X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvcf%2FVCFLoader.java;h=f965c4e2d4b093381ac29514326681bec075044c;hb=dc24bc768061f6e08be77d7e18709da98c6f9428;hp=1eeb922981a2c5153e2741321e1bd7e4d8a77a7c;hpb=65740880573a48adc758bec3939ece9d9ae104dd;p=jalview.git diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java index 1eeb922..f965c4e 100644 --- a/src/jalview/io/vcf/VCFLoader.java +++ b/src/jalview/io/vcf/VCFLoader.java @@ -20,27 +20,6 @@ */ package jalview.io.vcf; -import jalview.analysis.Dna; -import jalview.api.AlignViewControllerGuiI; -import jalview.bin.Cache; -import jalview.datamodel.DBRefEntry; -import jalview.datamodel.GeneLociI; -import jalview.datamodel.Mapping; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceI; -import jalview.datamodel.features.FeatureAttributeType; -import jalview.datamodel.features.FeatureSource; -import jalview.datamodel.features.FeatureSources; -import jalview.ext.ensembl.EnsemblMap; -import jalview.ext.htsjdk.HtsContigDb; -import jalview.ext.htsjdk.VCFReader; -import jalview.io.gff.Gff3Helper; -import jalview.io.gff.SequenceOntologyI; -import jalview.util.MapList; -import jalview.util.MappingUtils; -import jalview.util.MessageManager; -import jalview.util.StringUtils; - import java.io.File; import java.io.IOException; import java.util.ArrayList; @@ -67,6 +46,26 @@ import htsjdk.variant.vcf.VCFHeaderLine; import htsjdk.variant.vcf.VCFHeaderLineCount; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; +import jalview.analysis.Dna; +import jalview.api.AlignViewControllerGuiI; +import jalview.bin.Cache; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.GeneLociI; +import jalview.datamodel.Mapping; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.datamodel.features.FeatureAttributeType; +import jalview.datamodel.features.FeatureSource; +import jalview.datamodel.features.FeatureSources; +import jalview.ext.ensembl.EnsemblMap; +import jalview.ext.htsjdk.HtsContigDb; +import jalview.ext.htsjdk.VCFReader; +import jalview.io.gff.Gff3Helper; +import jalview.io.gff.SequenceOntologyI; +import jalview.util.MapList; +import jalview.util.MappingUtils; +import jalview.util.MessageManager; +import jalview.util.StringUtils; /** * A class to read VCF data (using the htsjdk) and add variants as sequence @@ -674,7 +673,6 @@ public class VCFLoader /** * Transfers VCF features to sequences to which this sequence has a mapping. - * If the mapping is 3:1, computes peptide variants from nucleotide variants. * * @param seq */ @@ -897,12 +895,19 @@ public class VCFLoader int[] featureRange = map.map.locateInFrom(variant.getStart(), variant.getEnd()); + /* + * only take features whose range is fully mappable to sequence positions + */ if (featureRange != null) { int featureStart = Math.min(featureRange[0], featureRange[1]); int featureEnd = Math.max(featureRange[0], featureRange[1]); - count += addAlleleFeatures(seq, variant, featureStart, - featureEnd, forwardStrand); + if (featureEnd - featureStart == variant.getEnd() + - variant.getStart()) + { + count += addAlleleFeatures(seq, variant, featureStart, + featureEnd, forwardStrand); + } } } variants.close(); @@ -912,7 +917,7 @@ public class VCFLoader * RuntimeException throwable by htsjdk */ String msg = String.format("Error reading VCF for %s:%d-%d: %s ", - map.chromosome, vcfStart, vcfEnd); + map.chromosome, vcfStart, vcfEnd,e.getLocalizedMessage()); Cache.log.error(msg); } }