<commit_before>#!/bin/bash -e

. /var/cache/build/packages-manual/common.sh

download_and_verify \
    snpeff \
    snpeff \
    4_3k \
    396fadbefb4994838713c9a3e96393d16e7ec833254a962834e7cbd699b9f35e \
    https://sourceforge.net/projects/snpeff/files/snpEff_v\${version}_core.zip \
    snpEff

rm -rf clinEff examples
java -jar snpEff.jar download GRCh37.75 -v

mkdir bin

echo '#!/bin/sh' > bin/snpEff
echo 'exec java -Xmx16g -jar /opt/snpeff/snpeff/snpEff.jar "$@"' >> bin/snpEff
chmod +x bin/snpEff

echo '#!/bin/sh' > bin/SnpSift
echo 'exec java -Xmx16g -jar /opt/snpeff/snpeff/SnpSift.jar "$@"' > bin/SnpSift
chmod +x bin/SnpSift

add_binary_path \
    snpeff \
    snpeff \
    bin<commit_msg>Ensure snpeff data is downloaded during build<commit_after>#!/bin/bash -e

. /var/cache/build/packages-manual/common.sh

download_and_verify \
    snpeff \
    snpeff \
    4_3k \
    396fadbefb4994838713c9a3e96393d16e7ec833254a962834e7cbd699b9f35e \
    https://sourceforge.net/projects/snpeff/files/snpEff_v\${version}_core.zip \
    snpEff

rm -rf clinEff examples
java -jar snpEff.jar download GRCh37.75 -v

mkdir bin

echo '#!/bin/sh' > bin/snpEff
echo 'exec java -Xmx16g -jar /opt/snpeff/snpeff/snpEff.jar "$@"' >> bin/snpEff
chmod +x bin/snpEff

echo '#!/bin/sh' > bin/SnpSift
echo 'exec java -Xmx16g -jar /opt/snpeff/snpeff/SnpSift.jar "$@"' > bin/SnpSift
chmod +x bin/SnpSift

# Ensure data is downloaded during build. If not, fail.
test -d data

add_binary_path \
    snpeff \
    snpeff \
    bin
{'fraction_non_alphanumeric': 0.12764550264550265, 'fraction_numerical': 0.06878306878306878, 'mean_word_length': 3.202777777777778, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 13, 'https://': 2, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 6, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3519786', 'n_tokens_mistral': 748, 'n_tokens_neox': 677, 'n_words': 121}