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Hotfix converter default compression #11

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Merged
AxisAlexNT merged 2 commits into from
Feb 23, 2026
Merged

Hotfix converter default compression #11

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0672d6f
Enable Deflate 6 compression level by default
AxisAlexNT Feb 23, 2026
63f0e89
Merge branch 'master' of github.com:ctlab/HiCT_JVM into migrate-conve…
AxisAlexNT Feb 23, 2026
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6 changes: 3 additions & 3 deletions ...ain/java/ru/itmo/ctlab/hict/hict_server/handlers/conversion/ConversionHandlersHolder.java
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Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,7 @@ public void addHandlersToRouter(final @NotNull Router router) {

final var resolutionCsv = req.getParam("resolutions");
final var resolutions = parseResolutions(resolutionCsv);
final var compression = parseInteger(req.getParam("compression"), 0);
final var compression = parseInteger(req.getParam("compression"), 6);
final var compressionAlgorithm = ConversionOptions.CompressionAlgorithm.parse(req.getParam("compressionAlgorithm") == null ? "deflate" : req.getParam("compressionAlgorithm"));
final var chunkSize = parseInteger(req.getParam("chunkSize"), 8192);
final var applyAgpRaw = Boolean.parseBoolean(req.getParam("applyAgp"));
Expand Down Expand Up @@ -99,7 +99,7 @@ public void addHandlersToRouter(final @NotNull Router router) {
final var direction = requestJson.getString("direction", "mcool-to-hict");
final var parallelism = requestJson.getInteger("parallelism", Runtime.getRuntime().availableProcessors());
final var resolutions = parseResolutions(requestJson.getString("resolutions"));
final var compression = requestJson.getInteger("compression", 0);
final var compression = requestJson.getInteger("compression", 6);
final var compressionAlgorithm = ConversionOptions.CompressionAlgorithm.parse(requestJson.getString("compressionAlgorithm", "deflate"));
final var chunkSize = requestJson.getInteger("chunkSize", 8192);

Expand Down Expand Up @@ -143,7 +143,7 @@ public void addHandlersToRouter(final @NotNull Router router) {
final var parallelJobs = Math.max(1, requestJson.getInteger("parallelJobs", 1));
final var parallelism = requestJson.getInteger("parallelism", Runtime.getRuntime().availableProcessors());
final var resolutions = parseResolutions(requestJson.getString("resolutions"));
final var compression = requestJson.getInteger("compression", 0);
final var compression = requestJson.getInteger("compression", 6);
final var compressionAlgorithm = ConversionOptions.CompressionAlgorithm.parse(requestJson.getString("compressionAlgorithm", "deflate"));
final var chunkSize = requestJson.getInteger("chunkSize", 8192);

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6 changes: 3 additions & 3 deletions src/main/java/ru/itmo/ctlab/hict/hict_server/tools/ConversionCliLauncher.java
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Expand Up @@ -29,7 +29,7 @@ public static void main(String[] args) throws Exception {
Path.of(parser.require("output")),
parser.listOfLong("resolutions"),
parser.integer("chunk-size", 8192),
parser.integer("compression", 0),
parser.integer("compression", 6),
ConversionOptions.CompressionAlgorithm.parse(parser.value("compression-algorithm", "deflate")),
parser.value("agp", ConversionOptions.NO_AGP),
parser.flag("apply-agp"),
Expand All @@ -54,8 +54,8 @@ private static Consumer<String> stdoutLogger() {

private static void printHelp() {
System.out.println("Usage:");
System.out.println(" hict-to-mcool --input=<in.hict> --output=<out.mcool> [--resolutions=10000,50000] [--compression=0..9] [--compression-algorithm=deflate|zstd|lzf] [--chunk-size=8192] [--agp=foo.agp --apply-agp] [--parallelism=N]");
System.out.println(" mcool-to-hict --input=<in.mcool> --output=<out.hict> [--resolutions=10000,50000] [--compression=0..9] [--compression-algorithm=deflate|zstd|lzf] [--chunk-size=8192] [--parallelism=N]");
System.out.println(" hict-to-mcool --input=<in.hict> --output=<out.mcool> [--resolutions=10000,50000] [--compression=0..9 (default: 6)] [--compression-algorithm=deflate|zstd|lzf] [--chunk-size=8192] [--agp=foo.agp --apply-agp] [--parallelism=N]");
System.out.println(" mcool-to-hict --input=<in.mcool> --output=<out.hict> [--resolutions=10000,50000] [--compression=0..9 (default: 6)] [--compression-algorithm=deflate|zstd|lzf] [--chunk-size=8192] [--parallelism=N]");
}

private record ArgParser(String[] args) {
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2 changes: 1 addition & 1 deletion src/main/java/ru/itmo/ctlab/hict/hict_server/tools/HictCli.java
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Expand Up @@ -122,7 +122,7 @@ abstract static class BaseConvert implements Callable<Integer> {
@Option(names = "--chunk-size", defaultValue = "8192", description = "HDF5 chunk size (default: 8192).")
int chunkSize;

@Option(names = "--compression", defaultValue = "0", description = "Compression level 0..9 (default: 0).")
@Option(names = "--compression", defaultValue = "6", description = "Compression level 0..9 (default: 6).")
int compression;

@Option(
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