LICENSE
MANIFEST.in
README.md
commands.md
gemini_install.py
heaper.py
make.sh
master-test.sh
requirements.txt
setup.py
t.py
t.sh
to-sample.py
docs/EXAMPLES.rst
docs/Makefile
docs/TODO.rst
docs/build.sh
docs/conf.py
docs/gemini.ai
docs/gemini.png
docs/index.rst
docs/requirements.txt
docs/_static/labibi.css
docs/_static/labibi.js
docs/content/acknowledgements.rst
docs/content/api.rst
docs/content/browser.rst
docs/content/caveats.rst
docs/content/database_schema.rst
docs/content/faq.rst
docs/content/functional_annotation.rst
docs/content/genotype_query_engines.rst
docs/content/history.rst
docs/content/installation.rst
docs/content/other.rst
docs/content/preprocessing.rst
docs/content/querying.rst
docs/content/quick_start.rst
docs/content/tools.rst
docs/images/browser-query.png
docs/images/gene_wise_example.png
docs/images/overview.png
docs/images/query-speed.png
docs/templates/layout.html
docs/templates/page.html
docs/templates/sidebar-intro.html
docs/themes/rtd/theme.conf
docs/themes/rtd/static/rtd.css_t
gemini/GeminiQuery.py
gemini/__init__.py
gemini/anno_info.py
gemini/annotations.py
gemini/compression.py
gemini/config.py
gemini/database.py
gemini/dgidb.py
gemini/gemini_actionable_mutations.py
gemini/gemini_amend.py
gemini/gemini_annotate.py
gemini/gemini_bcolz.py
gemini/gemini_browser.py
gemini/gemini_constants.py
gemini/gemini_dbinfo.py
gemini/gemini_dump.py
gemini/gemini_load.py
gemini/gemini_load_chunk.py
gemini/gemini_main.py
gemini/gemini_merge_chunks.py
gemini/gemini_plot.py
gemini/gemini_query.py
gemini/gemini_region.py
gemini/gemini_set_somatic.py
gemini/gemini_stats.py
gemini/gemini_subjects.py
gemini/gemini_update.py
gemini/gemini_utils.py
gemini/gemini_windower.py
gemini/gene_table.py
gemini/genewise.py
gemini/gim.py
gemini/infotag.py
gemini/install-data.py
gemini/mendelianerror.py
gemini/pdict.py
gemini/ped.py
gemini/popgen.py
gemini/sql_utils.py
gemini/stats.py
gemini/structural_variants.py
gemini/tool_burden_tests.py
gemini/tool_fusions.py
gemini/tool_homozygosity_runs.py
gemini/tool_interactions.py
gemini/tool_lof_sieve.py
gemini/tool_pathways.py
gemini/tool_qc.py
gemini/version.py
gemini.egg-info/PKG-INFO
gemini.egg-info/SOURCES.txt
gemini.egg-info/dependency_links.txt
gemini.egg-info/not-zip-safe
gemini.egg-info/requires.txt
gemini.egg-info/top_level.txt
gemini/data/__init__.py
gemini/data/gemini.conf
gemini/scripts/__init__.py
gemini/scripts/__init__.pyc
gemini/scripts/gemini
gemini/scripts/gemini_install.py
gemini/static/css/gemini.css
gemini/static/img/gemini.png
gemini/static/third_party/bootstrap/css/bootstrap-responsive.css
gemini/static/third_party/bootstrap/css/bootstrap-responsive.min.css
gemini/static/third_party/bootstrap/css/bootstrap-rowlink.css
gemini/static/third_party/bootstrap/css/bootstrap-rowlink.min.css
gemini/static/third_party/bootstrap/css/bootstrap.css
gemini/static/third_party/bootstrap/css/bootstrap.min.css
gemini/static/third_party/bootstrap/img/glyphicons-halflings-white.png
gemini/static/third_party/bootstrap/img/glyphicons-halflings.png
gemini/static/third_party/bootstrap/js/bootstrap-rowlink.js
gemini/static/third_party/bootstrap/js/bootstrap-rowlink.min.js
gemini/static/third_party/bootstrap/js/bootstrap.js
gemini/static/third_party/bootstrap/js/bootstrap.min.js
gemini/static/third_party/jquery/jquery-1.7.1.js
gemini/static/third_party/jquery-ui/jquery-ui.min.js
gemini/tests/__init__.py
gemini/views/auto_dom.j2.html
gemini/views/auto_rec.j2.html
gemini/views/base.j2.html
gemini/views/db_schema.j2.html
gemini/views/de_novo.j2.html
gemini/views/index.j2.html
gemini/views/query.j2.html
test/.temp.11438
test/.temp.11494
test/.temp.2322
test/ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites.snippet.snpEff.vcf
test/ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites.snippet.vcf
test/_err
test/anno.bed.gz
test/anno.bed.gz.tbi
test/bcolz-setup.sh
test/bcolz-test.sh
test/check.sh
test/clinvar_annotate_error_20170818.ped
test/data-setup.sh
test/drop-gl-columns.py
test/err
test/exp.10554
test/exp.13272
test/exp.13870
test/exp.14012
test/exp.16758
test/exp.17524
test/exp.17564
test/exp.20665
test/exp.22442
test/exp.24703
test/exp.2498
test/exp.25808
test/exp.27504
test/exp.28228
test/exp.3624
test/exp.4675
test/exp.5623
test/exp.6795
test/exp.8350
test/expz
test/from_inheritance.ped
test/from_inheritance.vcf
test/inherited-dn.ped
test/inherited-dn.vcf
test/obs.10554
test/obs.13272
test/obs.13870
test/obs.14012
test/obs.16758
test/obs.17524
test/obs.17564
test/obs.20665
test/obs.22442
test/obs.24703
test/obs.2498
test/obs.25808
test/obs.27504
test/obs.28228
test/obs.3624
test/obs.4675
test/obs.5623
test/obs.6795
test/obs.8350
test/obsz
test/t.py
test/t.sh
test/test-amend.sh
test/test-annotate-tool-vcf.sh
test/test-annotate-tool.sh
test/test-auto-dom.sh
test/test-auto-rec.sh
test/test-bcolz.sh
test/test-cadd.sh
test/test-clinvar.sh
test/test-columns.sh
test/test-comphet.sh
test/test-cosmic.sh
test/test-dashes.sh
test/test-de-novo.sh
test/test-dump.sh
test/test-eff.sh
test/test-effstring.sh
test/test-encode.sh
test/test-esp.sh
test/test-exac.sh
test/test-fitcons.sh
test/test-fusions.sh
test/test-genewise.sh
test/test-geno2mp.sh
test/test-genome.sh
test/test-genotype-likelihoods.sh
test/test-genotypes.sh
test/test-gerp.sh
test/test-gnomad.sh
test/test-load.sh
test/test-lof.vcf
test/test-lofsieve.sh
test/test-map.sh
test/test-mendel-error.sh
test/test-multi-col.sh
test/test-multiple-alts.sh
test/test-no-gls.sh
test/test-pathtool.sh
test/test-pfam.sh
test/test-pop.sh
test/test-query.sh
test/test-region.sh
test/test-roh.sh
test/test-somatic.sh
test/test-stats.sh
test/test-t-all.sh
test/test-vcf-output.sh
test/test-vep-extra.sh
test/test-vep-extra.vcf
test/test-wildcards.sh
test/test-windower.sh
test/test-x-linked.sh
test/test.PLs.vcf
test/test.auto_dom.no_parents.2.ped
test/test.auto_dom.no_parents.2.vcf
test/test.auto_dom.no_parents.3.ped
test/test.auto_dom.no_parents.3.vcf
test/test.auto_dom.no_parents.4.ped
test/test.auto_dom.no_parents.4.vcf
test/test.auto_dom.no_parents.5.ped
test/test.auto_dom.no_parents.5.vcf
test/test.auto_dom.no_parents.ped
test/test.auto_dom.no_parents.vcf
test/test.auto_dom.ped
test/test.auto_dom.vcf
test/test.auto_rec.no_parents.2.ped
test/test.auto_rec.no_parents.2.vcf
test/test.auto_rec.no_parents.3.ped
test/test.auto_rec.no_parents.3.vcf
test/test.auto_rec.no_parents.4.ped
test/test.auto_rec.no_parents.4.vcf
test/test.auto_rec.no_parents.5.ped
test/test.auto_rec.no_parents.5.vcf
test/test.auto_rec.no_parents.ped
test/test.auto_rec.no_parents.vcf
test/test.auto_rec.ped
test/test.auto_rec.vcf
test/test.burden.ped
test/test.burden.vcf
test/test.cadd.vcf
test/test.clinvar.vcf
test/test.clinvar_gene_pheno.vcf
test/test.comp_het.2.ped
test/test.comp_het.2.vcf
test/test.comp_het.3.vcf
test/test.comp_het.4.vcf
test/test.comp_het.5.vcf
test/test.comp_het.6.vcf
test/test.comp_het.7.vcf
test/test.comp_het.ped
test/test.comp_het.singleton.vcf
test/test.comp_het.unphase.vcf
test/test.comp_het.vcf
test/test.cosmic.vcf
test/test.dashes.ped
test/test.dashes.vcf
test/test.de_novo.affected.and.unaffected.ped
test/test.de_novo.affected.and.unaffected.vcf
test/test.de_novo.ped
test/test.de_novo.vcf
test/test.eff.vcf
test/test.esp.zero.vcf
test/test.exac.vcf
test/test.family.vcf
test/test.fusions.ped
test/test.fusions.vcf
test/test.geno2mp.vcf
test/test.mendel.ped
test/test.mendel.vcf
test/test.multiple-alts.decomp.snpeff.vcf
test/test.passonly.vcf
test/test.query.vcf
test/test.region.vep.vcf
test/test.roh.vcf
test/test.snpeff.vcf
test/test.somatic.ped
test/test.somatic.vcf
test/test.vcf_id.snpeff.vcf
test/test.x-linked.ped
test/test.x-linked.vcf
test/test1.snpeff.vcf
test/test2.snpeff.vcf
test/test3.snpeff.vcf
test/test4.snpeff.ped
test/test4.vep.snpeff.vcf
test/test5.vep.snpeff.vcf
test/test_amend2_sample.ped
test/test_amend_sample.ped
test/test_extended_ped.ped
test/unicode.ped