gunzip file because we need the raw fasta file to use our samtools indexer. use the command line not java for memory reasons.
@@ -84,7 +84,11 @@ public class GenomeDownloadManager extends AbstractDownloadManager {
logger.info("Saving reference genome version data at {}", sequenceFolder.resolve("genomeVersion.json"));
saveVersionData(EtlCommons.GENOME_DATA, ENSEMBL_NAME, ensemblVersion, getTimeStamp(),
Collections.singletonList(url), sequenceFolder.resolve("genomeVersion.json"));
- return Collections.singletonList(downloadFile(url, outputPath.toString()));
+ List<DownloadFile> downloadFiles = Collections.singletonList(downloadFile(url, outputPath.toString()));
+ logger.info("Unzipping file: " + outputFileName);
+ //CompressionUtils.gunzip(IOUtils.toByteArray(new FileInputStream(outputPath.toString())));
+ EtlCommons.runCommandLineProcess(null, "gunzip", Collections.singletonList(outputPath.toString()), null);
+ return downloadFiles;
}
/**
