wip

src/freqs/cli/query.rs

@@ -237,8 +237,13 @@ mod test {
     }
 
     #[rstest::rstest]
+    #[case("1:55516885:G:A", "grch37", "2.1")]
+    #[case("1:55039933:G:A", "grch38", "4.0")]
     fn smoke_query_exomes_var_single_match_chr_1(
-        #[with("1:55516885:G:A", "grch37", "2.1")] args_freqs: ArgsFreqs,
+        #[case] _variant: &str,
+        #[case] _genome: &str,
+        #[case] _version: &str,
+        #[with(_variant, _genome, _version)] args_freqs: ArgsFreqs,
     ) -> Result<(), anyhow::Error> {
         let ArgsFreqs {
             common_args,
@@ -261,8 +266,13 @@ mod test {
     }
 
     #[rstest::rstest]
+    #[case("X:69902557:G:T", "grch37", "2.1")]
+    #[case("X:17434:A:AC", "grch38", "4.0")]
     fn smoke_query_exomes_var_single_match_chr_x(
-        #[with("X:69902557:G:T", "grch37", "2.1")] args_freqs: ArgsFreqs,
+        #[case] _variant: &str,
+        #[case] _genome: &str,
+        #[case] _version: &str,
+        #[with(_variant, _genome, _version)] args_freqs: ArgsFreqs,
     ) -> Result<(), anyhow::Error> {
         let ArgsFreqs {
             common_args,
@@ -285,8 +295,13 @@ mod test {
     }
 
     #[rstest::rstest]
+    #[case("Y:4967199:G:T", "grch37", "2.1")]
+    #[case("Y:2782947:C:T", "grch38", "4.0")]
     fn smoke_query_exomes_var_single_match_chr_y(
-        #[with("Y:4967199:G:T", "grch37", "2.1")] args_freqs: ArgsFreqs,
+        #[case] _variant: &str,
+        #[case] _genome: &str,
+        #[case] _version: &str,
+        #[with(_variant, _genome, _version)] args_freqs: ArgsFreqs,
     ) -> Result<(), anyhow::Error> {
         let ArgsFreqs {
             common_args,
@@ -309,8 +324,13 @@ mod test {
     }
 
     #[rstest::rstest]
+    #[case("M:11:C:T", "grch37", "2.1")]
+    #[case("M:11:C:T", "grch38", "4.0")]
     fn smoke_query_exomes_var_single_match_chr_mt(
-        #[with("M:11:C:T", "grch37", "2.1")] args_freqs: ArgsFreqs,
+        #[case] _variant: &str,
+        #[case] _genome: &str,
+        #[case] _version: &str,
+        #[with(_variant, _genome, _version)] args_freqs: ArgsFreqs,
     ) -> Result<(), anyhow::Error> {
         let ArgsFreqs {
             common_args,
@@ -334,6 +354,7 @@ mod test {
 
     #[rstest::rstest]
     #[case("1:55516885:G:TT", "grch37", "2.1")]
+    #[case("1:55516885:G:TT", "grch38", "4.0")]
     fn smoke_query_exomes_var_single_nomatch(
         #[case] _variant: &str,
         #[case] _genome: &str,

src/freqs/cli/snapshots/annonars__freqs__cli__query__test__smoke_query_exomes_var_single_match_chr_1@grch37-2.1-1_55516885_G_A.snap

@@ -0,0 +1,6 @@
+---
+source: src/freqs/cli/query.rs
+expression: "&out_data"
+---
+{"gnomad_exomes":{"an":128256,"ac_hom":0,"ac_het":1},"gnomad_genomes":{"an":0,"ac_hom":0,"ac_het":0}}
+

src/freqs/cli/snapshots/annonars__freqs__cli__query__test__smoke_query_exomes_var_single_match_chr_1@grch38-4.0-1_55039933_G_A.snap

@@ -0,0 +1,6 @@
+---
+source: src/freqs/cli/query.rs
+expression: "&out_data"
+---
+{"gnomad_exomes":{"an":586534,"ac_hom":0,"ac_het":1},"gnomad_genomes":{"an":0,"ac_hom":0,"ac_het":0}}
+

src/freqs/cli/snapshots/annonars__freqs__cli__query__test__smoke_query_exomes_var_single_match_chr_mt@grch37-2.1-M_11_C_T.snap

@@ -0,0 +1,6 @@
+---
+source: src/freqs/cli/query.rs
+expression: "&out_data"
+---
+{"gnomad_mtdna":{"an":0,"ac_hom":0,"ac_het":0},"helixmtdb":{"an":196554,"ac_hom":0,"ac_het":1}}
+

src/freqs/cli/snapshots/annonars__freqs__cli__query__test__smoke_query_exomes_var_single_match_chr_mt@grch38-4.0-M_11_C_T.snap

@@ -0,0 +1,6 @@
+---
+source: src/freqs/cli/query.rs
+expression: "&out_data"
+---
+{"gnomad_mtdna":{"an":0,"ac_hom":0,"ac_het":0},"helixmtdb":{"an":196554,"ac_hom":0,"ac_het":1}}
+

src/freqs/cli/snapshots/annonars__freqs__cli__query__test__smoke_query_exomes_var_single_match_chr_x@grch37-2.1-X_69902557_G_T.snap

@@ -0,0 +1,6 @@
+---
+source: src/freqs/cli/query.rs
+expression: "&out_data"
+---
+{"gnomad_exomes":{"an":179321,"ac_hom":0,"ac_het":1,"ac_hemi":0},"gnomad_genomes":{"an":0,"ac_hom":0,"ac_het":0,"ac_hemi":0}}
+

src/freqs/cli/snapshots/annonars__freqs__cli__query__test__smoke_query_exomes_var_single_match_chr_x@grch38-4.0-X_17434_A_AC.snap

@@ -0,0 +1,6 @@
+---
+source: src/freqs/cli/query.rs
+expression: "&out_data"
+---
+{"gnomad_exomes":{"an":0,"ac_hom":0,"ac_het":0,"ac_hemi":0},"gnomad_genomes":{"an":45836,"ac_hom":0,"ac_het":0,"ac_hemi":0}}
+

src/freqs/cli/snapshots/annonars__freqs__cli__query__test__smoke_query_exomes_var_single_match_chr_y@grch37-2.1-Y_4967199_G_T.snap

@@ -0,0 +1,6 @@
+---
+source: src/freqs/cli/query.rs
+expression: "&out_data"
+---
+{"gnomad_exomes":{"an":67766,"ac_hom":0,"ac_het":0,"ac_hemi":1},"gnomad_genomes":{"an":0,"ac_hom":0,"ac_het":0,"ac_hemi":0}}
+

src/freqs/cli/snapshots/annonars__freqs__cli__query__test__smoke_query_exomes_var_single_match_chr_y@grch38-4.0-Y_2782947_C_T.snap

@@ -0,0 +1,6 @@
+---
+source: src/freqs/cli/query.rs
+expression: "&out_data"
+---
+{"gnomad_exomes":{"an":0,"ac_hom":0,"ac_het":0,"ac_hemi":0},"gnomad_genomes":{"an":33081,"ac_hom":0,"ac_het":0,"ac_hemi":1}}
+

src/freqs/cli/snapshots/annonars__freqs__cli__query__test__smoke_query_exomes_var_single_nomatch@grch37-2.1-1_55516885_G_TT.snap

@@ -0,0 +1,5 @@
+---
+source: src/freqs/cli/query.rs
+expression: "&out_data"
+---
+

src/freqs/cli/snapshots/annonars__freqs__cli__query__test__smoke_query_exomes_var_single_nomatch@grch38-4.0-1_55516885_G_TT.snap

@@ -0,0 +1,5 @@
+---
+source: src/freqs/cli/query.rs
+expression: "&out_data"
+---
+

tests/freqs/grch37/v2.1/bootstrap.sh

@@ -0,0 +1,70 @@
+#!/usr/bin/env bash
+
+set -euo pipefail
+set -x
+
+if [[ "${EXTRACT-false}" == "true" ]]; then
+    EXOMES=https://storage.googleapis.com/gcp-public-data--gnomad/release/2.1.1/vcf/exomes
+    tabix --print-header \
+        $EXOMES/gnomad.exomes.r2.1.1.sites.1.vcf.bgz \
+        1:55505599-55516888 \
+    > tests/freqs/grch37/v2.1/gnomad-exomes.1.vcf
+    bgzip -c tests/freqs/grch37/v2.1/gnomad-exomes.1.vcf \
+    > tests/freqs/grch37/v2.1/gnomad-exomes.1.vcf.bgz
+    tabix -f tests/freqs/grch37/v2.1/gnomad-exomes.1.vcf.bgz
+
+    tabix --print-header \
+        $EXOMES/gnomad.exomes.r2.1.1.sites.X.vcf.bgz \
+        X:69902557-69902557 \
+    > tests/freqs/grch37/v2.1/gnomad-exomes.X.vcf
+    bgzip -c tests/freqs/grch37/v2.1/gnomad-exomes.X.vcf \
+    > tests/freqs/grch37/v2.1/gnomad-exomes.X.vcf.bgz
+    tabix -f tests/freqs/grch37/v2.1/gnomad-exomes.X.vcf.bgz
+
+    tabix --print-header \
+        $EXOMES/gnomad.exomes.r2.1.1.sites.Y.vcf.bgz \
+        Y:4967199-4967199 \
+    > tests/freqs/grch37/v2.1/gnomad-exomes.Y.vcf
+    bgzip -c tests/freqs/grch37/v2.1/gnomad-exomes.Y.vcf \
+    > tests/freqs/grch37/v2.1/gnomad-exomes.Y.vcf.bgz
+    tabix -f tests/freqs/grch37/v2.1/gnomad-exomes.Y.vcf.bgz
+
+    GENOMES=https://storage.googleapis.com/gcp-public-data--gnomad/release/2.1.1/vcf/genomes
+    tabix --print-header \
+        $GENOMES/gnomad.genomes.r2.1.1.sites.1.vcf.bgz \
+        1:55505599-55505599 \
+    > tests/freqs/grch37/v2.1/gnomad-genomes.1.vcf
+    bgzip -c tests/freqs/grch37/v2.1/gnomad-genomes.1.vcf \
+    > tests/freqs/grch37/v2.1/gnomad-genomes.1.vcf.bgz
+    tabix -f tests/freqs/grch37/v2.1/gnomad-genomes.1.vcf.bgz
+
+    tabix --print-header \
+        $GENOMES/gnomad.genomes.r2.1.1.sites.X.vcf.bgz \
+        X:69902634-69902634 \
+    > tests/freqs/grch37/v2.1/gnomad-genomes.X.vcf
+    bgzip -c tests/freqs/grch37/v2.1/gnomad-genomes.X.vcf \
+    > tests/freqs/grch37/v2.1/gnomad-genomes.X.vcf.bgz
+    tabix -f tests/freqs/grch37/v2.1/gnomad-genomes.X.vcf.bgz
+fi
+
+rm -rf tests/freqs/grch37/v2.1/example/freqs.db
+cargo run --all-features -- \
+    freqs import \
+    -vvv \
+    --genome-release grch37 \
+    --path-out-rocksdb tests/freqs/grch37/v2.1/example/freqs.db \
+    \
+    --gnomad-exomes-version "2.1.1" \
+    --path-gnomad-exomes-auto tests/freqs/grch37/v2.1/gnomad-exomes.1.vcf.bgz \
+    --path-gnomad-exomes-xy tests/freqs/grch37/v2.1/gnomad-exomes.X.vcf.bgz \
+    --path-gnomad-exomes-xy tests/freqs/grch37/v2.1/gnomad-exomes.Y.vcf.bgz \
+    \
+    --gnomad-genomes-version "2.1.1" \
+    --path-gnomad-genomes-auto tests/freqs/grch37/v2.1/gnomad-genomes.1.vcf.bgz \
+    --path-gnomad-genomes-xy tests/freqs/grch37/v2.1/gnomad-genomes.X.vcf.bgz \
+    \
+    --gnomad-mtdna-version "3.1.1" \
+    --path-gnomad-mtdna tests/freqs/grch37/v2.1/reading/gnomad.chrM.vcf.bgz \
+    \
+    --helixmtdb-version "20200327" \
+    --path-helixmtdb tests/freqs/grch37/v2.1/reading/helix.chrM.vcf.bgz