fix: additional github tests

jeffersonfparil · Jul 1, 2024 · df94c0d · df94c0d
1 parent aed3abc
commit df94c0d
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Showing 3 changed files with 7 additions and 7 deletions.
diff --git a/src/imputation/adaptive_ld_knn_imputation.rs b/src/imputation/adaptive_ld_knn_imputation.rs
@@ -613,7 +613,7 @@ mod tests {
 //     --phen-pool-size-col 1 \
 //     --phen-value-col 2 \
 //     --min-allele-frequency 0.0001 \
-//     --min-coverage 0 \
+//     --min-coverage-depth 0 \
 //     --min-quality 0.01 \
 //     --max-missingness-rate 0.2 \
 //     --min-depth-set-to-missing 5 \

diff --git a/src/imputation/mean_imputation.rs b/src/imputation/mean_imputation.rs
@@ -266,7 +266,7 @@ mod tests {
 //     --phen-pool-size-col 1 \
 //     --phen-value-col 2 \
 //     --min-allele-frequency 0.0001 \
-//     --min-coverage 0 \
+//     --min-coverage-depth 0 \
 //     --min-quality 0.01 \
 //     --max-missingness-rate 0.75 \
 //     --min-depth-set-to-missing 5 \

diff --git a/src/main.rs b/src/main.rs
@@ -157,13 +157,13 @@ struct Args {
 /// ## Examples
 /// ```shell
 /// cargo run -- pileup2sync -f ./tests/test.pileup -p ./tests/test.csv
-/// cargo run -- fisher_exact_test -f ./tests/test.sync -p ./tests/test.csv --n-threads 32 --min-coverage 10 --min-allele-frequency 0.01
-/// cargo run -- chisq_test -f ./tests/test.sync -p ./tests/test.csv --n-threads 32 --min-coverage 10 --min-allele-frequency 0.01
-/// cargo run -- pearson_corr -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3  --n-threads 32 --min-coverage 10 --min-allele-frequency 0.01
+/// cargo run -- fisher_exact_test -f ./tests/test.sync -p ./tests/test.csv --n-threads 32 --min-coverage-depth 10 --min-allele-frequency 0.01
+/// cargo run -- chisq_test -f ./tests/test.sync -p ./tests/test.csv --n-threads 32 --min-coverage-depth 10 --min-allele-frequency 0.01
+/// cargo run -- pearson_corr -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3  --n-threads 32 --min-coverage-depth 10 --min-allele-frequency 0.01
 /// cargo run -- fst -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3  --n-threads 32
 /// cargo run -- heterozygosity -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3  --n-threads 32
-/// cargo run -- ols_iter -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3  --n-threads 32 --min-coverage 10 --min-allele-frequency 0.01
-/// cargo run -- mle_iter -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3  --n-threads 32 --min-coverage 10 --min-allele-frequency 0.01
+/// cargo run -- ols_iter -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3  --n-threads 32 --min-coverage-depth 10 --min-allele-frequency 0.01
+/// cargo run -- mle_iter -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3  --n-threads 32 --min-coverage-depth 10 --min-allele-frequency 0.01
 /// cargo run -- gwalpha  -f ./tests/test.sync -p ./tests/test.py --n-threads 32 --gwalpha-method ML
 /// cargo run -- sync2csv -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3  --n-threads 32 --keep-p-minus-1
 /// # cargo run -- genomic_prediction_cross_validation -f ./tests/test_MORE_POOLS.sync -p ./tests/test_MORE_POOLS.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3  --n-threads 32