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kebab case some arguments in LocusWalker and Spark walkers #5770

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Merged
merged 2 commits into from
Mar 7, 2019
Merged

kebab case some arguments in LocusWalker and Spark walkers #5770

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197c0c2
kebab ases some arguments in LocusWalker and Spark walkers
davidbenjamin Mar 6, 2019
32408be
extract
davidbenjamin Mar 6, 2019
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7 changes: 3 additions & 4 deletions src/main/java/org/broadinstitute/hellbender/engine/LocusWalker.java
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Original file line number Diff line number Diff line change
Expand Up @@ -38,8 +38,9 @@
* @author Daniel Gomez-Sanchez (magicDGS)
*/
public abstract class LocusWalker extends GATKTool {
public static final String MAX_DEPTH_PER_SAMPLE_NAME = "max-depth-per-sample";

@Argument(fullName = "maxDepthPerSample", shortName = "maxDepthPerSample", doc = "Maximum number of reads to retain per sample per locus. Reads above this threshold will be downsampled. Set to 0 to disable.", optional = true)
@Argument(fullName = MAX_DEPTH_PER_SAMPLE_NAME, shortName = MAX_DEPTH_PER_SAMPLE_NAME, doc = "Maximum number of reads to retain per sample per locus. Reads above this threshold will be downsampled. Set to 0 to disable.", optional = true)
protected int maxDepthPerSample = defaultMaxDepthPerSample();

/**
Expand Down Expand Up @@ -122,9 +123,7 @@ public List<ReadFilter> getDefaultReadFilters() {
/** Returns the downsampling info using {@link #maxDepthPerSample} as target coverage. */
protected final LIBSDownsamplingInfo getDownsamplingInfo() {
if (maxDepthPerSample < 0) {
throw new CommandLineException.BadArgumentValue("maxDepthPerSample",
String.valueOf(maxDepthPerSample),
"should be a positive number");
throw new CommandLineException.BadArgumentValue(MAX_DEPTH_PER_SAMPLE_NAME, String.valueOf(maxDepthPerSample), "should be a positive number");
}
return (maxDepthPerSample == 0) ? LocusIteratorByState.NO_DOWNSAMPLING : new LIBSDownsamplingInfo(true, maxDepthPerSample);
}
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4 changes: 2 additions & 2 deletions ...org/broadinstitute/hellbender/engine/spark/AssemblyRegionReadShardArgumentCollection.java
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Expand Up @@ -10,9 +10,9 @@ public class AssemblyRegionReadShardArgumentCollection implements Serializable {
public static final int DEFAULT_READSHARD_SIZE = 5000;
public static final int DEFAULT_READSHARD_PADDING_SIZE = 100;

@Argument(fullName="readShardSize", shortName="readShardSize", doc = "Maximum size of each read shard, in bases. For good performance, this should be much larger than the maximum assembly region size.", optional = true)
@Argument(fullName="read-shard-size", shortName="read-shard-size", doc = "Maximum size of each read shard, in bases. For good performance, this should be much larger than the maximum assembly region size.", optional = true)
public int readShardSize = DEFAULT_READSHARD_SIZE;

@Argument(fullName="readShardPadding", shortName="readShardPadding", doc = "Each read shard has this many bases of extra context on each side. Read shards must have as much or more padding than assembly regions.", optional = true)
@Argument(fullName="read-shard-padding", shortName="read-shard-padding", doc = "Each read shard has this many bases of extra context on each side. Read shards must have as much or more padding than assembly regions.", optional = true)
public int readShardPadding = DEFAULT_READSHARD_PADDING_SIZE;
}
8 changes: 3 additions & 5 deletions src/main/java/org/broadinstitute/hellbender/engine/spark/LocusWalkerSpark.java
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Expand Up @@ -30,7 +30,7 @@
public abstract class LocusWalkerSpark extends GATKSparkTool {
private static final long serialVersionUID = 1L;

@Argument(fullName = "maxDepthPerSample", shortName = "maxDepthPerSample", doc = "Maximum number of reads to retain per sample per locus. Reads above this threshold will be downsampled. Set to 0 to disable.", optional = true)
@Argument(fullName = LocusWalker.MAX_DEPTH_PER_SAMPLE_NAME, shortName = LocusWalker.MAX_DEPTH_PER_SAMPLE_NAME, doc = "Maximum number of reads to retain per sample per locus. Reads above this threshold will be downsampled. Set to 0 to disable.", optional = true)
protected int maxDepthPerSample = defaultMaxDepthPerSample();

/**
Expand All @@ -41,7 +41,7 @@ protected int defaultMaxDepthPerSample() {
return 0;
}

@Argument(fullName="readShardSize", shortName="readShardSize", doc = "Maximum size of each read shard, in bases.", optional = true)
@Argument(fullName="read-shard-size", shortName="read-shard-size", doc = "Maximum size of each read shard, in bases.", optional = true)
public int readShardSize = 10000;

@Argument(doc = "whether to use the shuffle implementation or overlaps partitioning (the default)", shortName = "shuffle", fullName = "shuffle", optional = true)
Expand All @@ -57,9 +57,7 @@ public boolean requiresReads() {
/** Returns the downsampling info using {@link #maxDepthPerSample} as target coverage. */
protected final LIBSDownsamplingInfo getDownsamplingInfo() {
if (maxDepthPerSample < 0) {
throw new CommandLineException.BadArgumentValue("maxDepthPerSample",
String.valueOf(maxDepthPerSample),
"should be a positive number");
throw new CommandLineException.BadArgumentValue(LocusWalker.MAX_DEPTH_PER_SAMPLE_NAME, String.valueOf(maxDepthPerSample), "should be a positive number");
}
return (maxDepthPerSample == 0) ? LocusIteratorByState.NO_DOWNSAMPLING : new LIBSDownsamplingInfo(true, maxDepthPerSample);
}
Expand Down