#!/bin/bash
# Copyright 2018 Google LLC.
#
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# 1. Redistributions of source code must retain the above copyright notice,
#    this list of conditions and the following disclaimer.
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#    software without specific prior written permission.
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
#
# This script processes our test_cram.sam file into CRAM formatted and indexed
# files used in our tests.
#
# usage: ./make_cram_testdata.sh from the nucleus root directory.
#
set -euo pipefail

for version in 3.0; do
for embed_ref in 0 1; do
  filename="test_cram.embed_ref_${embed_ref}_version_${version}.cram"
  samtools view -C \
    --output-fmt cram \
    --output-fmt-option version="${version}" \
    --output-fmt-option embed_ref="${embed_ref}" \
    third_party/nucleus/testdata/test_cram.sam \
    -T third_party/nucleus/testdata/test.fasta \
    -o "third_party/nucleus/testdata/${filename}"
  samtools index "third_party/nucleus/testdata/${filename}"
done
done