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Improve exception message for unset VCF output type #1357

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merged 4 commits into from
Apr 23, 2019
Merged

Improve exception message for unset VCF output type #1357

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a76fc8f
Improve exception message for unset VCF output type
clintval Apr 22, 2019
146fd1a
Add valid VCF extensions and attempted outPath to exception message
clintval Apr 23, 2019
6207124
outPath can be null for streams
clintval Apr 23, 2019
022db1e
Better formatting on message
clintval Apr 23, 2019
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2 changes: 1 addition & 1 deletion src/main/java/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.java
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Original file line number Diff line number Diff line change
Expand Up @@ -453,7 +453,7 @@ else if (STREAM_TYPES.contains(this.outType))

switch (typeToBuild) {
case UNSPECIFIED:
throw new IllegalArgumentException("Must specify file or stream output type.");
throw new IllegalArgumentException("Output format type is not set, or could not be inferred from the output path. If a path was used, does it have a valid VCF extension?");
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if you're at it, why not take htsjdk.samtools.util.IOUtil#VCF_EXTENSIONS_LIST and present it to the user for reference?

case VCF:
if ((refDict == null) && (options.contains(Options.INDEX_ON_THE_FLY)))
throw new IllegalArgumentException("A reference dictionary is required for creating Tribble indices on the fly");
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