diff --git a/dorado/cli/polish.cpp b/dorado/cli/polish.cpp index 8cb9340d..ee73cad9 100644 --- a/dorado/cli/polish.cpp +++ b/dorado/cli/polish.cpp @@ -588,9 +588,6 @@ const polisher::ModelConfig resolve_model(const polisher::BamInfo& bam_info, // Example: dna_r10.4.1_e8.2_400bps_hac@v5.0.0_polish_rl_mv std::string model_name = basecaller_model + polish_model_suffix; - // Example: dna_r10.4.1_e8.2_400bps_hac_v5.0.0_polish_rl_mv - std::replace(std::begin(model_name), std::end(model_name), '@', '_'); - spdlog::info("Downloading model: '{}'", model_name); model_dir = download_model(model_name); @@ -613,9 +610,6 @@ const polisher::ModelConfig resolve_model(const polisher::BamInfo& bam_info, // Example: dna_r10.4.1_e8.2_400bps_hac@v5.0.0_polish_rl_mv std::string model_name = basecaller_model + polish_model_suffix; - // Example: dna_r10.4.1_e8.2_400bps_hac_v5.0.0_polish_rl_mv - std::replace(std::begin(model_name), std::end(model_name), '@', '_'); - spdlog::info("Downloading model: '{}'", model_name); model_dir = download_model(model_name); diff --git a/dorado/models/models.cpp b/dorado/models/models.cpp index d60cf525..a6161f42 100644 --- a/dorado/models/models.cpp +++ b/dorado/models/models.cpp @@ -1121,29 +1121,29 @@ namespace polisher { const std::vector models = { ModelInfo{ - "dna_r10.4.1_e8.2_400bps_hac_v5.0.0_polish_rl", - "fdb6d18fe7e93f141c8e15f1b014e338e7cdd2b3f390abd0ff85cede33b50cc7", + "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_polish_rl", + "d343b4394b904d219257ad188c82ece63b935f15d78f09f551e591b2275da4b9", CC::UNKNOWN, ModelVariantPair{}, ModsVariantPair{}, }, ModelInfo{ - "dna_r10.4.1_e8.2_400bps_hac_v5.0.0_polish_rl_mv", - "719389cf723a4ddbd020690c20708885ed6b5000c51a2144a5af5b8064a055d2", + "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_polish_rl_mv", + "928d9bcf3d68162eff479ada5839c5df3faa0ad393658729511aedffe65f089c", CC::UNKNOWN, ModelVariantPair{}, ModsVariantPair{}, }, ModelInfo{ - "dna_r10.4.1_e8.2_400bps_sup_v5.0.0_polish_rl", - "3c0c7fbf2f204390ca6dfafaefc25a3f999870368e4a7b5d238eb600aa7e781b", + "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_polish_rl", + "6d8c5a8ce45311c25f824453d0af997fbe2f63a5f734fdb4d884d285ddafec33", CC::UNKNOWN, ModelVariantPair{}, ModsVariantPair{}, }, ModelInfo{ - "dna_r10.4.1_e8.2_400bps_sup_v5.0.0_polish_rl_mv", - "eb9b4691bda3133e9b991aa1a2666cc632bbd5c2f803dff704ef1265f4315a90", + "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_polish_rl_mv", + "0e0cb175aa41636de835d2abb5330b91fed14a00f811804edf983bc086cf477a", CC::UNKNOWN, ModelVariantPair{}, ModsVariantPair{}, diff --git a/tests/cram/polish/cram-polish-01-model-download.t b/tests/cram/polish/cram-polish-01-model-download.t index 204325f9..e706af5e 100755 --- a/tests/cram/polish/cram-polish-01-model-download.t +++ b/tests/cram/polish/cram-polish-01-model-download.t @@ -27,8 +27,8 @@ Negative test: BAM has a model which is not available for download in auto mode. > echo "Exit code: $?" > grep "\[error\]" out/out.fasta.stderr | sed -E 's/.*\[error\] //g' Exit code: 1 - Selected model doesn't exist: dna_r10.4.1_e8.2_400bps_hac_v1.0.0_polish_rl_mv - Could not download model: dna_r10.4.1_e8.2_400bps_hac_v1.0.0_polish_rl_mv + Selected model doesn't exist: dna_r10.4.1_e8.2_400bps_hac@v1.0.0_polish_rl_mv + Could not download model: dna_r10.4.1_e8.2_400bps_hac@v1.0.0_polish_rl_mv Negative test: BAM has no models listed (no RG tags). $ rm -rf out; mkdir -p out @@ -101,7 +101,7 @@ Load a model from path. Download an explicit polishing model by name with `--skip-model-compatibility-check`. $ rm -rf out; mkdir -p out > in_dir=${TEST_DATA_DIR}/polish/test-01-supertiny - > model="dna_r10.4.1_e8.2_400bps_hac_v5.0.0_polish_rl_mv" + > model="dna_r10.4.1_e8.2_400bps_hac@v5.0.0_polish_rl_mv" > ${DORADO_BIN} polish --skip-model-compatibility-check --model "${model}" --device cpu ${in_dir}/calls_to_draft.bam ${in_dir}/draft.fasta.gz -t 4 --infer-threads 1 -vv > out/out.fasta 2> out/out.fasta.stderr > echo "Exit code: $?" > ${DORADO_BIN} aligner ${in_dir}/ref.fasta.gz out/out.fasta 1> out/out.sam 2> out/out.sam.stderr diff --git a/tests/test_dorado_polish.sh b/tests/test_dorado_polish.sh index 537a94e1..dac3062f 100755 --- a/tests/test_dorado_polish.sh +++ b/tests/test_dorado_polish.sh @@ -49,7 +49,7 @@ CRAM=$(pwd)/cram-0.6/cram.py popd # Download the model once. -MODEL_NAME="dna_r10.4.1_e8.2_400bps_hac_v5.0.0_polish_rl_mv" +MODEL_NAME="dna_r10.4.1_e8.2_400bps_hac@v5.0.0_polish_rl_mv" MODEL_DIR=${output_dir}/${MODEL_NAME} if [[ ! -d "${MODEL_DIR}" ]]; then ${DORADO_BIN} download --model "${MODEL_NAME}" --models-directory ${output_dir}