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test: Add genome fasta file to test_data directory #178

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SamBryce-Smith opened this issue Sep 23, 2021 · 0 comments
Open

test: Add genome fasta file to test_data directory #178

SamBryce-Smith opened this issue Sep 23, 2021 · 0 comments
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@SamBryce-Smith
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As spotted by @mzavolan in the Aptardi PR review (#174), we don't currently have a genome FASTA file in the tests/test_data repository. This would also be useful for LABRAT and possibly other tools too.

This should be the same genome version used for alignment and be subsetted to the two chromosomes (chr6 and 16) that are present in the current test data. If the file is too large even with just two chromosomes, we should consider gzip-ing the file and shipping that with the repo, providing a note in the README to tell the downstream user to unzip if the tool requires uncompressed FASTA.

It would also be useful to generate two versions of the test file with the chr chromosome name prefix resent/absent for compatibility with the existing noChr test files and the prospective test files with the chr prefix added (#177).

@mrgazzara - Can you confirm the genome versions used please? From the other test file names I suspect GRCm38/mm10

@ninsch3000 ninsch3000 changed the title Add genome fasta file to test_data directory test: Add genome fasta file to test_data directory Aug 10, 2023
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