A 0 ENSG00000113916 ENST00000496823 processed_transcript PUTATIVE None None None None 187453975 187463247 -1 LAZ3,ZNF51,BCL6,BCL5,ZBTB27 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL6 1 ENSG00000113916 ENST00000496823 processed_transcript PUTATIVE None 1001 None None 187453975 187463247 -1 LAZ3,ZNF51,ZBTB27,BCL5,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 ZBTB27 0 ENSG00000113916 ENST00000496823 processed_transcript PUTATIVE None None None None 187453975 187463247 -1 LAZ3,ZNF51,BCL6,BCL5,BCL6A 23.5727766 604 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/encode.6celltypes.consensus.bedg.gz
Binary file test-data/test-cache/gemini/data/encode.6celltypes.consensus.bedg.gz has changed
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/encode.6celltypes.consensus.bedg.gz.tbi
Binary file test-data/test-cache/gemini/data/encode.6celltypes.consensus.bedg.gz.tbi has changed
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/genetic_map_HapMapII_GRCh37.gz
Binary file test-data/test-cache/gemini/data/genetic_map_HapMapII_GRCh37.gz has changed
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/genetic_map_HapMapII_GRCh37.gz.tbi
Binary file test-data/test-cache/gemini/data/genetic_map_HapMapII_GRCh37.gz.tbi has changed
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/geno2mp.variants.tidy.vcf.gz
Binary file test-data/test-cache/gemini/data/geno2mp.variants.tidy.vcf.gz has changed
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/geno2mp.variants.tidy.vcf.gz.tbi
Binary file test-data/test-cache/gemini/data/geno2mp.variants.tidy.vcf.gz.tbi has changed
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz
Binary file test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz has changed
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz.tbi
Binary file test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz.tbi has changed
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/hg19.CpG.bed.gz
Binary file test-data/test-cache/gemini/data/hg19.CpG.bed.gz has changed
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/hg19.CpG.bed.gz.tbi
Binary file test-data/test-cache/gemini/data/hg19.CpG.bed.gz.tbi has changed
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/hg19.cytoband.bed.gz
Binary file test-data/test-cache/gemini/data/hg19.cytoband.bed.gz has changed
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/hg19.cytoband.bed.gz.tbi
Binary file test-data/test-cache/gemini/data/hg19.cytoband.bed.gz.tbi has changed
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/hg19.dgv.bed.gz
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/hg19.dgv.bed.gz.tbi
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/hg19.gerp.elements.bed.gz
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/hg19.gerp.elements.bed.gz.tbi
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/hg19.gwas.bed.gz
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/hg19.gwas.bed.gz.tbi
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/hg19.pfam.ucscgenes.bed.gz
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/hg19.pfam.ucscgenes.bed.gz.tbi
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/hg19.rmsk.bed.gz
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/hg19.segdup.bed.gz
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/hg19.vista.enhancers.20131108.bed.gz
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/hg19_fitcons_fc-i6-0_V1-01.bed.gz
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/hg19_fitcons_fc-i6-0_V1-01.bed.gz.tbi
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/hprd_interaction_edges.gz
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diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/kegg_pathways_ensembl66
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-cache/gemini/data/kegg_pathways_ensembl66 Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,30 @@
+B8PSA7 BCL6 BCL6 ENSG00000113916 ENST00000450123 None None
+C9J1C7 MASP1 MASP1 ENSG00000127241 ENST00000439271 None None
+C9JCS5 BCL6 BCL6 ENSG00000113916 ENST00000430339 None None
+C9JCS5 BCL6 BCL6 ENSG00000113916 ENST00000450123 None None
+C9JL16 BCL6 BCL6 ENSG00000113916 ENST00000430339 None None
+C9JL16 BCL6 BCL6 ENSG00000113916 ENST00000438077 None None
+C9JL16 BCL6 BCL6 ENSG00000113916 ENST00000450123 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000169293 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000296280 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000392470 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000392475 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000425937 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000439271 None None
+C9JMA2 MASP1 MASP1 ENSG00000127241 ENST00000392475 None None
+F5H2J0 MASP1 MASP1 ENSG00000127241 ENST00000541896 None None
+F8W876 MASP1 MASP1 ENSG00000127241 ENST00000169293 None None
+F8W876 MASP1 MASP1 ENSG00000127241 ENST00000392470 None None
+P41182 BCL6 BCL6 ENSG00000113916 ENST00000232014 hsa:604 path:hsa05202;Transcriptional_misregulation_in_cancer
+P41182 BCL6 BCL6 ENSG00000113916 ENST00000406870 hsa:604 path:hsa05202;Transcriptional_misregulation_in_cancer
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000337774 hsa:5648 path:hsa04610;Complement_and_coagulation_cascades
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000337774 hsa:5648 path:hsa05150;Staphylococcus_aureus_infection
+P61278 SST SST ENSG00000157005 ENST00000287641 hsa:6750 path:hsa04080;Neuroactive_ligand_receptor_interaction
+P61278 SST SST ENSG00000157005 ENST00000287641 hsa:6750 path:hsa04971;Gastric_acid_secretion
+Q5HYM1 MASP1 MASP1 ENSG00000127241 ENST00000541896 None None
+Q5QGT7 RTP2 RTP2 ENSG00000198471 ENST00000358241 hsa:344892 None
+Q96DX8 RTP4 RTP4 ENSG00000136514 ENST00000259030 hsa:64108 None
+Q9NSY8 MASP1 MASP1 ENSG00000127241 ENST00000296280 None None
+Q9NSY8 MASP1 MASP1 ENSG00000127241 ENST00000392472 None None
+Q9NSY8 MASP1 MASP1 ENSG00000127241 ENST00000541811 None None
+none BCL6 BCL6 ENSG00000113916 ENST00000419510 None None
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/kegg_pathways_ensembl67
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-cache/gemini/data/kegg_pathways_ensembl67 Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,30 @@
+B8PSA7 BCL6 BCL6 ENSG00000113916 ENST00000450123 None None
+C9J1C7 MASP1 MASP1 ENSG00000127241 ENST00000439271 None None
+C9JCS5 BCL6 BCL6 ENSG00000113916 ENST00000430339 None None
+C9JCS5 BCL6 BCL6 ENSG00000113916 ENST00000450123 None None
+C9JL16 BCL6 BCL6 ENSG00000113916 ENST00000430339 None None
+C9JL16 BCL6 BCL6 ENSG00000113916 ENST00000438077 None None
+C9JL16 BCL6 BCL6 ENSG00000113916 ENST00000450123 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000169293 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000296280 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000392470 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000392475 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000425937 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000439271 None None
+C9JMA2 MASP1 MASP1 ENSG00000127241 ENST00000392475 None None
+F5H2J0 MASP1 MASP1 ENSG00000127241 ENST00000541896 None None
+F8W876 MASP1 MASP1 ENSG00000127241 ENST00000169293 None None
+F8W876 MASP1 MASP1 ENSG00000127241 ENST00000392470 None None
+P41182 BCL6 BCL6 ENSG00000113916 ENST00000232014 hsa:604 path:hsa05202;Transcriptional_misregulation_in_cancer
+P41182 BCL6 BCL6 ENSG00000113916 ENST00000406870 hsa:604 path:hsa05202;Transcriptional_misregulation_in_cancer
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000337774 hsa:5648 path:hsa04610;Complement_and_coagulation_cascades
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000337774 hsa:5648 path:hsa05150;Staphylococcus_aureus_infection
+P61278 SST SST ENSG00000157005 ENST00000287641 hsa:6750 path:hsa04080;Neuroactive_ligand_receptor_interaction
+P61278 SST SST ENSG00000157005 ENST00000287641 hsa:6750 path:hsa04971;Gastric_acid_secretion
+Q5HYM1 MASP1 MASP1 ENSG00000127241 ENST00000541896 None None
+Q5QGT7 RTP2 RTP2 ENSG00000198471 ENST00000358241 hsa:344892 None
+Q96DX8 RTP4 RTP4 ENSG00000136514 ENST00000259030 hsa:64108 None
+Q9NSY8 MASP1 MASP1 ENSG00000127241 ENST00000296280 None None
+Q9NSY8 MASP1 MASP1 ENSG00000127241 ENST00000392472 None None
+Q9NSY8 MASP1 MASP1 ENSG00000127241 ENST00000541811 None None
+none BCL6 BCL6 ENSG00000113916 ENST00000419510 None None
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/kegg_pathways_ensembl68
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-cache/gemini/data/kegg_pathways_ensembl68 Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,26 @@
+C9J1C7 MASP1 MASP1 ENSG00000127241 ENST00000439271 None None
+C9JCS5 BCL6 BCL6 ENSG00000113916 ENST00000430339 None None
+C9JL16 BCL6 BCL6 ENSG00000113916 ENST00000430339 None None
+C9JL16 BCL6 BCL6 ENSG00000113916 ENST00000438077 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000392470 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000392475 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000425937 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000439271 None None
+C9JMA2 MASP1 MASP1 ENSG00000127241 ENST00000392475 None None
+F8W876 MASP1 MASP1 ENSG00000127241 ENST00000392470 None None
+P41182 BCL6 BCL6 ENSG00000113916 ENST00000232014 hsa:604 path:hsa05202;Transcriptional_misregulation_in_cancer
+P41182 BCL6 BCL6 ENSG00000113916 ENST00000406870 hsa:604 path:hsa05202;Transcriptional_misregulation_in_cancer
+P41182 BCL6 BCL6 ENSG00000113916 ENST00000450123 hsa:604 path:hsa05202;Transcriptional_misregulation_in_cancer
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000169293 hsa:5648 path:hsa04610;Complement_and_coagulation_cascades
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000169293 hsa:5648 path:hsa05150;Staphylococcus_aureus_infection
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000296280 hsa:5648 path:hsa04610;Complement_and_coagulation_cascades
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000296280 hsa:5648 path:hsa05150;Staphylococcus_aureus_infection
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000337774 hsa:5648 path:hsa04610;Complement_and_coagulation_cascades
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000337774 hsa:5648 path:hsa05150;Staphylococcus_aureus_infection
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000392472 hsa:5648 path:hsa04610;Complement_and_coagulation_cascades
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000392472 hsa:5648 path:hsa05150;Staphylococcus_aureus_infection
+P61278 SST SST ENSG00000157005 ENST00000287641 hsa:6750 path:hsa04080;Neuroactive_ligand_receptor_interaction
+P61278 SST SST ENSG00000157005 ENST00000287641 hsa:6750 path:hsa04971;Gastric_acid_secretion
+Q5QGT7 RTP2 RTP2 ENSG00000198471 ENST00000358241 hsa:344892 None
+Q96DX8 RTP4 RTP4 ENSG00000136514 ENST00000259030 hsa:64108 None
+none BCL6 BCL6 ENSG00000113916 ENST00000419510 None None
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/kegg_pathways_ensembl69
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-cache/gemini/data/kegg_pathways_ensembl69 Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,26 @@
+C9J1C7 MASP1 MASP1 ENSG00000127241 ENST00000439271 None None
+C9JCS5 BCL6 BCL6 ENSG00000113916 ENST00000430339 None None
+C9JL16 BCL6 BCL6 ENSG00000113916 ENST00000430339 None None
+C9JL16 BCL6 BCL6 ENSG00000113916 ENST00000438077 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000392470 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000392475 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000425937 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000439271 None None
+C9JMA2 MASP1 MASP1 ENSG00000127241 ENST00000392475 None None
+F8W876 MASP1 MASP1 ENSG00000127241 ENST00000392470 None None
+P41182 BCL6 BCL6 ENSG00000113916 ENST00000232014 hsa:604 path:hsa05202;Transcriptional_misregulation_in_cancer
+P41182 BCL6 BCL6 ENSG00000113916 ENST00000406870 hsa:604 path:hsa05202;Transcriptional_misregulation_in_cancer
+P41182 BCL6 BCL6 ENSG00000113916 ENST00000450123 hsa:604 path:hsa05202;Transcriptional_misregulation_in_cancer
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000169293 hsa:5648 path:hsa04610;Complement_and_coagulation_cascades
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000169293 hsa:5648 path:hsa05150;Staphylococcus_aureus_infection
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000296280 hsa:5648 path:hsa04610;Complement_and_coagulation_cascades
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000296280 hsa:5648 path:hsa05150;Staphylococcus_aureus_infection
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000337774 hsa:5648 path:hsa04610;Complement_and_coagulation_cascades
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000337774 hsa:5648 path:hsa05150;Staphylococcus_aureus_infection
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000392472 hsa:5648 path:hsa04610;Complement_and_coagulation_cascades
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000392472 hsa:5648 path:hsa05150;Staphylococcus_aureus_infection
+P61278 SST SST ENSG00000157005 ENST00000287641 hsa:6750 path:hsa04080;Neuroactive_ligand_receptor_interaction
+P61278 SST SST ENSG00000157005 ENST00000287641 hsa:6750 path:hsa04971;Gastric_acid_secretion
+Q5QGT7 RTP2 RTP2 ENSG00000198471 ENST00000358241 hsa:344892 None
+Q96DX8 RTP4 RTP4 ENSG00000136514 ENST00000259030 hsa:64108 None
+none BCL6 BCL6 ENSG00000113916 ENST00000419510 None None
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/kegg_pathways_ensembl70
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-cache/gemini/data/kegg_pathways_ensembl70 Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,25 @@
+C9J1C7 MASP1 MASP1 ENSG00000127241 ENST00000439271 None None
+C9JL16 BCL6 BCL6 ENSG00000113916 ENST00000430339 None None
+C9JL16 BCL6 BCL6 ENSG00000113916 ENST00000438077 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000392470 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000392475 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000425937 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000439271 None None
+C9JMA2 MASP1 MASP1 ENSG00000127241 ENST00000392475 None None
+F8W876 MASP1 MASP1 ENSG00000127241 ENST00000392470 None None
+P41182 BCL6 BCL6 ENSG00000113916 ENST00000232014 hsa:604 path:hsa05202;Transcriptional_misregulation_in_cancer
+P41182 BCL6 BCL6 ENSG00000113916 ENST00000406870 hsa:604 path:hsa05202;Transcriptional_misregulation_in_cancer
+P41182 BCL6 BCL6 ENSG00000113916 ENST00000450123 hsa:604 path:hsa05202;Transcriptional_misregulation_in_cancer
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000169293 hsa:5648 path:hsa04610;Complement_and_coagulation_cascades
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000169293 hsa:5648 path:hsa05150;Staphylococcus_aureus_infection
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000296280 hsa:5648 path:hsa04610;Complement_and_coagulation_cascades
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000296280 hsa:5648 path:hsa05150;Staphylococcus_aureus_infection
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000337774 hsa:5648 path:hsa04610;Complement_and_coagulation_cascades
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000337774 hsa:5648 path:hsa05150;Staphylococcus_aureus_infection
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000392472 hsa:5648 path:hsa04610;Complement_and_coagulation_cascades
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000392472 hsa:5648 path:hsa05150;Staphylococcus_aureus_infection
+P61278 SST SST ENSG00000157005 ENST00000287641 hsa:6750 path:hsa04080;Neuroactive_ligand_receptor_interaction
+P61278 SST SST ENSG00000157005 ENST00000287641 hsa:6750 path:hsa04971;Gastric_acid_secretion
+Q5QGT7 RTP2 RTP2 ENSG00000198471 ENST00000358241 hsa:344892 None
+Q96DX8 RTP4 RTP4 ENSG00000136514 ENST00000259030 hsa:64108 None
+none BCL6 BCL6 ENSG00000113916 ENST00000419510 None None
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/kegg_pathways_ensembl71
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-cache/gemini/data/kegg_pathways_ensembl71 Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,26 @@
+C9J1C7 MASP1 MASP1 ENSG00000127241 ENST00000439271 None None
+C9JCS5 BCL6 BCL6 ENSG00000113916 ENST00000430339 None None
+C9JL16 BCL6 BCL6 ENSG00000113916 ENST00000430339 None None
+C9JL16 BCL6 BCL6 ENSG00000113916 ENST00000438077 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000392470 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000392475 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000425937 None None
+C9JLU5 MASP1 MASP1 ENSG00000127241 ENST00000439271 None None
+C9JMA2 MASP1 MASP1 ENSG00000127241 ENST00000392475 None None
+F8W876 MASP1 MASP1 ENSG00000127241 ENST00000392470 None None
+P41182 BCL6 BCL6 ENSG00000113916 ENST00000232014 hsa:604 path:hsa05202;Transcriptional_misregulation_in_cancer
+P41182 BCL6 BCL6 ENSG00000113916 ENST00000406870 hsa:604 path:hsa05202;Transcriptional_misregulation_in_cancer
+P41182 BCL6 BCL6 ENSG00000113916 ENST00000450123 hsa:604 path:hsa05202;Transcriptional_misregulation_in_cancer
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000169293 hsa:5648 path:hsa04610;Complement_and_coagulation_cascades
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000169293 hsa:5648 path:hsa05150;Staphylococcus_aureus_infection
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000296280 hsa:5648 path:hsa04610;Complement_and_coagulation_cascades
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000296280 hsa:5648 path:hsa05150;Staphylococcus_aureus_infection
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000337774 hsa:5648 path:hsa04610;Complement_and_coagulation_cascades
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000337774 hsa:5648 path:hsa05150;Staphylococcus_aureus_infection
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000392472 hsa:5648 path:hsa04610;Complement_and_coagulation_cascades
+P48740 MASP1 MASP1 ENSG00000127241 ENST00000392472 hsa:5648 path:hsa05150;Staphylococcus_aureus_infection
+P61278 SST SST ENSG00000157005 ENST00000287641 hsa:6750 path:hsa04080;Neuroactive_ligand_receptor_interaction
+P61278 SST SST ENSG00000157005 ENST00000287641 hsa:6750 path:hsa04971;Gastric_acid_secretion
+Q5QGT7 RTP2 RTP2 ENSG00000198471 ENST00000358241 hsa:344892 None
+Q96DX8 RTP4 RTP4 ENSG00000136514 ENST00000259030 hsa:64108 None
+none BCL6 BCL6 ENSG00000113916 ENST00000419510 None None
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/stam.125cells.dnaseI.hg19.bed.gz
Binary file test-data/test-cache/gemini/data/stam.125cells.dnaseI.hg19.bed.gz has changed
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/stam.125cells.dnaseI.hg19.bed.gz.tbi
Binary file test-data/test-cache/gemini/data/stam.125cells.dnaseI.hg19.bed.gz.tbi has changed
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/summary_gene_table_v75
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-cache/gemini/data/summary_gene_table_v75 Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,23 @@
+Chromosome Gene_name Is_hgnc Ensembl_gene_id HGNC_id Synonyms Rvis_pct Strand Transcript_min_start Transcript_max_end Mammalian_phenotype_id
+chr3 None 0 ENSG00000239093 None None None 1 187141103 187141207 None
+chr3 None 0 ENSG00000228952 None None None 1 187166633 187167238 None
+chr3 None 0 ENSG00000223401 None None None 1 187461474 187463208 None
+chr3 MASP 0 ENSG00000127241 None PRSS5,MASP1,CRARF 16.8141071 -1 186935942 187009810 None
+chr3 PRSS5 0 ENSG00000127241 None MASP1,CRARF,MASP 16.8141071 -1 186935942 187009810 None
+chr3 MASP1 1 ENSG00000127241 6901 PRSS5,CRARF,MASP 16.8141071 -1 186935942 187009810 None
+chr3 CRARF 0 ENSG00000127241 None PRSS5,MASP1,MASP 16.8141071 -1 186935942 187009810 None
+chr3 IFRG28 0 ENSG00000136514 None RTP4,Z3CXXC4 94.35008257 1 187086120 187089864 None
+chr3 RTP4 1 ENSG00000136514 23992 IFRG28,Z3CXXC4 94.35008257 1 187086120 187089864 None
+chr3 Z3CXXC4 0 ENSG00000136514 None IFRG28,RTP4 94.35008257 1 187086120 187089864 None
+chr3 SST 1 ENSG00000157005 11329 SMST 78.16112291 -1 187386694 187388187 MP:0002873,MP:0005386,MP:0005376,MP:0005381,MP:0003631,MP:0005378
+chr3 SMST 0 ENSG00000157005 None SST 78.16112291 -1 187386694 187388187 MP:0002873,MP:0005386,MP:0005376,MP:0005381,MP:0003631,MP:0005378
+chr3 Z3CXXC2 0 ENSG00000198471 None RTP2,MGC78665 69.20853975 -1 187416047 187420345 MP:0005389
+chr3 RTP2 1 ENSG00000198471 32486 Z3CXXC2,MGC78665 69.20853975 -1 187416047 187420345 MP:0005389
+chr3 MGC78665 0 ENSG00000198471 None Z3CXXC2,RTP2 69.20853975 -1 187416047 187420345 MP:0005389
+chr3 None 0 ENSG00000228804 None None None 1 187420101 187451637 None
+chr3 ZNF51 0 ENSG00000113916 None LAZ3,BCL5,BCL6,ZBTB27,BCL6A 23.5727766 -1 187439165 187463515 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 LAZ3 0 ENSG00000113916 None BCL5,ZNF51,BCL6,ZBTB27,BCL6A 23.5727766 -1 187439165 187463515 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL5 0 ENSG00000113916 None LAZ3,ZNF51,BCL6,ZBTB27,BCL6A 23.5727766 -1 187439165 187463515 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL6A 0 ENSG00000113916 None LAZ3,ZNF51,BCL6,BCL5,ZBTB27 23.5727766 -1 187439165 187463515 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 BCL6 1 ENSG00000113916 1001 LAZ3,ZNF51,ZBTB27,BCL5,BCL6A 23.5727766 -1 187439165 187463515 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3 ZBTB27 0 ENSG00000113916 None LAZ3,ZNF51,BCL6,BCL5,BCL6A 23.5727766 -1 187439165 187463515 MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/wgEncodeRegTfbsClusteredV2.cell_count.20130213.bed.gz
Binary file test-data/test-cache/gemini/data/wgEncodeRegTfbsClusteredV2.cell_count.20130213.bed.gz has changed
diff -r 000000000000 -r 3123ce7acd0e test-data/test-cache/gemini/data/wgEncodeRegTfbsClusteredV2.cell_count.20130213.bed.gz.tbi
Binary file test-data/test-cache/gemini/data/wgEncodeRegTfbsClusteredV2.cell_count.20130213.bed.gz.tbi has changed
diff -r 000000000000 -r 3123ce7acd0e test-data/util/README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/util/README.rst Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,25 @@
+Prepare Gemini annotation files and test databases for tool tests
+=================================================================
+
+Each version of GEMINI is tied to a particular set of annotation files and
+database version.
+
+The ``build-gemini-testdata.sh`` script in this folder should be used to
+regenerate the annotation files and the test databases whenever the GEMINI
+version required by the tool wrappers gets upgraded.
+
+The script requires a working GEMINI installation at the targeted version and
+a folder with GEMINI's original annotation files, and can be executed with::
+
+ sh build-gemini-testdata.sh path/to/gemini/annotation/files
+
+It will regenerate the annotation files inside test-data/test-cache/gemini/data
+and rebuild the *.db files in test-data.
+
+.. Note::
+
+ If the version of GEMINI that you are upgrading to uses a gemini-config.yaml
+ file that is different from the one found in test-data/test-cache you will
+ have to upgrade this file manually (make sure you leave the line
+ ``annotation_dir: gemini/data`` unchanged in the process).
+
diff -r 000000000000 -r 3123ce7acd0e test-data/util/build-data/anno.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/util/build-data/anno.bed Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,3 @@
+chr3 187000000 187150000
+chr3 187150000 187300000
+chr3 187300000 187450000
diff -r 000000000000 -r 3123ce7acd0e test-data/util/build-data/anno.bed.gz
Binary file test-data/util/build-data/anno.bed.gz has changed
diff -r 000000000000 -r 3123ce7acd0e test-data/util/build-data/anno.bed.gz.tbi
Binary file test-data/util/build-data/anno.bed.gz.tbi has changed
diff -r 000000000000 -r 3123ce7acd0e test-data/util/build-data/gemini_load_input.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/util/build-data/gemini_load_input.vcf Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,70 @@
+##fileformat=VCFv4.1
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##ALT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##reference=GRCh37
+##SnpEffVersion="SnpEff 3.0f (build 2012-08-23), by Pablo Cingolani"
+##SnpEffCmd="SnpEff GRCh37.66 -i vcf -o vcf -c /Users/arq5x/src/other/snpEff_3_0/snpEff.config ALL.wgs.integrated_phase1_v3.20101123.snps_indels_sv.sites.vcf.gz "
+##INFO=
+#CHROM POS ID REF ALT QUAL FILTER INFO
+1 10583 rs58108140 G A 100.0 PASS AVGPOST=0.7707;RSQ=0.4319;LDAF=0.2327;ERATE=0.0161;AN=2184;VT=SNP;AA=.;THETA=0.0046;AC=314;SNPSOURCE=LOWCOV;AF=0.14;ASN_AF=0.13;AMR_AF=0.17;AFR_AF=0.04;EUR_AF=0.21;EFF=DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),UPSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|)
+1 10611 rs189107123 C G 100.0 PASS AN=2184;THETA=0.0077;VT=SNP;AA=.;AC=41;ERATE=0.0048;SNPSOURCE=LOWCOV;AVGPOST=0.9330;LDAF=0.0479;RSQ=0.3475;AF=0.02;ASN_AF=0.01;AMR_AF=0.03;AFR_AF=0.01;EUR_AF=0.02;EFF=DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),UPSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|)
+1 13302 rs180734498 C T 100.0 PASS THETA=0.0048;AN=2184;AC=249;VT=SNP;AA=.;RSQ=0.6281;LDAF=0.1573;SNPSOURCE=LOWCOV;AVGPOST=0.8895;ERATE=0.0058;AF=0.11;ASN_AF=0.02;AMR_AF=0.08;AFR_AF=0.21;EUR_AF=0.14;EFF=DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),EXON(MODIFIER||||209|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),EXON(MODIFIER||||550|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),EXON(MODIFIER||||551|DDX11L1|processed_transcript|NON_CODING|ENST00000456328|),INTRON(MODIFIER||||493|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|)
+1 13327 rs144762171 G C 100.0 PASS AVGPOST=0.9698;AN=2184;VT=SNP;AA=.;RSQ=0.6482;AC=59;SNPSOURCE=LOWCOV;ERATE=0.0012;LDAF=0.0359;THETA=0.0204;AF=0.03;ASN_AF=0.02;AMR_AF=0.03;AFR_AF=0.02;EUR_AF=0.04;EFF=DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),EXON(MODIFIER||||209|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),EXON(MODIFIER||||550|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),EXON(MODIFIER||||551|DDX11L1|processed_transcript|NON_CODING|ENST00000456328|),INTRON(MODIFIER||||493|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|)
+1 13957 . TC T 28.0 PASS AA=TC;AC=35;AN=2184;VT=INDEL;AVGPOST=0.8711;RSQ=0.2501;LDAF=0.0788;THETA=0.0100;ERATE=0.0065;AF=0.02;ASN_AF=0.01;AMR_AF=0.02;AFR_AF=0.02;EUR_AF=0.02;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),EXON(MODIFIER||||493|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|),EXON(MODIFIER||||550|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),EXON(MODIFIER||||551|DDX11L1|processed_transcript|NON_CODING|ENST00000456328|)
+1 13980 rs151276478 T C 100.0 PASS AN=2184;AC=45;ERATE=0.0034;THETA=0.0139;RSQ=0.3603;LDAF=0.0525;VT=SNP;AA=.;AVGPOST=0.9221;SNPSOURCE=LOWCOV;AF=0.02;ASN_AF=0.02;AMR_AF=0.02;AFR_AF=0.01;EUR_AF=0.02;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),EXON(MODIFIER||||493|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|),EXON(MODIFIER||||550|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),EXON(MODIFIER||||551|DDX11L1|processed_transcript|NON_CODING|ENST00000456328|)
+1 30923 rs140337953 G T 100.0 PASS AC=1584;AA=T;AN=2184;RSQ=0.5481;VT=SNP;THETA=0.0162;SNPSOURCE=LOWCOV;ERATE=0.0183;LDAF=0.6576;AVGPOST=0.7335;AF=0.73;ASN_AF=0.89;AMR_AF=0.80;AFR_AF=0.48;EUR_AF=0.73;EFF=DOWNSTREAM(MODIFIER|||||FAM138A|processed_transcript|CODING|ENST00000461467|),DOWNSTREAM(MODIFIER|||||FAM138A|protein_coding|CODING|ENST00000417324|),DOWNSTREAM(MODIFIER|||||MIR1302-10|miRNA|NON_CODING|ENST00000408384|),INTRON(MODIFIER||||177|MIR1302-10|antisense|NON_CODING|ENST00000469289|),INTRON(MODIFIER||||236|MIR1302-10|antisense|NON_CODING|ENST00000473358|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|)
+1 46402 . C CTGT 31.0 PASS AA=.;RSQ=0.0960;AN=2184;AC=8;VT=INDEL;AVGPOST=0.8325;THETA=0.0121;ERATE=0.0072;LDAF=0.0903;AF=0.0037;ASN_AF=0.0017;AFR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
+1 47190 . G GA 192.0 PASS AA=G;AVGPOST=0.9041;AN=2184;AC=29;VT=INDEL;LDAF=0.0628;THETA=0.0153;RSQ=0.2883;ERATE=0.0041;AF=0.01;AMR_AF=0.0028;AFR_AF=0.06;EFF=INTERGENIC(MODIFIER|||||||||)
+1 51476 rs187298206 T C 100.0 PASS ERATE=0.0021;AA=C;AC=18;AN=2184;VT=SNP;THETA=0.0103;LDAF=0.0157;SNPSOURCE=LOWCOV;AVGPOST=0.9819;RSQ=0.5258;AF=0.01;ASN_AF=0.01;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
+1 51479 rs116400033 T A 100.0 PASS RSQ=0.7414;AVGPOST=0.9085;AA=T;AN=2184;THETA=0.0131;AC=235;VT=SNP;LDAF=0.1404;SNPSOURCE=LOWCOV;ERATE=0.0012;AF=0.11;ASN_AF=0.0035;AMR_AF=0.16;AFR_AF=0.03;EUR_AF=0.22;EFF=INTERGENIC(MODIFIER|||||||||)
+1 51914 rs190452223 T G 100.0 PASS ERATE=0.0004;AVGPOST=0.9985;THETA=0.0159;AA=T;AN=2184;VT=SNP;SNPSOURCE=LOWCOV;AC=1;RSQ=0.4089;LDAF=0.0012;AF=0.0005;ASN_AF=0.0017;EFF=INTERGENIC(MODIFIER|||||||||)
+1 51935 rs181754315 C T 100.0 PASS THETA=0.0126;AA=C;AN=2184;RSQ=0.1888;AVGPOST=0.9972;LDAF=0.0015;VT=SNP;AC=0;SNPSOURCE=LOWCOV;ERATE=0.0006;AF=0;EFF=INTERGENIC(MODIFIER|||||||||)
+1 51954 rs185832753 G C 100.0 PASS LDAF=0.0021;AA=G;AN=2184;RSQ=0.4692;AVGPOST=0.9975;VT=SNP;SNPSOURCE=LOWCOV;THETA=0.0029;ERATE=0.0006;AC=2;AF=0.0009;AMR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
+1 52058 rs62637813 G C 100.0 PASS AA=C;ERATE=0.0057;AN=2184;AVGPOST=0.9264;VT=SNP;RSQ=0.4882;AC=64;SNPSOURCE=LOWCOV;LDAF=0.0620;THETA=0.0069;AF=0.03;ASN_AF=0.0017;AMR_AF=0.04;AFR_AF=0.02;EUR_AF=0.05;EFF=INTERGENIC(MODIFIER|||||||||)
+1 52144 rs190291950 T A 100.0 PASS THETA=0.0093;ERATE=0.0013;LDAF=0.0156;AA=T;AN=2184;VT=SNP;RSQ=0.5220;AVGPOST=0.9811;SNPSOURCE=LOWCOV;AC=21;AF=0.01;ASN_AF=0.0035;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
+1 52185 . TTAA T 244.0 PASS AA=.;AN=2184;LDAF=0.0124;VT=INDEL;AC=10;THETA=0.0232;RSQ=0.4271;AVGPOST=0.9840;ERATE=0.0037;AF=0.0046;ASN_AF=0.0035;AMR_AF=0.02;AFR_AF=0.0020;EFF=INTERGENIC(MODIFIER|||||||||)
+1 52238 rs150021059 T G 100.0 PASS THETA=0.0132;AA=G;AN=2184;RSQ=0.6256;VT=SNP;ERATE=0.0026;AVGPOST=0.8617;SNPSOURCE=LOWCOV;AC=1941;LDAF=0.8423;AF=0.89;ASN_AF=0.99;AMR_AF=0.93;AFR_AF=0.64;EUR_AF=0.95;EFF=INTERGENIC(MODIFIER|||||||||)
+1 53234 . CAT C 227.0 PASS AA=CAT;AVGPOST=0.9936;AN=2184;VT=INDEL;THETA=0.0119;AC=10;LDAF=0.0074;RSQ=0.6237;ERATE=0.0007;AF=0.0046;AMR_AF=0.0028;AFR_AF=0.02;EFF=INTERGENIC(MODIFIER|||||||||)
+1 54353 rs140052487 C A 100.0 PASS THETA=0.0026;AA=C;AN=2184;AC=16;VT=SNP;RSQ=0.5074;SNPSOURCE=LOWCOV;AVGPOST=0.9844;LDAF=0.0146;ERATE=0.0058;AF=0.01;ASN_AF=0.01;AMR_AF=0.0028;AFR_AF=0.02;EUR_AF=0.0013;EFF=INTERGENIC(MODIFIER|||||||||)
+1 54421 rs146477069 A G 100.0 PASS ERATE=0.0013;AN=2184;AC=220;VT=SNP;RSQ=0.7869;AVGPOST=0.9461;AA=A;THETA=0.0025;SNPSOURCE=LOWCOV;LDAF=0.1190;AF=0.10;ASN_AF=0.25;AMR_AF=0.12;AFR_AF=0.03;EUR_AF=0.02;EFF=INTERGENIC(MODIFIER|||||||||)
+1 54490 rs141149254 G A 100.0 PASS ERATE=0.0004;THETA=0.0074;AA=G;AN=2184;VT=SNP;RSQ=0.8366;AVGPOST=0.9646;AC=175;SNPSOURCE=LOWCOV;LDAF=0.0929;AF=0.08;ASN_AF=0.0035;AMR_AF=0.12;AFR_AF=0.03;EUR_AF=0.15;EFF=INTERGENIC(MODIFIER|||||||||)
+1 54676 rs2462492 C T 100.0 PASS LDAF=0.1528;RSQ=0.6989;AA=T;AN=2184;AC=267;VT=SNP;AVGPOST=0.8998;SNPSOURCE=LOWCOV;THETA=0.0110;ERATE=0.0037;AF=0.12;ASN_AF=0.02;AMR_AF=0.20;AFR_AF=0.09;EUR_AF=0.18;EFF=INTERGENIC(MODIFIER|||||||||)
+1 54753 rs143174675 T G 100.0 PASS AA=T;AN=2184;RSQ=0.6820;AC=65;VT=SNP;THETA=0.0080;ERATE=0.0016;SNPSOURCE=LOWCOV;AVGPOST=0.9697;LDAF=0.0399;AF=0.03;AMR_AF=0.04;AFR_AF=0.07;EUR_AF=0.03;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55164 rs3091274 C A 100.0 PASS AN=2184;VT=SNP;ERATE=0.0045;AA=A;THETA=0.0162;SNPSOURCE=LOWCOV;AC=1955;RSQ=0.6373;AVGPOST=0.8686;LDAF=0.8489;AF=0.90;ASN_AF=0.99;AMR_AF=0.94;AFR_AF=0.65;EUR_AF=0.96;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55249 . C CTATGG 443.0 PASS AA=C;AVGPOST=0.9073;ERATE=0.0063;RSQ=0.5891;AN=2184;THETA=0.0038;VT=INDEL;AC=151;LDAF=0.0968;AF=0.07;ASN_AF=0.16;AMR_AF=0.08;AFR_AF=0.03;EUR_AF=0.02;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55299 rs10399749 C T 100.0 PASS RSQ=0.7602;LDAF=0.2954;AN=2184;VT=SNP;ERATE=0.0051;AA=c;AC=554;SNPSOURCE=LOWCOV;AVGPOST=0.8845;THETA=0.0070;AF=0.25;ASN_AF=0.33;AMR_AF=0.21;AFR_AF=0.39;EUR_AF=0.13;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55313 rs182462964 A T 100.0 PASS ERATE=0.0004;RSQ=0.6112;AVGPOST=0.9994;AN=2184;VT=SNP;THETA=0.0057;AA=A;SNPSOURCE=LOWCOV;AC=1;LDAF=0.0008;AF=0.0005;AFR_AF=0.0020;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55326 rs3107975 T C 100.0 PASS AA=C;ERATE=0.0074;AN=2184;THETA=0.0085;VT=SNP;SNPSOURCE=LOWCOV;AVGPOST=0.9622;AC=90;RSQ=0.6901;LDAF=0.0562;AF=0.04;ASN_AF=0.07;AMR_AF=0.02;AFR_AF=0.07;EUR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55330 rs185215913 G A 100.0 PASS ERATE=0.0005;AA=G;AN=2184;VT=SNP;THETA=0.0086;AVGPOST=0.9988;LDAF=0.0011;SNPSOURCE=LOWCOV;AC=1;RSQ=0.4701;AF=0.0005;AFR_AF=0.0020;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55367 rs190850374 G A 100.0 PASS ERATE=0.0004;THETA=0.0044;AA=G;AN=2184;VT=SNP;LDAF=0.0029;RSQ=0.3860;SNPSOURCE=LOWCOV;AVGPOST=0.9961;AC=2;AF=0.0009;AMR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55388 rs182711216 C T 100.0 PASS THETA=0.0102;ERATE=0.0005;AA=C;AVGPOST=0.9983;AN=2184;LDAF=0.0010;VT=SNP;RSQ=0.2348;SNPSOURCE=LOWCOV;AC=1;AF=0.0005;ASN_AF=0.0017;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55394 rs2949420 T A 100.0 PASS AC=18;AN=2184;VT=SNP;AA=A;RSQ=0.4995;AVGPOST=0.9784;LDAF=0.0171;SNPSOURCE=LOWCOV;ERATE=0.0012;THETA=0.0063;AF=0.01;AMR_AF=0.01;AFR_AF=0.0041;EUR_AF=0.02;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55416 rs193242050 G A 100.0 PASS AA=G;AN=2184;AVGPOST=0.9944;VT=SNP;LDAF=0.0064;AC=9;THETA=0.0019;RSQ=0.6553;SNPSOURCE=LOWCOV;ERATE=0.0006;AF=0.0041;AFR_AF=0.02;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55427 rs183189405 T C 100.0 PASS THETA=0.0054;AA=T;AN=2184;VT=SNP;AVGPOST=0.9969;LDAF=0.0020;SNPSOURCE=LOWCOV;AC=1;RSQ=0.2759;ERATE=0.0007;AF=0.0005;AFR_AF=0.0020;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55816 rs187434873 G A 100.0 PASS AN=2184;THETA=0.0119;VT=SNP;AC=10;RSQ=0.4578;AA=A;SNPSOURCE=LOWCOV;AVGPOST=0.9844;LDAF=0.0108;ERATE=0.0007;AF=0.0046;AMR_AF=0.01;EUR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55850 rs191890754 C G 100.0 PASS AVGPOST=0.9921;AA=G;AN=2184;VT=SNP;RSQ=0.4083;THETA=0.0045;LDAF=0.0056;AC=5;SNPSOURCE=LOWCOV;ERATE=0.0006;AF=0.0023;EUR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
+1 55852 rs184233019 G C 100.0 PASS THETA=0.0137;AA=G;AN=2184;RSQ=0.5433;ERATE=0.0009;LDAF=0.0046;VT=SNP;AVGPOST=0.9953;AC=5;SNPSOURCE=LOWCOV;AF=0.0023;AMR_AF=0.01;EUR_AF=0.0013;EFF=INTERGENIC(MODIFIER|||||||||)
diff -r 000000000000 -r 3123ce7acd0e test-data/util/build-data/test.auto_dom.ped
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/util/build-data/test.auto_dom.ped Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,9 @@
+1 1_dad 0 0 -1 1
+1 1_mom 0 0 -1 1
+1 1_kid 1_dad 1_mom -1 2
+2 2_dad 0 0 -1 1
+2 2_mom 0 0 -1 2
+2 2_kid 2_dad 2_mom -1 2
+3 3_dad 0 0 -1 2
+3 3_mom 0 0 -1 -9
+3 3_kid 3_dad 3_mom -1 2
diff -r 000000000000 -r 3123ce7acd0e test-data/util/build-data/test.auto_dom.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/util/build-data/test.auto_dom.vcf Fri Jan 11 17:50:55 2019 -0500
@@ -0,0 +1,127 @@
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