From ffbcef24f540e5840fb77c487a5fb46fbb9da133 Mon Sep 17 00:00:00 2001
From: Tom Clegg <tom@curii.com>
Date: Thu, 11 Apr 2024 14:16:52 -0400
Subject: [PATCH] 21543: Move Go code into go-lightning subdir.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
---
 .licenseignore                                |  6 +-
 docker/lightning/Dockerfile                   |  6 +-
 example-su92l-1kg.sh                          | 93 -------------------
 Makefile => go-lightning/Makefile             |  0
 anno2vcf.go => go-lightning/anno2vcf.go       |  0
 annotate.go => go-lightning/annotate.go       |  2 +-
 arvados.go => go-lightning/arvados.go         |  0
 batchargs.go => go-lightning/batchargs.go     |  0
 chisquare.go => go-lightning/chisquare.go     |  0
 .../chisquare_test.go                         |  0
 .../choosesamples.go                          |  0
 cmd.go => go-lightning/cmd.go                 |  0
 diff.go => go-lightning/diff.go               |  2 +-
 diff_test.go => go-lightning/diff_test.go     |  0
 dump.go => go-lightning/dump.go               |  0
 dumpgob.go => go-lightning/dumpgob.go         |  0
 export.go => go-lightning/export.go           |  2 +-
 export_test.go => go-lightning/export_test.go |  0
 exportnumpy.go => go-lightning/exportnumpy.go |  2 +-
 .../exportnumpy_test.go                       |  0
 filter.go => go-lightning/filter.go           |  0
 flake.go => go-lightning/flake.go             |  0
 glm.go => go-lightning/glm.go                 |  0
 glm_test.go => go-lightning/glm_test.go       |  0
 go.mod => go-lightning/go.mod                 |  4 +-
 go.sum => go-lightning/go.sum                 |  0
 gob.go => go-lightning/gob.go                 |  0
 {hgvs => go-lightning/hgvs}/diff.go           |  0
 {hgvs => go-lightning/hgvs}/diff_test.go      |  0
 import.go => go-lightning/import.go           |  0
 {lightning => go-lightning/lightning}/main.go |  2 +-
 lis.go => go-lightning/lis.go                 |  0
 lis_test.go => go-lightning/lis_test.go       |  0
 manhattan.go => go-lightning/manhattan.go     |  0
 manhattan.py => go-lightning/manhattan.py     |  0
 mask.go => go-lightning/mask.go               |  0
 mask_test.go => go-lightning/mask_test.go     |  0
 merge.go => go-lightning/merge.go             |  0
 numpycomvar.go => go-lightning/numpycomvar.go |  0
 pca_plot.go => go-lightning/pca_plot.go       |  0
 pca_plot.py => go-lightning/pca_plot.py       |  0
 .../pipeline_test.go                          |  0
 profile.go => go-lightning/profile.go         |  0
 ref2genome.go => go-lightning/ref2genome.go   |  0
 slice.go => go-lightning/slice.go             |  0
 slice_test.go => go-lightning/slice_test.go   |  0
 slicenumpy.go => go-lightning/slicenumpy.go   |  2 +-
 stats.go => go-lightning/stats.go             |  0
 taglib.go => go-lightning/taglib.go           |  0
 taglib_test.go => go-lightning/taglib_test.go |  0
 {testdata => go-lightning/testdata}/a.1.fasta |  0
 {testdata => go-lightning/testdata}/a.2.fasta |  0
 .../testdata}/pipeline1/input1.1.fasta        |  0
 .../testdata}/pipeline1/input1.2.fasta        |  0
 .../testdata}/pipeline1/input2.1.fasta        |  0
 .../testdata}/pipeline1/input2.2.fasta        |  0
 {testdata => go-lightning/testdata}/ref.fasta |  0
 .../testdata}/spanningtile/input1.1.fasta     |  0
 .../testdata}/spanningtile/input1.2.fasta     |  0
 .../testdata}/spanningtile/input2.1.fasta     |  0
 .../testdata}/spanningtile/input2.2.fasta     |  0
 {testdata => go-lightning/testdata}/tags      |  0
 .../testdata}/tinyref.fasta                   |  0
 throttle.go => go-lightning/throttle.go       |  0
 tilelib.go => go-lightning/tilelib.go         |  0
 .../tilelib_test.go                           |  0
 tilestats.go => go-lightning/tilestats.go     |  0
 vcf2fasta.go => go-lightning/vcf2fasta.go     |  0
 version.sh => go-lightning/version.sh         |  0
 69 files changed, 14 insertions(+), 107 deletions(-)
 delete mode 100755 example-su92l-1kg.sh
 rename Makefile => go-lightning/Makefile (100%)
 rename anno2vcf.go => go-lightning/anno2vcf.go (100%)
 rename annotate.go => go-lightning/annotate.go (99%)
 rename arvados.go => go-lightning/arvados.go (100%)
 rename batchargs.go => go-lightning/batchargs.go (100%)
 rename chisquare.go => go-lightning/chisquare.go (100%)
 rename chisquare_test.go => go-lightning/chisquare_test.go (100%)
 rename choosesamples.go => go-lightning/choosesamples.go (100%)
 rename cmd.go => go-lightning/cmd.go (100%)
 rename diff.go => go-lightning/diff.go (97%)
 rename diff_test.go => go-lightning/diff_test.go (100%)
 rename dump.go => go-lightning/dump.go (100%)
 rename dumpgob.go => go-lightning/dumpgob.go (100%)
 rename export.go => go-lightning/export.go (99%)
 rename export_test.go => go-lightning/export_test.go (100%)
 rename exportnumpy.go => go-lightning/exportnumpy.go (99%)
 rename exportnumpy_test.go => go-lightning/exportnumpy_test.go (100%)
 rename filter.go => go-lightning/filter.go (100%)
 rename flake.go => go-lightning/flake.go (100%)
 rename glm.go => go-lightning/glm.go (100%)
 rename glm_test.go => go-lightning/glm_test.go (100%)
 rename go.mod => go-lightning/go.mod (97%)
 rename go.sum => go-lightning/go.sum (100%)
 rename gob.go => go-lightning/gob.go (100%)
 rename {hgvs => go-lightning/hgvs}/diff.go (100%)
 rename {hgvs => go-lightning/hgvs}/diff_test.go (100%)
 rename import.go => go-lightning/import.go (100%)
 rename {lightning => go-lightning/lightning}/main.go (74%)
 rename lis.go => go-lightning/lis.go (100%)
 rename lis_test.go => go-lightning/lis_test.go (100%)
 rename manhattan.go => go-lightning/manhattan.go (100%)
 rename manhattan.py => go-lightning/manhattan.py (100%)
 rename mask.go => go-lightning/mask.go (100%)
 rename mask_test.go => go-lightning/mask_test.go (100%)
 rename merge.go => go-lightning/merge.go (100%)
 rename numpycomvar.go => go-lightning/numpycomvar.go (100%)
 rename pca_plot.go => go-lightning/pca_plot.go (100%)
 rename pca_plot.py => go-lightning/pca_plot.py (100%)
 rename pipeline_test.go => go-lightning/pipeline_test.go (100%)
 rename profile.go => go-lightning/profile.go (100%)
 rename ref2genome.go => go-lightning/ref2genome.go (100%)
 rename slice.go => go-lightning/slice.go (100%)
 rename slice_test.go => go-lightning/slice_test.go (100%)
 rename slicenumpy.go => go-lightning/slicenumpy.go (99%)
 rename stats.go => go-lightning/stats.go (100%)
 rename taglib.go => go-lightning/taglib.go (100%)
 rename taglib_test.go => go-lightning/taglib_test.go (100%)
 rename {testdata => go-lightning/testdata}/a.1.fasta (100%)
 rename {testdata => go-lightning/testdata}/a.2.fasta (100%)
 rename {testdata => go-lightning/testdata}/pipeline1/input1.1.fasta (100%)
 rename {testdata => go-lightning/testdata}/pipeline1/input1.2.fasta (100%)
 rename {testdata => go-lightning/testdata}/pipeline1/input2.1.fasta (100%)
 rename {testdata => go-lightning/testdata}/pipeline1/input2.2.fasta (100%)
 rename {testdata => go-lightning/testdata}/ref.fasta (100%)
 rename {testdata => go-lightning/testdata}/spanningtile/input1.1.fasta (100%)
 rename {testdata => go-lightning/testdata}/spanningtile/input1.2.fasta (100%)
 rename {testdata => go-lightning/testdata}/spanningtile/input2.1.fasta (100%)
 rename {testdata => go-lightning/testdata}/spanningtile/input2.2.fasta (100%)
 rename {testdata => go-lightning/testdata}/tags (100%)
 rename {testdata => go-lightning/testdata}/tinyref.fasta (100%)
 rename throttle.go => go-lightning/throttle.go (100%)
 rename tilelib.go => go-lightning/tilelib.go (100%)
 rename tilelib_test.go => go-lightning/tilelib_test.go (100%)
 rename tilestats.go => go-lightning/tilestats.go (100%)
 rename vcf2fasta.go => go-lightning/vcf2fasta.go (100%)
 rename version.sh => go-lightning/version.sh (100%)

diff --git a/.licenseignore b/.licenseignore
index 0d77b26cc4..752f7f8f7e 100644
--- a/.licenseignore
+++ b/.licenseignore
@@ -1,6 +1,6 @@
 .licenseignore
 AUTHORS
-go.mod
-go.sum
-testdata/*
+go-lightning/go.mod
+go-lightning/go.sum
+go-lightning/testdata/*
 readme.md
diff --git a/docker/lightning/Dockerfile b/docker/lightning/Dockerfile
index a6df7bb3d3..7175ffc33b 100644
--- a/docker/lightning/Dockerfile
+++ b/docker/lightning/Dockerfile
@@ -3,7 +3,7 @@
 # SPDX-License-Identifier: AGPL-3.0
 
 # build instruction:
-# docker build -t dockername --file=/path/to/lightning/docker/lightning/Dockerfile /path/to/lightning
+# docker build -t dockername --file=/path/to/lightning/docker/lightning/Dockerfile /path/to/lightning/go-lightning
 
 FROM python:3.11-buster
 USER root
@@ -26,8 +26,8 @@ RUN apt-get install -qy --no-install-recommends wget \
 
 RUN pip install --upgrade pip matplotlib numpy pandas scikit-learn scipy
 
-RUN wget --progress=dot:giga https://go.dev/dl/go1.20.10.linux-amd64.tar.gz && \
-    tar -C /usr/local -xzf go1.20.10.linux-amd64.tar.gz
+RUN wget --progress=dot:giga https://go.dev/dl/go1.22.2.linux-amd64.tar.gz && \
+    tar -C /usr/local -xzf go1.22.2.linux-amd64.tar.gz
 
 ENV PATH $PATH:/usr/local/go/bin:/root/go/bin
 
diff --git a/example-su92l-1kg.sh b/example-su92l-1kg.sh
deleted file mode 100755
index c60e8fc93d..0000000000
--- a/example-su92l-1kg.sh
+++ /dev/null
@@ -1,93 +0,0 @@
-#!/bin/bash
-
-set -ex
-
-PATH="${GOPATH:-${HOME}/go}/bin:${PATH}"
-go install
-lightning build-docker-image
-arv keep docker lightning-runtime
-
-priority=501
-project=su92l-j7d0g-jzei0m9yvgauhjf
-ref_fa=su92l-4zz18-u77iyyy7cb05xqv/hg38.fa.gz
-ref37_fa=su92l-4zz18-caw3g2ji89jxix8/human_g1k_v37.fasta.gz
-gvcf=${HOME}/keep/by_id/su92l-4zz18-bgyq36m6gctk63q
-info=su92l-4zz18-ykpcoea5nisz74f
-tagset=su92l-4zz18-92bx4zjg5hgs3yc/tagset.fa.gz
-
-genome=$(lightning     ref2genome   -project ${project} -priority ${priority} -ref ${ref_fa})                                                          ; echo genome=${genome}
-fasta=$(lightning      vcf2fasta    -project ${project} -priority ${priority} -ref ${ref_fa} -genome ${genome} -mask=true ${gvcf})                     ; echo fasta=${fasta}
-# fasta=su92l-4zz18-9nq05jifgz7iult
-
-ref37_lib=$(lightning  import       -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true -save-incomplete-tiles=true ${ref37_fa}) ; echo ref37_lib=${ref37_lib}
-# ref37_lib=su92l-4zz18-vnhlv3g6yp1azls/library.gob
-# 539s
-# ref37_lib=su92l-4zz18-v0xfm2o1tu3u1w3/library.gob.gz
-# 2751s @ 4a3899f
-
-ref38_lib=$(lightning  import       -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true -save-incomplete-tiles=true ${ref_fa}) ; echo ref38_lib=${ref38_lib}
-# ref38_lib=su92l-4zz18-swebknshfwsvys6/library.gob
-
-bed37=$(lightning export       -project ${project} -priority ${priority} -i ${ref37_lib} -output-format hgvs -ref /mnt/$ref37_fa -output-bed hg37.bed) ; echo bed37=${bed37}
-# bed37=su92l-4zz18-gb3hihiiaz0xaz9/export.csv
-# 463s @ 870319f
-bed38=$(lightning export       -project ${project} -priority ${priority} -i ${ref38_lib} -output-format hgvs -ref /mnt/$ref_fa -output-bed hg38.bed) ; echo bed38=${bed38}
-
-unfiltered=$(lightning import       -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true ${fasta})       ; echo unfiltered=${unfiltered}
-# unfiltered=su92l-4zz18-mz3546bib6oj1gg/library.gob
-# unfiltered=su92l-4zz18-72ovi5qrderxudv/library.gob
-# 24674s @ pre-38e6e7c
-# unfiltered=su92l-4zz18-ywhkc1hgdzxwp5u/library.gob
-# 18497s @ 64vcpu bf0968a
-# _____s @ 32vcpu 83983ad
-
-
-merged=$(lightning     merge        -project ${project} -priority ${priority} ${unfiltered} ${ref37_lib})                                              ; echo merged=${merged}
-# merged=su92l-4zz18-svw5xqe5g0ct2v1/library.gob
-# 2400s
-
-exportvcf=$(lightning  export       -project ${project} -priority ${priority} -i ${merged} -output-format vcf -ref /mnt/su92l-4zz18-caw3g2ji89jxix8/human_g1k_v37.fasta.gz -output-bed export.bed) ; echo exportvcf=${exportvcf}
-# exportvcf=su92l-4zz18-gz4svr6zyvipueu/export.csv
-# 5506s
-
-exporthgvs=$(lightning export       -project ${project} -priority ${priority} -i ${merged38} -output-format hgvs -ref /mnt/su92l-4zz18-u77iyyy7cb05xqv/hg38.fa.gz -output-bed hg38.bed) ; echo exporthgvs=${exporthgvs}
-# 
-# 
-
-stats=$(lightning      stats        -project ${project} -priority ${priority} -i ${merged})                                                            ; echo stats=${stats}
-
-filtered=$(lightning   filter       -project ${project} -priority ${priority} -i ${merged} -min-coverage "0.9" -max-variants "30")                     ; echo filtered=${filtered}
-
-annotations=$(lightning annotate    -project ${project} -priority ${priority} -i ${merged})                                                            ; echo annotations=${annotations}
-
-pca=$(lightning        pca-go       -project ${project} -priority ${priority} -i ${unfiltered} -min-coverage "0.9" -max-variants "30")                 ; echo pca=${pca}
-# pca=su92l-4zz18-e3xhi2mzp8rqevd/pca.npy
-# 3987s @ c237c16
-plot=$(lightning       plot         -project ${project} -priority ${priority} -i ${pca} -labels-csv ${info}/sample_info.csv -sample-fasta-dir ${fasta})
-echo >&2 "https://workbench2.${plot%%-*}.arvadosapi.com/collections/${plot}"
-echo ${plot%%/*}
-# plot=su92l-4zz18-xyei3lnyxmgo7lh/plot.png
-# 535s @ c237c16
-
-merged38=$(lightning   merge        -project ${project} -priority ${priority} ${unfiltered} ${ref38_lib})                                              ; echo merged38=${merged38}
-# merged38=su92l-4zz18-xq17gtaltjxbm3n/library.gob
-# 1602s
-# merged38=su92l-4zz18-5kcaci3hqzukjv2/library.gob
-# 2815s @ 83983ad
-# merged38=su92l-4zz18-nq8dmtng68ozovu/library.gob.gz
-# 9803s @ 69b71af
-
-numpy=$(lightning      export-numpy -project ${project} -priority ${priority} -i ${merged38})                                                          ; echo numpy=${numpy}
-# numpy=su92l-4zz18-w3dx5k79mtbz6qt/matrix.npy
-# 6155s
-# numpy=su92l-4zz18-g1y2eg9qvngvkkq/matrix.npy
-# 6633s @ 83983ad
-# numpy=su92l-4zz18-cpw0i3z7wery77o/matrix.npy
-# 6311s @ 4e6ada0
-# numpy=su92l-4zz18-hljgbqs6c87wles/matrix.npy
-# 6824s @ 2e1cb2e
-# numpy=su92l-4zz18-vw31l0qzenyb44l/matrix.npy
-# 7403s @ 6785271
-# pcapy=$(lightning      pca          -project ${project} -priority ${priority} -i ${numpy})                                                             ; echo pcapy=${pcapy}
-comvar=$(lightning     numpy-comvar -project ${project} -priority ${priority} -i ${numpy} -annotations ${numpy%/matrix.npy}/annotations.tsv)           ; echo comvar=${comvar}
-# comvar=su92l-4zz18-s1yhngobdvcoc2e/commonvariants.csv
diff --git a/Makefile b/go-lightning/Makefile
similarity index 100%
rename from Makefile
rename to go-lightning/Makefile
diff --git a/anno2vcf.go b/go-lightning/anno2vcf.go
similarity index 100%
rename from anno2vcf.go
rename to go-lightning/anno2vcf.go
diff --git a/annotate.go b/go-lightning/annotate.go
similarity index 99%
rename from annotate.go
rename to go-lightning/annotate.go
index 00f1cad155..b8bee8182f 100644
--- a/annotate.go
+++ b/go-lightning/annotate.go
@@ -22,7 +22,7 @@ import (
 	"sync"
 
 	"git.arvados.org/arvados.git/sdk/go/arvados"
-	"github.com/arvados/lightning/hgvs"
+	"github.com/arvados/lightning/go-lightning/hgvs"
 	log "github.com/sirupsen/logrus"
 )
 
diff --git a/arvados.go b/go-lightning/arvados.go
similarity index 100%
rename from arvados.go
rename to go-lightning/arvados.go
diff --git a/batchargs.go b/go-lightning/batchargs.go
similarity index 100%
rename from batchargs.go
rename to go-lightning/batchargs.go
diff --git a/chisquare.go b/go-lightning/chisquare.go
similarity index 100%
rename from chisquare.go
rename to go-lightning/chisquare.go
diff --git a/chisquare_test.go b/go-lightning/chisquare_test.go
similarity index 100%
rename from chisquare_test.go
rename to go-lightning/chisquare_test.go
diff --git a/choosesamples.go b/go-lightning/choosesamples.go
similarity index 100%
rename from choosesamples.go
rename to go-lightning/choosesamples.go
diff --git a/cmd.go b/go-lightning/cmd.go
similarity index 100%
rename from cmd.go
rename to go-lightning/cmd.go
diff --git a/diff.go b/go-lightning/diff.go
similarity index 97%
rename from diff.go
rename to go-lightning/diff.go
index 4999643e99..a10d6d8180 100644
--- a/diff.go
+++ b/go-lightning/diff.go
@@ -12,7 +12,7 @@ import (
 	"io"
 	"os"
 
-	"github.com/arvados/lightning/hgvs"
+	"github.com/arvados/lightning/go-lightning/hgvs"
 )
 
 type diffFasta struct{}
diff --git a/diff_test.go b/go-lightning/diff_test.go
similarity index 100%
rename from diff_test.go
rename to go-lightning/diff_test.go
diff --git a/dump.go b/go-lightning/dump.go
similarity index 100%
rename from dump.go
rename to go-lightning/dump.go
diff --git a/dumpgob.go b/go-lightning/dumpgob.go
similarity index 100%
rename from dumpgob.go
rename to go-lightning/dumpgob.go
diff --git a/export.go b/go-lightning/export.go
similarity index 99%
rename from export.go
rename to go-lightning/export.go
index 39af631e9a..acb06a46e5 100644
--- a/export.go
+++ b/go-lightning/export.go
@@ -24,7 +24,7 @@ import (
 	"time"
 
 	"git.arvados.org/arvados.git/sdk/go/arvados"
-	"github.com/arvados/lightning/hgvs"
+	"github.com/arvados/lightning/go-lightning/hgvs"
 	"github.com/klauspost/pgzip"
 	"github.com/kshedden/gonpy"
 	"github.com/sirupsen/logrus"
diff --git a/export_test.go b/go-lightning/export_test.go
similarity index 100%
rename from export_test.go
rename to go-lightning/export_test.go
diff --git a/exportnumpy.go b/go-lightning/exportnumpy.go
similarity index 99%
rename from exportnumpy.go
rename to go-lightning/exportnumpy.go
index 698180b754..c0f3e55300 100644
--- a/exportnumpy.go
+++ b/go-lightning/exportnumpy.go
@@ -23,7 +23,7 @@ import (
 	"sync/atomic"
 
 	"git.arvados.org/arvados.git/sdk/go/arvados"
-	"github.com/arvados/lightning/hgvs"
+	"github.com/arvados/lightning/go-lightning/hgvs"
 	"github.com/kshedden/gonpy"
 	"github.com/sirupsen/logrus"
 	log "github.com/sirupsen/logrus"
diff --git a/exportnumpy_test.go b/go-lightning/exportnumpy_test.go
similarity index 100%
rename from exportnumpy_test.go
rename to go-lightning/exportnumpy_test.go
diff --git a/filter.go b/go-lightning/filter.go
similarity index 100%
rename from filter.go
rename to go-lightning/filter.go
diff --git a/flake.go b/go-lightning/flake.go
similarity index 100%
rename from flake.go
rename to go-lightning/flake.go
diff --git a/glm.go b/go-lightning/glm.go
similarity index 100%
rename from glm.go
rename to go-lightning/glm.go
diff --git a/glm_test.go b/go-lightning/glm_test.go
similarity index 100%
rename from glm_test.go
rename to go-lightning/glm_test.go
diff --git a/go.mod b/go-lightning/go.mod
similarity index 97%
rename from go.mod
rename to go-lightning/go.mod
index 8f8400a3b8..a38de1bee8 100644
--- a/go.mod
+++ b/go-lightning/go.mod
@@ -1,6 +1,6 @@
-module github.com/arvados/lightning
+module github.com/arvados/lightning/go-lightning
 
-go 1.17
+go 1.20
 
 require (
 	git.arvados.org/arvados.git v0.0.0-20221110193247-c80603fb6b95
diff --git a/go.sum b/go-lightning/go.sum
similarity index 100%
rename from go.sum
rename to go-lightning/go.sum
diff --git a/gob.go b/go-lightning/gob.go
similarity index 100%
rename from gob.go
rename to go-lightning/gob.go
diff --git a/hgvs/diff.go b/go-lightning/hgvs/diff.go
similarity index 100%
rename from hgvs/diff.go
rename to go-lightning/hgvs/diff.go
diff --git a/hgvs/diff_test.go b/go-lightning/hgvs/diff_test.go
similarity index 100%
rename from hgvs/diff_test.go
rename to go-lightning/hgvs/diff_test.go
diff --git a/import.go b/go-lightning/import.go
similarity index 100%
rename from import.go
rename to go-lightning/import.go
diff --git a/lightning/main.go b/go-lightning/lightning/main.go
similarity index 74%
rename from lightning/main.go
rename to go-lightning/lightning/main.go
index 5d5ec6cb12..7d4ca168e5 100644
--- a/lightning/main.go
+++ b/go-lightning/lightning/main.go
@@ -4,7 +4,7 @@
 
 package main
 
-import "github.com/arvados/lightning"
+import "github.com/arvados/lightning/go-lightning"
 
 func main() {
 	lightning.Main()
diff --git a/lis.go b/go-lightning/lis.go
similarity index 100%
rename from lis.go
rename to go-lightning/lis.go
diff --git a/lis_test.go b/go-lightning/lis_test.go
similarity index 100%
rename from lis_test.go
rename to go-lightning/lis_test.go
diff --git a/manhattan.go b/go-lightning/manhattan.go
similarity index 100%
rename from manhattan.go
rename to go-lightning/manhattan.go
diff --git a/manhattan.py b/go-lightning/manhattan.py
similarity index 100%
rename from manhattan.py
rename to go-lightning/manhattan.py
diff --git a/mask.go b/go-lightning/mask.go
similarity index 100%
rename from mask.go
rename to go-lightning/mask.go
diff --git a/mask_test.go b/go-lightning/mask_test.go
similarity index 100%
rename from mask_test.go
rename to go-lightning/mask_test.go
diff --git a/merge.go b/go-lightning/merge.go
similarity index 100%
rename from merge.go
rename to go-lightning/merge.go
diff --git a/numpycomvar.go b/go-lightning/numpycomvar.go
similarity index 100%
rename from numpycomvar.go
rename to go-lightning/numpycomvar.go
diff --git a/pca_plot.go b/go-lightning/pca_plot.go
similarity index 100%
rename from pca_plot.go
rename to go-lightning/pca_plot.go
diff --git a/pca_plot.py b/go-lightning/pca_plot.py
similarity index 100%
rename from pca_plot.py
rename to go-lightning/pca_plot.py
diff --git a/pipeline_test.go b/go-lightning/pipeline_test.go
similarity index 100%
rename from pipeline_test.go
rename to go-lightning/pipeline_test.go
diff --git a/profile.go b/go-lightning/profile.go
similarity index 100%
rename from profile.go
rename to go-lightning/profile.go
diff --git a/ref2genome.go b/go-lightning/ref2genome.go
similarity index 100%
rename from ref2genome.go
rename to go-lightning/ref2genome.go
diff --git a/slice.go b/go-lightning/slice.go
similarity index 100%
rename from slice.go
rename to go-lightning/slice.go
diff --git a/slice_test.go b/go-lightning/slice_test.go
similarity index 100%
rename from slice_test.go
rename to go-lightning/slice_test.go
diff --git a/slicenumpy.go b/go-lightning/slicenumpy.go
similarity index 99%
rename from slicenumpy.go
rename to go-lightning/slicenumpy.go
index 34cd777458..654ee6f26b 100644
--- a/slicenumpy.go
+++ b/go-lightning/slicenumpy.go
@@ -28,7 +28,7 @@ import (
 	"unsafe"
 
 	"git.arvados.org/arvados.git/sdk/go/arvados"
-	"github.com/arvados/lightning/hgvs"
+	"github.com/arvados/lightning/go-lightning/hgvs"
 	"github.com/james-bowman/nlp"
 	"github.com/kshedden/gonpy"
 	"github.com/sirupsen/logrus"
diff --git a/stats.go b/go-lightning/stats.go
similarity index 100%
rename from stats.go
rename to go-lightning/stats.go
diff --git a/taglib.go b/go-lightning/taglib.go
similarity index 100%
rename from taglib.go
rename to go-lightning/taglib.go
diff --git a/taglib_test.go b/go-lightning/taglib_test.go
similarity index 100%
rename from taglib_test.go
rename to go-lightning/taglib_test.go
diff --git a/testdata/a.1.fasta b/go-lightning/testdata/a.1.fasta
similarity index 100%
rename from testdata/a.1.fasta
rename to go-lightning/testdata/a.1.fasta
diff --git a/testdata/a.2.fasta b/go-lightning/testdata/a.2.fasta
similarity index 100%
rename from testdata/a.2.fasta
rename to go-lightning/testdata/a.2.fasta
diff --git a/testdata/pipeline1/input1.1.fasta b/go-lightning/testdata/pipeline1/input1.1.fasta
similarity index 100%
rename from testdata/pipeline1/input1.1.fasta
rename to go-lightning/testdata/pipeline1/input1.1.fasta
diff --git a/testdata/pipeline1/input1.2.fasta b/go-lightning/testdata/pipeline1/input1.2.fasta
similarity index 100%
rename from testdata/pipeline1/input1.2.fasta
rename to go-lightning/testdata/pipeline1/input1.2.fasta
diff --git a/testdata/pipeline1/input2.1.fasta b/go-lightning/testdata/pipeline1/input2.1.fasta
similarity index 100%
rename from testdata/pipeline1/input2.1.fasta
rename to go-lightning/testdata/pipeline1/input2.1.fasta
diff --git a/testdata/pipeline1/input2.2.fasta b/go-lightning/testdata/pipeline1/input2.2.fasta
similarity index 100%
rename from testdata/pipeline1/input2.2.fasta
rename to go-lightning/testdata/pipeline1/input2.2.fasta
diff --git a/testdata/ref.fasta b/go-lightning/testdata/ref.fasta
similarity index 100%
rename from testdata/ref.fasta
rename to go-lightning/testdata/ref.fasta
diff --git a/testdata/spanningtile/input1.1.fasta b/go-lightning/testdata/spanningtile/input1.1.fasta
similarity index 100%
rename from testdata/spanningtile/input1.1.fasta
rename to go-lightning/testdata/spanningtile/input1.1.fasta
diff --git a/testdata/spanningtile/input1.2.fasta b/go-lightning/testdata/spanningtile/input1.2.fasta
similarity index 100%
rename from testdata/spanningtile/input1.2.fasta
rename to go-lightning/testdata/spanningtile/input1.2.fasta
diff --git a/testdata/spanningtile/input2.1.fasta b/go-lightning/testdata/spanningtile/input2.1.fasta
similarity index 100%
rename from testdata/spanningtile/input2.1.fasta
rename to go-lightning/testdata/spanningtile/input2.1.fasta
diff --git a/testdata/spanningtile/input2.2.fasta b/go-lightning/testdata/spanningtile/input2.2.fasta
similarity index 100%
rename from testdata/spanningtile/input2.2.fasta
rename to go-lightning/testdata/spanningtile/input2.2.fasta
diff --git a/testdata/tags b/go-lightning/testdata/tags
similarity index 100%
rename from testdata/tags
rename to go-lightning/testdata/tags
diff --git a/testdata/tinyref.fasta b/go-lightning/testdata/tinyref.fasta
similarity index 100%
rename from testdata/tinyref.fasta
rename to go-lightning/testdata/tinyref.fasta
diff --git a/throttle.go b/go-lightning/throttle.go
similarity index 100%
rename from throttle.go
rename to go-lightning/throttle.go
diff --git a/tilelib.go b/go-lightning/tilelib.go
similarity index 100%
rename from tilelib.go
rename to go-lightning/tilelib.go
diff --git a/tilelib_test.go b/go-lightning/tilelib_test.go
similarity index 100%
rename from tilelib_test.go
rename to go-lightning/tilelib_test.go
diff --git a/tilestats.go b/go-lightning/tilestats.go
similarity index 100%
rename from tilestats.go
rename to go-lightning/tilestats.go
diff --git a/vcf2fasta.go b/go-lightning/vcf2fasta.go
similarity index 100%
rename from vcf2fasta.go
rename to go-lightning/vcf2fasta.go
diff --git a/version.sh b/go-lightning/version.sh
similarity index 100%
rename from version.sh
rename to go-lightning/version.sh
-- 
2.30.2