private void parseRemainingFields(ConsequenceType consequenceType, String[] lineFields) { consequenceType.setEnsemblGeneId(lineFields[3]); // fill Ensembl gene id consequenceType.setEnsemblTranscriptId(lineFields[4]); // fill Ensembl transcript id ProteinVariantAnnotation proteinVariantAnnotation = new ProteinVariantAnnotation(); if(!lineFields[7].equals("-")) { consequenceType.setCdnaPosition(parseStringInterval(lineFields[7])); // fill cdna position } if(!lineFields[8].equals("-")) { consequenceType.setCdsPosition(parseStringInterval(lineFields[8])); // fill cds position } if(!lineFields[9].equals("-")) { proteinVariantAnnotation.setPosition(parseStringInterval(lineFields[9])); // fill aa position } if(!lineFields[10].equals("-")) { String parts[] = lineFields[10].split("/"); if(parts.length == 2) { proteinVariantAnnotation.setReference(parts[0]); // fill aa change proteinVariantAnnotation.setAlternate(parts[1]); // fill aa change } } consequenceType.setProteinVariantAnnotation(proteinVariantAnnotation); consequenceType.setCodon(lineFields[11]); // fill codon change if(!lineFields[6].equals("") && !lineFields.equals("-")) { // VEP may leave this field empty consequenceType.setSequenceOntologyTerms( getSequenceOntologyTerms(Arrays.asList(lineFields[6].split(",")))); // fill so terms // consequenceType.setSoTermsFromSoNames(Arrays.asList(lineFields[6].split(","))); // fill so terms } }
if (variant.getStart() <= exon.getEnd()) { // Variant start within the exon cdnaVariantPosition = cdnaExonEnd - (exon.getEnd() - variant.getStart()); consequenceType.setCdnaPosition(cdnaVariantPosition); exonOverlap = new ExonOverlap( (new StringBuilder()).append(exon.getExonNumber()).append("/").append(transcript.getExons() if (variant.getStart() <= exon.getEnd()) { // Variant within the exon cdnaVariantPosition = cdnaExonEnd - (exon.getEnd() - variant.getStart()); consequenceType.setCdnaPosition(cdnaVariantPosition); exonOverlap = new ExonOverlap( (new StringBuilder()).append(exon.getExonNumber()).append("/").append(transcript.getExons()
consequenceType.setCdnaPosition(cdnaVariantPosition); exonOverlap = new ExonOverlap( (new StringBuilder()).append(exon.getExonNumber()).append("/").append(transcript.getExons().size()) if (variant.getStart() >= exon.getStart()) { // Variant end within the exon cdnaVariantPosition = cdnaExonEnd - (variant.getStart() - exon.getStart()); consequenceType.setCdnaPosition(cdnaVariantPosition); exonOverlap = new ExonOverlap( (new StringBuilder()).append(exon.getExonNumber()).append("/").append(transcript.getExons().size())
if (variant.getStart() <= exon.getEnd()) { // Variant start within the exon cdnaVariantPosition = cdnaExonEnd - (exon.getEnd() - variant.getStart()); consequenceType.setCdnaPosition(cdnaVariantPosition); exonOverlap = new ExonOverlap( (new StringBuilder()).append(exon.getExonNumber()).append("/").append(transcript.getExons() if (variant.getStart() <= exon.getEnd()) { // Variant within the exon cdnaVariantPosition = cdnaExonEnd - (exon.getEnd() - variant.getStart()); consequenceType.setCdnaPosition(cdnaVariantPosition); exonOverlap = new ExonOverlap( (new StringBuilder()).append(exon.getExonNumber()).append("/").append(transcript.getExons()
consequenceType.setCdnaPosition(cdnaVariantPosition); exonOverlap = new ExonOverlap( (new StringBuilder()).append(exon.getExonNumber()).append("/").append(transcript.getExons().size()) if (variant.getStart() >= exon.getStart()) { // Variant end within the exon cdnaVariantPosition = cdnaExonEnd - (variant.getStart() - exon.getStart()); consequenceType.setCdnaPosition(cdnaVariantPosition); exonOverlap = new ExonOverlap( (new StringBuilder()).append(exon.getExonNumber()).append("/").append(transcript.getExons().size())
consequenceType.setCdnaPosition(cdnaVariantPosition); exonOverlap = new ExonOverlap( (new StringBuilder()).append(exon.getExonNumber()).append("/").append(transcript.getExons().size()) if (variant.getStart() <= exon.getEnd()) { // Variant within the exon cdnaVariantPosition = cdnaExonEnd - (exon.getEnd() - variant.getStart()); consequenceType.setCdnaPosition(cdnaVariantPosition); exonOverlap = new ExonOverlap( (new StringBuilder()).append(exon.getExonNumber()).append("/").append(transcript.getExons()
consequenceType.setCdnaPosition(cdnaVariantPosition); exonOverlap = new ExonOverlap( (new StringBuilder()).append(exon.getExonNumber()).append("/").append(transcript.getExons().size()) if (variant.getStart() <= exon.getEnd()) { // Variant within the exon cdnaVariantPosition = cdnaExonEnd - (exon.getEnd() - variant.getStart()); consequenceType.setCdnaPosition(cdnaVariantPosition); exonOverlap = new ExonOverlap( (new StringBuilder()).append(exon.getExonNumber()).append("/").append(transcript.getExons()
consequenceType.setCdnaPosition(cdnaVariantPosition); exonOverlap = new ExonOverlap( (new StringBuilder()).append(exon.getExonNumber()).append("/").append(transcript.getExons().size()) if (variant.getStart() >= exon.getStart()) { // Variant end within the exon cdnaVariantPosition = cdnaExonEnd - (variant.getStart() - exon.getStart()); consequenceType.setCdnaPosition(cdnaVariantPosition); exonOverlap = new ExonOverlap( (new StringBuilder()).append(exon.getExonNumber()).append("/").append(transcript.getExons()
consequenceType.setCdnaPosition(cdnaVariantPosition); exonOverlap = new ExonOverlap( (new StringBuilder()).append(exon.getExonNumber()).append("/").append(transcript.getExons().size()) if (variant.getStart() >= exon.getStart()) { // Variant end within the exon cdnaVariantPosition = cdnaExonEnd - (variant.getStart() - exon.getStart()); consequenceType.setCdnaPosition(cdnaVariantPosition); exonOverlap = new ExonOverlap( (new StringBuilder()).append(exon.getExonNumber()).append("/").append(transcript.getExons()
if (variantEnd >= exon.getStart()) { // Variant end within the exon cdnaVariantStart = cdnaExonEnd - (variantEnd - exon.getStart()); consequenceType.setCdnaPosition(cdnaVariantStart); exonNumber = exon.getExonNumber(); if (variantEnd >= exon.getStart()) { // Variant end within the exon cdnaVariantStart = cdnaExonEnd - (variantEnd - exon.getStart()); consequenceType.setCdnaPosition(cdnaVariantStart); exonNumber = exon.getExonNumber();
if (variantEnd >= exon.getStart()) { // Variant end within the exon cdnaVariantStart = cdnaExonEnd - (variantEnd - exon.getStart()); consequenceType.setCdnaPosition(cdnaVariantStart); exonNumber = exon.getExonNumber(); if (variantEnd >= exon.getStart()) { // Variant end within the exon cdnaVariantStart = cdnaExonEnd - (variantEnd - exon.getStart()); consequenceType.setCdnaPosition(cdnaVariantStart); exonNumber = exon.getExonNumber();
if (variantStart <= exon.getEnd()) { // Variant start within the exon (this is a insertion, variantEnd=variantStart+1) cdnaVariantStart = cdnaExonEnd - (exon.getEnd() - variantStart); consequenceType.setCdnaPosition(cdnaVariantStart); exonNumber = exon.getExonNumber(); if (variantStart <= exon.getEnd()) { // Variant start within the exon cdnaVariantStart = cdnaExonEnd - (exon.getEnd() - variantStart); consequenceType.setCdnaPosition(cdnaVariantStart); exonNumber = exon.getExonNumber();
if (variantEnd >= exon.getStart()) { // Variant end within the exon cdnaVariantStart = cdnaExonEnd - (variantEnd - exon.getStart()); consequenceType.setCdnaPosition(cdnaVariantStart); exonNumber = exon.getExonNumber(); if (variantEnd >= exon.getStart()) { // Variant end within the exon cdnaVariantStart = cdnaExonEnd - (variantEnd - exon.getStart()); consequenceType.setCdnaPosition(cdnaVariantStart); exonNumber = exon.getExonNumber();
if (variantStart <= exon.getEnd()) { // Variant start within the exon (this is a insertion, variantEnd=variantStart+1) cdnaVariantStart = cdnaExonEnd - (exon.getEnd() - variantStart); consequenceType.setCdnaPosition(cdnaVariantStart); exonNumber = exon.getExonNumber(); if (variantStart <= exon.getEnd()) { // Variant start within the exon cdnaVariantStart = cdnaExonEnd - (exon.getEnd() - variantStart); consequenceType.setCdnaPosition(cdnaVariantStart); exonNumber = exon.getExonNumber();
if (variantEnd >= exon.getStart()) { // Variant end within the exon cdnaVariantStart = cdnaExonEnd - (variantEnd - exon.getStart()); consequenceType.setCdnaPosition(cdnaVariantStart); exonNumber = exon.getExonNumber(); if (variantEnd >= exon.getStart()) { // Variant end within the exon cdnaVariantStart = cdnaExonEnd - (variantEnd - exon.getStart()); consequenceType.setCdnaPosition(cdnaVariantStart); exonNumber = exon.getExonNumber();
if (variantStart <= exon.getEnd()) { // Variant start within the exon (this is a insertion, variantEnd=variantStart+1) cdnaVariantStart = cdnaExonEnd - (exon.getEnd() - variantStart); consequenceType.setCdnaPosition(cdnaVariantStart); exonNumber = exon.getExonNumber(); if (variantStart <= exon.getEnd()) { // Variant start within the exon cdnaVariantStart = cdnaExonEnd - (exon.getEnd() - variantStart); consequenceType.setCdnaPosition(cdnaVariantStart); exonNumber = exon.getExonNumber();
if (variantStart <= exon.getEnd()) { // Variant start within the exon cdnaVariantStart = cdnaExonEnd - (exon.getEnd() - variantStart); consequenceType.setCdnaPosition(cdnaVariantStart); if (variantStart <= exon.getEnd()) { // Variant start within the exon cdnaVariantStart = cdnaExonEnd - (exon.getEnd() - variantStart); consequenceType.setCdnaPosition(cdnaVariantStart);
if (variantEnd >= exon.getStart()) { // Variant end within the exon cdnaVariantStart = cdnaExonEnd - (variantEnd - exon.getStart()); consequenceType.setCdnaPosition(cdnaVariantStart); if (variantEnd >= exon.getStart()) { // Variant end within the exon cdnaVariantStart = cdnaExonEnd - (variantEnd - exon.getStart()); consequenceType.setCdnaPosition(cdnaVariantStart);
if (variantEnd >= exon.getStart()) { // Variant end within the exon cdnaVariantStart = cdnaExonEnd - (variantEnd - exon.getStart()); consequenceType.setCdnaPosition(cdnaVariantStart); if (variantEnd >= exon.getStart()) { // Variant end within the exon cdnaVariantStart = cdnaExonEnd - (variantEnd - exon.getStart()); consequenceType.setCdnaPosition(cdnaVariantStart);
if (variantEnd >= exon.getStart()) { // Variant end within the exon cdnaVariantStart = cdnaExonEnd - (variantEnd - exon.getStart()); consequenceType.setCdnaPosition(cdnaVariantStart); if (variantEnd >= exon.getStart()) { // Variant end within the exon cdnaVariantStart = cdnaExonEnd - (variantEnd - exon.getStart()); consequenceType.setCdnaPosition(cdnaVariantStart);