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Use samtools to index bzgipped chromosome file
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Refs pombase/website#2038
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@kimrutherford
kimrutherford committed Jan 28, 2025
1 parent b3e8d92 commit 05cb0f0
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3 changes: 2 additions & 1 deletion etc/load-all.sh
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Expand Up @@ -1116,7 +1116,8 @@ zstd -9q --rm $CURRENT_BUILD_DIR/api_maps.sqlite3

mkdir $CURRENT_BUILD_DIR/fasta/bgzip_chromosomes
cp -r $CURRENT_BUILD_DIR/fasta/chromosomes/Schizosaccharomyces_pombe_all_chromosomes.fa $CURRENT_BUILD_DIR/fasta/bgzip_chromosomes
bgzip -i -l 9 $CURRENT_BUILD_DIR/fasta/chromosomes/Schizosaccharomyces_pombe_all_chromosomes.fa
bgzip -l 9 $CURRENT_BUILD_DIR/fasta/chromosomes/Schizosaccharomyces_pombe_all_chromosomes.fa
samtools faidx $CURRENT_BUILD_DIR/fasta/chromosomes/Schizosaccharomyces_pombe_all_chromosomes.fa

find $CURRENT_BUILD_DIR/fasta/ -name '*.fa' | xargs gzip -9

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