Add keep-contig-names parameter #8865
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droazen
suggested changes
Jun 24, 2024
| @@ -73,6 +73,10 @@ public class FastaReferenceMaker extends ReferenceWalker { | |||
| @Argument(fullName= LINE_WIDTH_LONG_NAME, doc="Maximum length of sequence to write per line", optional=true) | |||
| public int basesPerLine = FastaReferenceWriter.DEFAULT_BASES_PER_LINE; | |||
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| public static final String KEEP_CONTIG_NAMES = "keep-contig-names"; | |||
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Add an integration test that uses this new argument, with an expected output
droazen
reviewed
Jun 24, 2024
| writer.appendSequence(lastPosition.getContig(), description, basesPerLine, Bytes.toArray(sequence)); | ||
| } | ||
| else { | ||
| writer.appendSequence(String.valueOf(contigCount), description, basesPerLine, Bytes.toArray(sequence)); |
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If you're using just a slice of a contig, perhaps the name should include the full genomic coordinates
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A forum topic asked whether we can have a behavior to keep original contig names in FastaAlternateReferenceMaker tool.
A new parameter
--keep-contig-namesis added.New optional behavior is to set contig names as
>originalcontigname descriptionHere is my small local test and its result
VCF
Original Fasta
New Fasta with new optional behavior
Sequence dictionary created for the new Fasta.
Default value is false therefore original behavior is kept. Should not hurt any current tests.