├── .gitignore ├── LICENSE.txt ├── README.md ├── aortagene └── v20230529 │ └── aorta_gene.R ├── aortascore ├── deprecated │ └── v20220307 │ │ └── aorta_score.R └── v20220503 │ └── aorta_score.R ├── applyprsgcp ├── bgi_tempfile.go ├── bgi_tempfile_locked.go ├── prsworker │ └── open.go └── tasker │ ├── tasker.go │ └── types.go ├── bim.go ├── bimrow.go ├── cardiaccycle ├── cardiaccycle.go ├── entry.go ├── list.go ├── result.go ├── runfile.go ├── runslice.go └── seriessample.go ├── chrpos ├── lookups │ ├── README.md │ ├── grch37 │ └── grch38 ├── splitchrpos.go ├── splitchrpos_test.go └── type_tabixlocus.go ├── cmd ├── animategcp │ ├── README.md │ ├── main.go │ ├── makegif.go │ └── manifest.go ├── animateunjitter │ ├── main.go │ └── sortable.go ├── animatezip │ ├── README.md │ ├── label.go │ ├── main.go │ ├── makegif.go │ └── manifest.go ├── applyprsbasic │ ├── bgen.go │ ├── build-linux.sh │ ├── errors.go │ ├── main.go │ ├── prs.go │ ├── type_sample.go │ └── vcf.go ├── applyprsgcp │ ├── dsub │ │ ├── dsub-example.sh │ │ ├── make-tasks.sh │ │ ├── result-query.sql │ │ └── worker.sh │ ├── prsreducer │ │ └── main.go │ ├── prsworker │ │ ├── accumulatescore.go │ │ ├── bgenpreprocess.go │ │ ├── errors.go │ │ ├── main.go │ │ ├── prs.go │ │ └── type_sample.go │ └── tasker │ │ └── main.go ├── batcher │ ├── dicom.go │ ├── functions.go │ └── main.go ├── bgen2bigquery │ ├── build-linux.sh │ └── main.go ├── bgenreadsnp │ ├── allelecount │ │ └── main.go │ └── main.go ├── bimfixduplicatesnpids │ └── main.go ├── bimmanglesnpids │ └── main.go ├── bolt2ldhub │ └── main.go ├── cardiaccycle │ ├── entry.go │ ├── list.go │ ├── main.go │ └── sample.go ├── cardiaccyclev2 │ ├── entry.go │ ├── list.go │ ├── main.go │ └── sample.go ├── clinvartab2bigquery │ ├── README.txt │ └── main.go ├── combine-spreadsheet │ ├── README.md │ └── main.go ├── critic │ ├── cmd │ │ └── critic │ │ │ ├── annotations.go │ │ │ ├── critic.exe │ │ │ ├── default.labels.json │ │ │ ├── demo.tsv │ │ │ ├── errors.go │ │ │ ├── fetchimage.go │ │ │ ├── functions.go │ │ │ ├── globals.go │ │ │ ├── handler.go │ │ │ ├── handlers.go │ │ │ ├── labels.go │ │ │ ├── main.go │ │ │ ├── manifest.go │ │ │ ├── render.go │ │ │ ├── router.go │ │ │ ├── templates │ │ │ ├── DMCA.html │ │ │ ├── TOS.html │ │ │ ├── _base.html │ │ │ ├── about.html │ │ │ ├── critic-POST.html │ │ │ ├── critic.html │ │ │ ├── error.html │ │ │ ├── index.html │ │ │ ├── listproject.html │ │ │ ├── privacy.html │ │ │ └── static │ │ │ │ ├── css │ │ │ │ ├── bootstrap.3.3.1.min.css │ │ │ │ ├── darkly.bootstrap.3.4.0.min.css │ │ │ │ ├── flatly.bootstrap.3.3.0.min.css │ │ │ │ ├── nofont-flatly.bootstrap.3.3.0.min.css │ │ │ │ └── overrides.css │ │ │ │ ├── favicon.ico │ │ │ │ ├── img │ │ │ │ ├── 128px-Utah_teapot_simple_2.png │ │ │ │ └── unsplash_pubrank.jpg │ │ │ │ └── js │ │ │ │ ├── bootstrap.3.3.1.min.js │ │ │ │ ├── critic.js │ │ │ │ └── jquery.2.1.1.min.js │ │ │ ├── type_fastslice.go │ │ │ └── type_fastslice_test.go │ ├── demo │ │ ├── 128px-Utah_teapot_simple_2.png │ │ ├── bmp.js │ │ ├── demo.html │ │ ├── fill.js │ │ └── traceoverlay.js │ └── web │ │ ├── annotations.go │ │ ├── default.labels.json │ │ ├── errors.go │ │ ├── functions.go │ │ ├── globals.go │ │ ├── handler.go │ │ ├── handlers.go │ │ ├── labels.go │ │ ├── main.go │ │ ├── manifest.go │ │ ├── render.go │ │ ├── router.go │ │ ├── templates │ │ ├── DMCA.html │ │ ├── TOS.html │ │ ├── _base.html │ │ ├── about.html │ │ ├── critic-POST.html │ │ ├── critic.html │ │ ├── error.html │ │ ├── index.html │ │ ├── listproject.html │ │ ├── privacy.html │ │ └── static │ │ │ ├── css │ │ │ ├── bootstrap.3.3.1.min.css │ │ │ ├── darkly.bootstrap.3.4.0.min.css │ │ │ ├── flatly.bootstrap.3.3.0.min.css │ │ │ ├── nofont-flatly.bootstrap.3.3.0.min.css │ │ │ └── overrides.css │ │ │ ├── favicon.ico │ │ │ ├── img │ │ │ ├── 128px-Utah_teapot_simple_2.png │ │ │ └── unsplash_pubrank.jpg │ │ │ └── js │ │ │ ├── bootstrap.3.3.1.min.js │ │ │ ├── critic.js │ │ │ └── jquery.2.1.1.min.js │ │ ├── type_fastslice.go │ │ └── type_fastslice_test.go ├── deleteunknown │ └── main.go ├── dicom-mip │ ├── README.md │ ├── functions.go │ ├── main.go │ ├── makemip.go │ ├── makemip_nonsquare.go │ ├── makemovie.go │ ├── manifest.go │ └── process_entries.go ├── dicom2las │ ├── doc.go │ ├── main.go │ ├── makelas.go │ ├── manifest.go │ └── process_entries.go ├── dicom2png │ ├── main.go │ └── targz.go ├── dicomdump │ ├── dicom.go │ └── main.go ├── dicomvenc │ ├── functions.go │ ├── main.go │ ├── plot.go │ └── zip.go ├── enhanceratlas │ └── enhancergene │ │ └── main.go ├── gene2chrpos │ ├── grch38 │ │ ├── lookups │ │ │ └── ensembl.grch38.p12.genes │ │ └── main.go │ ├── lookups │ │ └── ensembl.grch37.p13.genes │ └── main.go ├── genes2sites │ ├── gene.go │ ├── lookups │ │ ├── ensembl.grch37.p13.genes │ │ ├── ensembl.grch38.p12.genes │ │ └── url.txt │ ├── main.go │ └── test.test ├── gtf2tsv │ └── main.go ├── gwasclump │ ├── 1.all-signif.sh │ ├── 2.clump-loci.sh │ ├── clump-by-p-and-distance.r │ └── genomewide-only.sh ├── interpolatecm │ ├── main.go │ ├── map.go │ └── pvar.go ├── liftover │ ├── io.go │ └── main.go ├── locusid │ └── main.go ├── mendeloverlap │ ├── README.md │ ├── gene.go │ ├── locus.go │ ├── lookups │ │ └── ensembl.grch37.p13.genes │ ├── main.go │ ├── permutation.go │ ├── results.go │ └── snpsnap.go ├── nearbygenes │ ├── gene.go │ ├── lookups │ │ ├── ensembl.grch37.p13.genes │ │ ├── ensembl.grch38.p12.genes │ │ └── url.txt │ ├── main.go │ └── test.test ├── nearestgene │ ├── gene.go │ ├── lookups │ │ ├── ensembl.grch37.p13.genes │ │ ├── ensembl.grch38.p12.genes │ │ └── url.txt │ ├── main.go │ └── test.test ├── nifti2png │ ├── main.go │ └── safely.go ├── pixelcounter │ ├── functions.go │ └── main.go ├── pixeloverlap │ ├── confusion.go │ ├── doc.go │ ├── functions.go │ └── main.go ├── pixeloverlapsummary │ └── main.go ├── pixelqc │ ├── file_covars.go │ ├── file_pixelcount.go │ ├── flags.go │ ├── main.go │ └── qc.go ├── pixelreplace │ ├── demo.replacements.json │ ├── doc.go │ ├── functions.go │ ├── main.go │ ├── replacement-ids.go │ └── targz.go ├── pngaverage │ ├── flagslice.go │ └── main.go ├── pngnorms │ └── main.go ├── pngoverlay │ └── main.go ├── pngreplace │ ├── demo-output │ │ └── demo.png │ ├── demo.png │ ├── demo.replacements.json │ ├── demo.sh │ ├── doc.go │ ├── functions.go │ ├── main.go │ ├── replacement-ids.go │ └── targz.go ├── pngtostack │ ├── loaders.go │ └── main.go ├── pngupsample │ └── main.go ├── printdisease │ ├── functions.go │ ├── importcoding.go │ ├── importdict.go │ ├── main.go │ ├── materialized_special.go │ ├── special_fields.go │ └── tabfile.go ├── rawdicom2png │ └── main.go ├── regenie2bolt │ ├── build-linux.sh │ └── main.go ├── regenie2exponent │ ├── build-linux.sh │ ├── gene.go │ ├── lookups │ │ ├── ensembl.grch37.p13.genes │ │ ├── ensembl.grch38.p12.genes │ │ └── url.txt │ └── main.go ├── saige2bolt │ └── main.go ├── ukbb2csv │ ├── censor │ │ ├── censor_result.go │ │ ├── main.go │ │ ├── query_counters.go │ │ ├── query_execute.go │ │ ├── query_template.go │ │ ├── query_template_aou.sql │ │ ├── query_template_ukbb.sql │ │ └── time_handling.go │ ├── convertcoding │ │ └── main.go │ ├── convertdict │ │ └── main.go │ ├── convertpheno │ │ └── main.go │ ├── convertsample │ │ └── main.go │ ├── downloader │ │ └── main.go │ ├── manifester │ │ ├── dicom.go │ │ ├── exerciseekg.go │ │ ├── main.go │ │ └── twelveleadekg.go │ ├── manifetcher │ │ ├── README.md │ │ └── main.go │ └── materialized_tables │ │ ├── hesin_and_gp │ │ ├── README.md │ │ ├── hesin.json │ │ ├── hesin_diag.json │ │ ├── hesin_oper.json │ │ ├── materialized_gp_dates.sql │ │ ├── materialized_hesin_dates.sql │ │ └── v1 │ │ │ ├── README.md │ │ │ └── materialized_hesin_dates.sql │ │ └── materialized_special_dates.sql ├── ukbb2disease │ ├── ARDS-demo-string.tab │ ├── ARDS-demo.tab │ ├── DATES.md │ ├── README.md │ ├── biobanks.go │ ├── main.go │ ├── materialized_special.go │ ├── query_template.go │ ├── query_template_aou.sql │ ├── query_template_ukbb.sql │ ├── result.go │ ├── special_fields.go │ └── tabfile.go ├── ukbb2recur │ ├── main.go │ ├── materialized_special.go │ ├── query.go │ ├── query_template.go │ ├── result.go │ ├── special_fields.go │ ├── statusenum.go │ ├── statusenum_string.go │ ├── tabfile.go │ └── time_handling.go ├── vcf2bigquery │ ├── flagslice.go │ ├── load │ │ ├── genotype.json │ │ ├── load_alt.sh │ │ └── load_missing.sh │ ├── lookups │ │ ├── README.md │ │ ├── grch37 │ │ └── grch38 │ ├── main.go │ ├── printer.go │ ├── qsub │ │ ├── qsub_alt.sh │ │ ├── qsub_missing.sh │ │ └── vcf2bigquery.sh │ ├── splitchrpos.go │ ├── type_tabixlocus.go │ └── work.go └── xml2ecg │ ├── cardiologyxml.go │ ├── functions.go │ └── main.go ├── compileinfo └── compileinfo.go ├── compileinfoprint └── compileinfoprint.go ├── detecreaddatatype.go ├── detectdelimiter.go ├── example └── bim │ └── main.go ├── expand.go ├── go.mod ├── go.sum ├── gsreaderatcloser.go ├── gsreadseeker.go ├── hwe ├── hwe_approx.go ├── hwe_exact.go ├── hwe_fast.go └── hwe_test.go ├── overlay ├── README.md ├── color_label.go ├── component.go ├── connected.go ├── connected_moments.go ├── demo-curved.png ├── demo-curved.png.overlay.png ├── demo.config.json ├── image_io.go ├── json-config.go ├── labelmap.go └── subset.go ├── prsparser ├── allele.go ├── layout.go ├── layout_test.go ├── prs.go └── prsparser.go ├── ramcsv └── randomaccesscsv.go ├── readeratcloser.go ├── ukbb ├── bulkprocess │ ├── README.md │ ├── dicom-metadata.go │ ├── dicom-overlay.go │ ├── dicom-safely-parse.go │ ├── dicom-tagmap.go │ ├── extractdicom.go │ ├── extractdicomfuncops.go │ ├── extractgif.go │ ├── extractimage.go │ ├── field-ids.go │ ├── gsreaderat.go │ ├── gsreaderat_test.go │ ├── imagegrid.go │ ├── process-zip.go │ ├── siemens.go │ ├── type_12_lead_ekg.go │ ├── type_exercise_ekg.go │ ├── venc.go │ └── zip-metadata.go ├── coding.go ├── csvquotefixreadcloser.go └── dict.go └── ukbb2csv └── convertpheno ├── convertpheno.go ├── datasource_bq.go 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