atg 0.8.7

Convert transcripts between different file formats
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#!/bin/bash

VERSION=$1

confirmation() {
    read confirm
    if [ "$confirm" != "y" ]
    then
      echo "Aborting";
      exit 1
    fi
}

echo -ne "Preparing for release ${VERSION}. Is this correct? [y/n] "
confirmation

if git rev-parse --quiet --verify $REVISION > /dev/null; then
    echo "Release branch exists already"
else
  echo "Creating release branch"
  git checkout main && \
  git pull && \
  git checkout -b release/${VERSION} && \
  git push -u origin release/${VERSION}
fi

echo -ne "Did you finish merging all features into 'release/${VERSION}'? [y/n] "
confirmation
git checkout release/${VERSION} && git pull

echo "Running linter and unittests"
cargo clippy && \
cargo fmt && \
cargo test

echo "Running basic check of GTF and RefGene convertion"
diff \
<( cargo run -- \
  -f gtf -i tests/data/example.gtf \
  -t refgene -o /dev/stdout 2> /dev/null | \
  sort ) \
tests/data/example.refgene

diff \
<( cargo run -- \
  -f refgene -i tests/data/example.refgene \
  -t gtf -g ncbiRefSeq.2021-05-17 \
  -o /dev/stdout 2> /dev/null | \
  cut -f1-5,7-8 | sort ) \
<( cut -f1-5,7-8 tests/data/example.gtf)


echo "Updating version number"
sed -i .bck "s/^version =.*$/version = \"${VERSION}\"/" ./Cargo.toml
cargo build

git commit -am "Release ${VERSION}"
git tag ${VERSION}
git push
git push --tags

echo -ne "Do you want to build the binaries now? [y/n] "
confirmation
cargo build --release --target=aarch64-apple-darwin
cp target/aarch64-apple-darwin/release/atg target/atg-${VERSION}-aarch64-apple-darwin
cargo build --release --target=x86_64-unknown-linux-gnu
cp target/x86_64-unknown-linux-gnu/release/atg target/atg-${VERSION}-x86_64-unknown-linux-gnu
cargo build --release --target=x86_64-unknown-linux-musl
cp target/x86_64-unknown-linux-musl/release/atg target/atg-${VERSION}-x86_64-unknown-linux-musl

echo "You can now merge release/${VERSION} into main, create a new release and upload the binaries"

echo -ne "Do you want to publish atg to crates.io now? [y/n] "
confirmation
cargo publish