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9 changes: 9 additions & 0 deletions
9
...tator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate/GenomeVersion.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,9 @@ | ||
| package com.github.bihealth.varfish_annotator.annotate; | ||
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| /** Enumerate known genome versions. */ | ||
| public enum GenomeVersion { | ||
| GRCH37, | ||
| HG19, | ||
| GRCH38, | ||
| HG38 | ||
| } |
17 changes: 17 additions & 0 deletions
17
...rc/main/java/com/github/bihealth/varfish_annotator/annotate/IncompatibleVcfException.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,17 @@ | ||
| package com.github.bihealth.varfish_annotator.annotate; | ||
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| /** Raised on incompatible VCF files. */ | ||
| public class IncompatibleVcfException extends Exception { | ||
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| public IncompatibleVcfException(String message, Throwable cause) { | ||
| super(message, cause); | ||
| } | ||
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| public IncompatibleVcfException(String message) { | ||
| super(message); | ||
| } | ||
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| public IncompatibleVcfException(Throwable cause) { | ||
| super(cause); | ||
| } | ||
| } |
80 changes: 80 additions & 0 deletions
80
...src/main/java/com/github/bihealth/varfish_annotator/annotate/VcfCompatibilityChecker.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,80 @@ | ||
| package com.github.bihealth.varfish_annotator.annotate; | ||
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| import htsjdk.samtools.SAMSequenceRecord; | ||
| import htsjdk.variant.vcf.VCFContigHeaderLine; | ||
| import htsjdk.variant.vcf.VCFFileReader; | ||
| import java.util.List; | ||
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| /** | ||
| * Check VCF file for compatibility with annotation. | ||
| * | ||
| * <p>At the moment, only a simple check is implemented that tests whether the dataset looks like | ||
| * GRCh37/hg19 as this is the Genome build that VarFish supports. | ||
| */ | ||
| public class VcfCompatibilityChecker { | ||
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| /** Length of chr1 in hg19. */ | ||
| private static final int CHR1_HG19_LENGTH = 249250621; | ||
| /** Length of chr1 in hg38. */ | ||
| private static final int CHR1_HG38_LENGTH = 248956422; | ||
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| /** The {@link VCFFileReader} that is to be used for checking. */ | ||
| private VCFFileReader reader; | ||
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| /** | ||
| * Construct a new {@link VcfCompatibilityChecker}. | ||
| * | ||
| * @param reader The {@link VCFFileReader} to use for checking headers etc. | ||
| */ | ||
| public VcfCompatibilityChecker(VCFFileReader reader) { | ||
| this.reader = reader; | ||
| } | ||
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| /** | ||
| * Check whether the VCF file given to the construtor as <tt>reader</tt> looks to be compatible. | ||
| * | ||
| * <p>Throws an exception in case of problems and otherwise just returns. Will print a warning to | ||
| * stderr if no reliable decision could be made. | ||
| * | ||
| * @throws IncompatibleVcfException If the VCF file looks to be incompatible. | ||
| */ | ||
| public void check() throws IncompatibleVcfException { | ||
| // Check whether this looks like GRCh37/h19. | ||
| GenomeVersion genomeVersion = this.guessGenomeVersion(); | ||
| if (genomeVersion == GenomeVersion.GRCH37 || genomeVersion == GenomeVersion.HG19) { | ||
| System.err.println( | ||
| "INFO: Genome looks like GRCh" + 37 + " (sequence only; regardless of 'chr' prefix)."); | ||
| } else if (genomeVersion == GenomeVersion.GRCH38 || genomeVersion == GenomeVersion.HG38) { | ||
| throw new IncompatibleVcfException( | ||
| "VCF file looks like hg38 by chr1 length but we only support hg19/GRCh37"); | ||
| } else { | ||
| System.err.println("WARNING: VCF file did not contain contig line for '1' or 'chr1'"); | ||
| System.err.println("WARNING: Will proceed as if it is hg19/GRCh37."); | ||
| } | ||
| } | ||
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| public GenomeVersion guessGenomeVersion() { | ||
| final List<VCFContigHeaderLine> contigLines = this.reader.getHeader().getContigLines(); | ||
| if (contigLines.isEmpty()) { | ||
| System.err.println("WARNING: VCF file did not contain any contig lines."); | ||
| return null; | ||
| } else { | ||
| for (VCFContigHeaderLine line : contigLines) { | ||
| final SAMSequenceRecord seqRecord = line.getSAMSequenceRecord(); | ||
| if (seqRecord.getSequenceName().equals("1") || seqRecord.getSequenceName().equals("chr1")) { | ||
| if (seqRecord.getSequenceLength() == CHR1_HG19_LENGTH) { | ||
| return seqRecord.getSequenceName().startsWith("chr") | ||
| ? GenomeVersion.HG19 | ||
| : GenomeVersion.GRCH37; | ||
| } else if (seqRecord.getSequenceLength() == CHR1_HG38_LENGTH) { | ||
| return seqRecord.getSequenceName().startsWith("chr") | ||
| ? GenomeVersion.HG38 | ||
| : GenomeVersion.GRCH37; | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| return null; | ||
| } | ||
| } |
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