ont_germline

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# This command assumes all the inputs are in the current working directory and all the outputs go to the same place.
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docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \
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    --workdir /workdir \
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    nvcr.io/nvidia/clara/clara-parabricks:4.7.1-1 \
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    pbrun ont_germline \
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    --ref /workdir/${REFERENCE_FILE} \
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    --in-fq /workdir/${INPUT_FASTQ} \
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    --out-bam /outputdir/${OUTPUT_BAM} \
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    --out-variants /outputdir/${OUTPUT_VCF}

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# Run minimap2 and pipe the output to create a sorted BAM.
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$ minimap2 -ax map-ont \
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    <INPUT_DIR>/${REFERENCE_FILE} \
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    <INPUT_DIR>/${INPUT_FASTQ} | \
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  gatk SortSam \
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    --java-options -Xmx30g \
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    --MAX_RECORDS_IN_RAM 5000000 \
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    -I /dev/stdin \
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    -O cpu.bam \
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    --SORT_ORDER coordinate
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 # Run deepvariant
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BIN_VERSION="1.9.0"
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sudo docker run \
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  -v "${PWD}":"/input" \
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  -v "${PWD}/output":"/output" \
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  -v "${PWD}/Ref":"/reference" \
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  google/deepvariant:"${BIN_VERSION}" \
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  /opt/deepvariant/bin/run_deepvariant \
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  --model_type ONT_R104 \
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  --ref /reference/${REFERENCE_FILE} \
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  --reads cpu.bam \
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  --output_vcf /output/"${OUTPUT_VCF_FILE}" \
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  --num_shards $(nproc) \
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  --disable_small_model=true \
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  --make_examples_extra_args "ws_use_window_selector_model=true"

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// loop fission: set scores first
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if (!(flag & KSW_EZ_GENERIC_SC)) {
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    for (t = st0; t <= en0; t += 16) {
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        __m128i sq, st, tmp, mask;
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        sq = _mm_loadu_si128((__m128i*)&sf[t]);
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        st = _mm_loadu_si128((__m128i*)&qrr[t]);
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        mask = _mm_or_si128(_mm_cmpeq_epi8(sq, m1_), _mm_cmpeq_epi8(st, m1_));
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        tmp = _mm_cmpeq_epi8(sq, st);
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    #ifdef __SSE4_1__
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                    tmp = _mm_blendv_epi8(sc_mis_, sc_mch_, tmp);
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                    tmp = _mm_blendv_epi8(tmp,     sc_N_,   mask);
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    #else
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                    tmp = _mm_or_si128(_mm_andnot_si128(tmp,  sc_mis_), _mm_and_si128(tmp,  sc_mch_));
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                    tmp = _mm_or_si128(_mm_andnot_si128(mask, tmp),     _mm_and_si128(mask, sc_N_));
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    #endif
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                    _mm_storeu_si128((__m128i*)((int8_t*)s + t), tmp);
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                }
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            } else {
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                for (t = st0; t <= en0; ++t)
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                    ((uint8_t*)s)[t] = mat[sf[t] * m + qrr[t]];
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            }

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// loop fission: set scores first
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int lf_start = st, lf_en = en;
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if (!(flag & KSW_EZ_GENERIC_SC)) {
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    for (t = lf_start; t <= lf_en; t += 16) {
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        __m128i sq, st, tmp, mask;
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        sq = _mm_loadu_si128((__m128i*)&sf[t]);
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        st = _mm_loadu_si128((__m128i*)&qrr[t]);
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        mask = _mm_or_si128(_mm_cmpeq_epi8(sq, m1_), _mm_cmpeq_epi8(st, m1_));
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        tmp = _mm_cmpeq_epi8(sq, st);
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    #ifdef __SSE4_1__
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                    tmp = _mm_blendv_epi8(sc_mis_, sc_mch_, tmp);
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                    tmp = _mm_blendv_epi8(tmp,     sc_N_,   mask);
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    #else
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                    tmp = _mm_or_si128(_mm_andnot_si128(tmp,  sc_mis_), _mm_and_si128(tmp,  sc_mch_));
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                    tmp = _mm_or_si128(_mm_andnot_si128(mask, tmp),     _mm_and_si128(mask, sc_N_));
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    #endif
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                    _mm_storeu_si128((__m128i*)((int8_t*)s + t), tmp);
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                }
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            } else {
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                for (t = lf_start; t <= lf_en; ++t)
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                    ((uint8_t*)s)[t] = mat[sf[t] * m + qrr[t]];
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            }