/**
* Add into to a hash
*
* @param hits
* @param marker
* @param hit2add
* @param showGeneDetails
* @param compareTemplate
*/
void regionsAddHit(
HashSet<String> hits,
Marker hit2add,
Marker marker,
boolean showGeneDetails,
boolean compareTemplate) {
String hitStr = hit2add.getClass().getSimpleName();
if (compareTemplate) {
Gene gene = (Gene) hit2add.findParent(Gene.class);
if (gene != null)
hitStr +=
(hit2add.isStrandPlus() == marker.isStrandPlus())
? "_TEMPLATE_STRAND"
: "_NON_TEMPLATE_STRAND";
}
if (showGeneDetails && (hit2add instanceof Gene)) {
Gene gene = (Gene) hit2add;
hitStr +=
"["
+ gene.getBioType()
+ ", "
+ gene.getGeneName()
+ ", "
+ (gene.isProteinCoding() ? "protein" : "not-protein")
+ "]";
}
hits.add(hitStr); // Add marker name to the list
}
/**
* Count number of bases, for a given chromosome and marker type
*
* @param mtype
* @param chr
* @param markers
* @return
*/
void countBases(String mtype, Chromosome chr, Markers markers) {
String chrName = chr.getChromosomeName();
if (verbose) System.err.print(" " + chrName);
// Initialize
byte busy[] = new byte[chr.size()];
for (int i = 0; i < busy.length; i++) busy[i] = 0;
for (Marker m : markers) {
// Same marker type & same chromo? Count bases
if (m.getChromosomeName().equals(chrName) && markerTypes.isType(m, mtype)) {
for (int i = m.getStart(); i <= m.getEnd(); i++) busy[i] = 1;
}
}
int latest = 0;
for (int i = 0; i < busy.length; i++) {
// Transition? Count another marker
if ((i > 0) && (busy[i] != 0) && (busy[i - 1] == 0)) {
if ((i - latest) <= readLength)
countBases.inc(mtype, i - latest); // Intervals are less than one read away? Unify them
else countMarkers.inc(mtype);
}
// Base busy? Count another base
if (busy[i] != 0) {
countBases.inc(mtype);
latest = i;
}
}
}
/**
* Predict the effect of a seqChange
*
* @param seqChange : Sequence change
* @param seqChangeRef : Before analyzing results, we have to change markers using seqChangerRef
* to create a new reference 'on the fly'
*/
public ChangeEffects seqChangeEffect(Variant seqChange, Variant seqChangeRef) {
ChangeEffects changeEffects = new ChangeEffects(seqChange, seqChangeRef);
// ---
// Chromosome missing?
// ---
if (Config.get().isErrorOnMissingChromo() && isChromosomeMissing(seqChange)) {
changeEffects.addErrorWarning(ErrorWarningType.ERROR_CHROMOSOME_NOT_FOUND);
return changeEffects;
}
// ---
// Check that this is not a huge deletion.
// Huge deletions would crash the rest of the algorithm, so we need to stop them here.
// ---
if (seqChange.isDel() && (seqChange.size() > HUGE_DELETION_SIZE_THRESHOLD)) {
// Get chromosome
String chromoName = seqChange.getChromosomeName();
Chromosome chr = genome.getChromosome(chromoName);
if (chr.size() > 0) {
double ratio = seqChange.size() / ((double) chr.size());
if (ratio > HUGE_DELETION_RATIO_THRESHOLD) {
changeEffects.add(chr, EffectType.CHROMOSOME_LARGE_DELETION, "");
return changeEffects;
}
}
}
// ---
// Query interval tree: Which intervals does seqChange intersect?
// ---
Markers intersects = query(seqChange);
// Show all results
boolean hitChromo = false, hitSomething = false;
if (intersects.size() > 0) {
for (Marker marker : intersects) {
if (marker instanceof Chromosome) hitChromo = true; // Do we hit any chromosome?
else { // Analyze all markers
marker.seqChangeEffect(seqChange, changeEffects, seqChangeRef);
hitSomething = true;
}
}
}
// Any errors or intergenic (i.e. did not hit any gene)
if (!hitChromo) {
if (Config.get().isErrorChromoHit())
changeEffects.addErrorWarning(ErrorWarningType.ERROR_OUT_OF_CHROMOSOME_RANGE);
} else if (!hitSomething) {
if (Config.get().isOnlyRegulation()) changeEffects.setEffectType(EffectType.NONE);
else changeEffects.setEffectType(EffectType.INTERGENIC);
}
return changeEffects;
}
/**
* Find the last position where a nonsense mediated decay is supposed to occurr This is 50 bases
* (MND_BASES_BEFORE_LAST_JUNCTION bases) before the last exon-exon junction.
*
* @param tr
* @return
*/
public int lastNmdPos(Transcript tr) {
// ---
// Get last exon
// ---
int cdsEnd = tr.getCdsEnd();
int cdsStart = tr.getCdsStart();
Marker cds =
new Marker(
tr.getChromosome(),
Math.min(cdsStart, cdsEnd),
Math.max(cdsStart, cdsEnd),
tr.getStrand(),
""); // Create a cds marker
Exon lastExon = null;
int countCodingExons = 0;
for (Exon exon : tr.sortedStrand()) {
if (exon.intersects(cdsEnd)) lastExon = exon;
if (cds.intersects(exon)) countCodingExons++;
}
// Only one coding exon? => No NMD
// Note: I'm assuming that we should have a splice event in a coding part of the transcript for
// NMD to happen.
if (countCodingExons <= 1) return -1;
// Sanity check
if (lastExon == null)
throw new RuntimeException(
"Cannot find last coding exon for transcript '"
+ tr.getId()
+ "' (cdsEnd: "
+ cdsEnd
+ ")\n\t"
+ tr);
// ---
// Find that position of MND_BASES_BEFORE_LAST_JUNCTION before the last exon-exon junction
// ---
int lastExonJunction = tr.isStrandPlus() ? lastExon.getStart() : lastExon.getEnd();
int chrPos[] = tr.baseNumberCds2Pos();
int lastNmdPos = -1;
for (int cdsi = chrPos.length - 1; cdsi >= 0; cdsi--) {
if (chrPos[cdsi] == lastExonJunction) {
if (cdsi > MND_BASES_BEFORE_LAST_JUNCTION)
lastNmdPos = chrPos[cdsi - MND_BASES_BEFORE_LAST_JUNCTION - 1];
else return tr.isStrandPlus() ? 0 : Integer.MAX_VALUE; // Out of CDS range
return lastNmdPos;
}
}
throw new RuntimeException(
"Cannot find last exon junction position for transcript '" + tr.getId() + "'\n\t" + tr);
// return -1;
}
/** Count bases covered for each marker type */
public void countBases() {
// ---
// Add all markers
// ---
Markers markers = new Markers();
markers.add(snpEffectPredictor.getMarkers());
for (Gene gene : snpEffectPredictor.getGenome().getGenes()) {
markers.add(gene);
markers.add(gene.markers());
}
for (Chromosome chr : snpEffectPredictor.getGenome()) markers.add(chr);
// ---
// Calculate raw counts
// ---
for (Marker m : markers) {
String mtype = markerTypes.getType(m);
String msubtype = markerTypes.getSubType(m);
rawCountMarkers.inc(mtype);
rawCountBases.inc(mtype, m.size());
// Count sub-types (if any)
if (msubtype != null) {
rawCountMarkers.inc(msubtype);
rawCountBases.inc(msubtype, m.size());
}
}
// ---
// Count number of bases for each marker type (overlap and join)
// ---
for (String mtype : rawCountMarkers.keysSorted()) {
if (mtype.equals(Chromosome.class.getSimpleName()))
continue; // We calculate chromosomes later (it's faster)
if (verbose) System.err.print(mtype + ":");
if (countMarkers.get(mtype) == 0) {
for (Chromosome chr : snpEffectPredictor.getGenome()) countBases(mtype, chr, markers);
}
if (verbose) System.err.println("");
}
// Show chromosomes length
String mtype = Chromosome.class.getSimpleName();
for (Chromosome chr : snpEffectPredictor.getGenome()) {
countBases.inc(mtype, chr.size());
countMarkers.inc(mtype);
}
}
public Gene getGene() {
if (marker != null) {
if (marker instanceof Gene) return (Gene) marker;
return (Gene) marker.findParent(Gene.class);
}
return null;
}
/** Get intron (if any) */
public Intron getIntron() {
if (marker != null) {
if (marker instanceof Intron) return (Intron) marker;
return (Intron) marker.findParent(Intron.class);
}
return null;
}
public Transcript getTranscript() {
if (marker != null) {
if (marker instanceof Transcript) return (Transcript) marker;
return (Transcript) marker.findParent(Transcript.class);
}
return null;
}
/** Get exon (if any) */
public Exon getExon() {
if (marker != null) {
if (marker instanceof Exon) return (Exon) marker;
return (Exon) marker.findParent(Exon.class);
}
return null;
}
/**
* Is this deletion a LOF?
*
* <p>Criteria: 1) First (coding) exon deleted 2) More than 50% of coding sequence deleted
*
* @param changeEffect
* @return
*/
protected boolean isLofDeletion(ChangeEffect changeEffect) {
Transcript tr = changeEffect.getTranscript();
if (tr == null)
throw new RuntimeException("Transcript not found for change:\n\t" + changeEffect);
// ---
// Criteria:
// 1) First (coding) exon deleted
// ---
if (changeEffect.getEffectType() == EffectType.EXON_DELETED) {
Variant seqChange = changeEffect.getSeqChange();
if (seqChange == null)
throw new RuntimeException("Cannot retrieve 'seqChange' from EXON_DELETED effect!");
if (seqChange.includes(tr.getFirstCodingExon())) return true;
}
// ---
// Criteria:
// 2) More than 50% of coding sequence deleted
// ---
// Find coding part of the transcript (i.e. no UTRs)
Variant seqChange = changeEffect.getSeqChange();
int cdsStart = tr.isStrandPlus() ? tr.getCdsStart() : tr.getCdsEnd();
int cdsEnd = tr.isStrandPlus() ? tr.getCdsEnd() : tr.getCdsStart();
Marker coding = new Marker(seqChange.getChromosome(), cdsStart, cdsEnd, 1, "");
// Create an interval intersecting the CDS and the deletion
int start = Math.max(cdsStart, seqChange.getStart());
int end = Math.min(cdsEnd, seqChange.getEnd());
if (start >= end) return false; // No intersections with coding part of the exon? => not LOF
Marker codingDeleted = new Marker(seqChange.getChromosome(), start, end, 1, "");
// Count:
// - number of coding bases deleted
// - number of coding bases
int codingBasesDeleted = 0, codingBases = 0;
for (Exon exon : tr) {
codingBasesDeleted += codingDeleted.intersectSize(exon);
codingBases += coding.intersectSize(exon);
}
// More than a threshold? => It is a LOF
double percDeleted = codingBasesDeleted / ((double) codingBases);
return (percDeleted > deleteProteinCodingBases);
}
/**
* Is the chromosome missing in this marker?
*
* @param marker
* @return
*/
boolean isChromosomeMissing(Marker marker) {
// Missing chromosome in marker?
if (marker.getChromosome() == null) return true;
// Missing chromosome in genome?
String chrName = marker.getChromosomeName();
Chromosome chr = genome.getChromosome(chrName);
if (chr == null) return true;
// Chromosome length is 1 or less?
if (chr.size() < 1) return true;
// Tree not found in interval forest?
if (!intervalForest.hasTree(chrName)) return true;
// OK, we have the chromosome
return false;
}
/** Save nextprot markers */
void save() {
String nextProtBinFile = config.getDirDataVersion() + "/nextProt.bin";
if (verbose) Timer.showStdErr("Saving database to file '" + nextProtBinFile + "'");
// Add chromosomes
HashSet<Chromosome> chromos = new HashSet<Chromosome>();
for (Marker m : markers) chromos.add(m.getChromosome());
// Create a set of all markers to be saved
Markers markersToSave = new Markers();
markersToSave.add(genome);
for (Chromosome chr : chromos) markersToSave.add(chr);
for (Marker m : markers) markersToSave.add(m);
// Save
MarkerSerializer markerSerializer = new MarkerSerializer();
markerSerializer.save(nextProtBinFile, markersToSave);
}
/** Set values for codons around change. */
public void setCodonsAround(String codonsLeft, String codonsRight) {
codonsAroundOld =
codonsLeft.toLowerCase() + codonsRef.toUpperCase() + codonsRight.toLowerCase();
codonsAroundNew =
codonsLeft.toLowerCase() + codonsAlt.toUpperCase() + codonsRight.toLowerCase();
// Amino acids surrounding the ones changed
CodonTable codonTable = marker.codonTable();
String aasLeft = codonTable.aa(codonsLeft);
String aasRigt = codonTable.aa(codonsRight);
aasAroundOld = aasLeft.toLowerCase() + aaRef.toUpperCase() + aasRigt.toLowerCase();
aasAroundNew = aasLeft.toLowerCase() + aaAlt.toUpperCase() + aasRigt.toLowerCase();
}
/** Return functional class of this effect (i.e. NONSENSE, MISSENSE, SILENT or NONE) */
public FunctionalClass getFunctionalClass() {
if (variant.isSnp()) {
if (!aaAlt.equals(aaRef)) {
CodonTable codonTable = marker.codonTable();
if (codonTable.isStop(codonsAlt)) return FunctionalClass.NONSENSE;
return FunctionalClass.MISSENSE;
}
if (!codonsAlt.equals(codonsRef)) return FunctionalClass.SILENT;
}
return FunctionalClass.NONE;
}
/**
* Find closest gene to this marker
*
* <p>In case more than one 'closest' gene is found (e.g. two or more genes at the same distance).
* The following rules apply:
*
* <p>i) If many genes have the same 'closest distance', coding genes are preferred.
*
* <p>ii) If more than one coding gene has the same 'closet distance', a random gene is returned.
*
* @param inputInterval
*/
public Gene queryClosestGene(Marker inputInterval) {
int initialExtension = 1000;
String chrName = inputInterval.getChromosomeName();
Chromosome chr = genome.getChromosome(chrName);
if (chr == null) return null;
if (chr.size() > 0) {
// Extend interval to capture 'close' genes
for (int extend = initialExtension; extend < chr.size(); extend *= 2) {
int start = Math.max(inputInterval.getStart() - extend, 0);
int end = inputInterval.getEnd() + extend;
Marker extended = new Marker(chr, start, end, 1, "");
// Find all genes that intersect with the interval
Markers markers = query(extended);
Markers genes = new Markers();
int minDist = Integer.MAX_VALUE;
for (Marker m : markers) {
if (m instanceof Gene) {
int dist = m.distance(inputInterval);
if (dist < minDist) {
genes.add(m);
minDist = dist;
}
}
}
// Found something?
if (genes.size() > 0) {
// Find a gene having distance 'minDist'. Prefer coding genes
Gene minDistGene = null;
for (Marker m : genes) {
int dist = m.distance(inputInterval);
if (dist == minDist) {
Gene gene = (Gene) m;
if (minDistGene == null) minDistGene = gene;
else if (!minDistGene.isProteinCoding() && gene.isProteinCoding()) minDistGene = gene;
}
}
return minDistGene;
}
}
}
// Nothing found
return null;
}
/** Set codon change. Calculate effect type based on codon changes (for SNPs & MNPs) */
public void setCodons(String codonsOld, String codonsNew, int codonNum, int codonIndex) {
codonsRef = codonsOld;
codonsAlt = codonsNew;
this.codonNum = codonNum;
this.codonIndex = codonIndex;
CodonTable codonTable = marker.codonTable();
// Calculate amino acids
if (codonsOld.isEmpty()) aaRef = "";
else {
aaRef = codonTable.aa(codonsOld);
codonDegeneracy = codonTable.degenerate(codonsOld, codonIndex); // Calculate codon degeneracy
}
if (codonsNew.isEmpty()) aaAlt = "";
else aaAlt = codonTable.aa(codonsNew);
}
/** Show a string with overall effect */
public String effect(
boolean shortFormat, boolean showAaChange, boolean showBioType, boolean useSeqOntology) {
String e = "";
String codonEffect = codonEffect(showAaChange, showBioType, useSeqOntology); // Codon effect
// Create effect string
if (!codonEffect.isEmpty()) e = codonEffect;
else if (isRegulation())
return getEffectTypeString(useSeqOntology) + "[" + ((Regulation) marker).getName() + "]";
else if (isNextProt())
return getEffectTypeString(useSeqOntology)
+ "["
+ VcfEffect.vcfEffSafe(((NextProt) marker).getId())
+ "]"; // Make sure this 'id' is not dangerous in a VCF 'EFF' field
else if (isMotif())
return getEffectTypeString(useSeqOntology)
+ "["
+ ((Motif) marker).getPwmId()
+ ":"
+ ((Motif) marker).getPwmName()
+ "]";
else if (isCustom()) {
// Custom interval
String label = ((Custom) marker).getLabel();
double score = ((Custom) marker).getScore();
if (!Double.isNaN(score)) label = label + ":" + score;
if (!label.isEmpty()) label = "[" + label + "]";
return getEffectTypeString(useSeqOntology) + label;
} else if (isIntergenic() || isIntron() || isSpliceSite())
e = getEffectTypeString(useSeqOntology);
else if (!message.isEmpty()) e = getEffectTypeString(useSeqOntology) + ": " + message;
else if (marker == null)
e =
getEffectTypeString(
useSeqOntology); // There are cases when no marker is associated (e.g. "Out of
// chromosome", "No such chromosome", etc.)
else e = getEffectTypeString(useSeqOntology) + ": " + marker.getId();
if (shortFormat) e = e.split(":")[0];
return e;
}
/**
* Name of the regions hit by a marker
*
* @param marker
* @param showGeneDetails
* @param compareTemplate
* @param id : Only use genes or transcripts matching this ID
* @return
*/
public Set<String> regions(
Marker marker, boolean showGeneDetails, boolean compareTemplate, String id) {
if (Config.get().isErrorOnMissingChromo() && isChromosomeMissing(marker))
throw new RuntimeEOFException("Chromosome missing for marker: " + marker);
boolean hitChromo = false;
HashSet<String> hits = new HashSet<String>();
Markers intersects = query(marker);
if (intersects.size() > 0) {
for (Marker markerInt : intersects) {
if (markerInt instanceof Chromosome) {
hitChromo = true; // OK (we have to hit a chromosome, otherwise it's an error
hits.add(markerInt.getClass().getSimpleName()); // Add marker name to the list
} else if (markerInt instanceof Gene) {
// Analyze Genes
Gene gene = (Gene) markerInt;
regionsAddHit(hits, gene, marker, showGeneDetails, compareTemplate);
// For all transcripts...
for (Transcript tr : gene) {
if ((id == null)
|| gene.getId().equals(id)
|| tr.getId().equals(id)) { // Mathes ID? (...or no ID to match)
// Does it intersect this transcript?
if (tr.intersects(marker)) {
regionsAddHit(hits, tr, marker, showGeneDetails, compareTemplate);
// Does it intersect a UTR?
for (Utr utr : tr.getUtrs())
if (utr.intersects(marker))
regionsAddHit(hits, utr, marker, showGeneDetails, compareTemplate);
// Does it intersect an exon?
for (Exon ex : tr)
if (ex.intersects(marker))
regionsAddHit(hits, ex, marker, showGeneDetails, compareTemplate);
// Does it intersect an intron?
for (Intron intron : tr.introns())
if (intron.intersects(marker))
regionsAddHit(hits, intron, marker, showGeneDetails, compareTemplate);
}
}
}
} else {
// No ID to match?
if (id == null) regionsAddHit(hits, markerInt, marker, showGeneDetails, compareTemplate);
else {
// Is ID from transcript?
Transcript tr = (Transcript) markerInt.findParent(Transcript.class);
if ((tr != null) && (tr.getId().equals(id))) {
regionsAddHit(
hits,
markerInt,
marker,
showGeneDetails,
compareTemplate); // Transcript ID matches => count
} else {
// Is ID from gene?
Gene gene = (Gene) markerInt.findParent(Gene.class);
if ((gene != null) && (gene.getId().equals(id)))
regionsAddHit(
hits,
markerInt,
marker,
showGeneDetails,
compareTemplate); // Gene ID matches => count
}
}
}
}
}
if (!hitChromo) throw new RuntimeException("ERROR: Out of chromosome range. " + marker);
return hits;
}
/** Show annotations counters in a table */
void analyzeSequenceConservation() {
if (verbose)
Timer.showStdErr(
"Sequence conservation analysis." //
+ "\n\tAA sequence length : "
+ 1 //
+ "\n\tMin AA count : "
+ HIGHLY_CONSERVED_AA_COUNT //
+ "\n\tMin AA conservation : "
+ HIGHLY_CONSERVED_AA_PERCENT //
);
ArrayList<String> keys = new ArrayList<String>();
keys.addAll(countAaSequenceByType.keySet());
Collections.sort(keys);
// Show title
StringBuilder title = new StringBuilder();
for (char aa : GprSeq.AMINO_ACIDS) title.append(aa + "\t");
title.append("\t" + title);
if (verbose)
System.out.println(
"Amino acid regions:\n\tTotal\tMax count\tAvg len\tConservation\tCatergory\tControlled Vocabulary\t"
+ title
+ "\tOther AA sequences:");
// Show AA counts for each 'key'
for (String key : keys) {
long seqLen = 0, totalSeqs = 0, maxCount = 0;
CountByType cbt = countAaSequenceByType.get(key);
long total = cbt.sum();
boolean highlyConservedAaSequence = false;
StringBuilder sb = new StringBuilder();
// For each single amino acid "sequence"
for (char aa : GprSeq.AMINO_ACIDS) {
long count = cbt.get("" + aa);
if (count > 0) {
seqLen += 1 * count;
totalSeqs += count;
maxCount = Math.max(maxCount, count);
sb.append(count);
double perc = ((double) count) / total;
// We estimate that if most AA are the same, then changing this AA can cause a high impact
// in protein coding
if ((perc > HIGHLY_CONSERVED_AA_PERCENT) && (total >= HIGHLY_CONSERVED_AA_COUNT))
highlyConservedAaSequence = true;
}
sb.append("\t");
}
// Sequences of more than one AA
for (String aas : cbt.keySet()) {
long count = cbt.get(aas);
double perc = ((double) count) / total;
if (aas.length() > 1) {
seqLen += aas.length() * count;
totalSeqs += count;
maxCount = Math.max(maxCount, count);
sb.append(String.format("\t" + aas + ":" + count));
if ((perc > HIGHLY_CONSERVED_AA_PERCENT) && (total >= HIGHLY_CONSERVED_AA_COUNT))
highlyConservedAaSequence = true;
}
}
long avgLen = seqLen / totalSeqs;
// Show line
if (verbose)
System.out.println( //
"\t"
+ total //
+ "\t"
+ maxCount //
+ "\t"
+ avgLen //
+ "\t"
+ (highlyConservedAaSequence ? "High" : "") //
+ "\t"
+ key //
+ "\t"
+ sb //
);
// Mark highly conserved
if (highlyConservedAaSequence) {
int count = 0;
for (Marker m : markers) {
NextProt nextProt = (NextProt) m;
if (m.getId().equals(key)) {
nextProt.setHighlyConservedAaSequence(true);
count++;
}
}
if (verbose)
Timer.showStdErr(
"NextProt "
+ count
+ " markers type '"
+ key
+ "' marked as highly conserved AA sequence");
}
}
}
public String toString(boolean useSeqOntology, boolean useHgvs) {
// Get data to show
String geneId = "", geneName = "", bioType = "", transcriptId = "", exonId = "", customId = "";
int exonRank = -1;
if (marker != null) {
// Gene Id, name and biotype
Gene gene = getGene();
Transcript tr = getTranscript();
// CDS size info
if (gene != null) {
geneId = gene.getId();
geneName = gene.getGeneName();
bioType = getBiotype();
}
// Update trId
if (tr != null) transcriptId = tr.getId();
// Exon rank information
Exon exon = getExon();
if (exon != null) {
exonId = exon.getId();
exonRank = exon.getRank();
}
// Regulation
if (isRegulation()) bioType = ((Regulation) marker).getCellType();
}
// Add seqChage's ID
if (!variant.getId().isEmpty()) customId += variant.getId();
// Add custom markers
if ((marker != null) && (marker instanceof Custom))
customId += (customId.isEmpty() ? "" : ";") + marker.getId();
// CDS length
int cdsSize = getCdsLength();
String errWarn = error + (error.isEmpty() ? "" : "|") + warning;
String aaChange = "";
if (useHgvs) aaChange = getHgvs();
else aaChange = ((aaRef.length() + aaAlt.length()) > 0 ? aaRef + "/" + aaAlt : "");
return errWarn //
+ "\t"
+ geneId //
+ "\t"
+ geneName //
+ "\t"
+ bioType //
+ "\t"
+ transcriptId //
+ "\t"
+ exonId //
+ "\t"
+ (exonRank >= 0 ? exonRank : "") //
+ "\t"
+ effect(false, false, false, useSeqOntology) //
+ "\t"
+ aaChange //
+ "\t"
+ ((codonsRef.length() + codonsAlt.length()) > 0 ? codonsRef + "/" + codonsAlt : "") //
+ "\t"
+ (codonNum >= 0 ? (codonNum + 1) : "") //
+ "\t"
+ (codonDegeneracy >= 0 ? codonDegeneracy + "" : "") //
+ "\t"
+ (cdsSize >= 0 ? cdsSize : "") //
+ "\t"
+ (codonsAroundOld.length() > 0 ? codonsAroundOld + " / " + codonsAroundNew : "") //
+ "\t"
+ (aasAroundOld.length() > 0 ? aasAroundOld + " / " + aasAroundNew : "") //
+ "\t"
+ customId //
;
}