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Fixing #408, indel parsing of nucleotides.
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@holtgrewe
holtgrewe committed Aug 24, 2018
1 parent e376023 commit d67c185
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,10 @@

## HEAD (unreleased)

### jannovar-hgvs

* Fixing parser issue for nucleotide indels (#408).

### jannovar-htsjdk

* Obey the `options.escapeAnnField` parameter for escaping the variant effect in the `ANN` field.
Expand Down
180 changes: 124 additions & 56 deletions ...s/src/main/java/de/charite/compbio/jannovar/hgvs/parser/Antlr4HGVSParserListenerImpl.java
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
package de.charite.compbio.jannovar.hgvs.parser;

import java.util.ArrayList;

import org.antlr.v4.runtime.ParserRuleContext;
import org.antlr.v4.runtime.tree.ParseTree;
import org.antlr.v4.runtime.tree.ParseTreeProperty;
import org.slf4j.Logger;
Expand Down Expand Up @@ -55,6 +55,7 @@
import de.charite.compbio.jannovar.hgvs.parser.Antlr4HGVSParser.Nt_multi_allele_varContext;
import de.charite.compbio.jannovar.hgvs.parser.Antlr4HGVSParser.Nt_multi_change_alleleContext;
import de.charite.compbio.jannovar.hgvs.parser.Antlr4HGVSParser.Nt_multi_change_allele_innerContext;
import de.charite.compbio.jannovar.hgvs.parser.Antlr4HGVSParser.Nt_numberContext;
import de.charite.compbio.jannovar.hgvs.parser.Antlr4HGVSParser.Nt_offsetContext;
import de.charite.compbio.jannovar.hgvs.parser.Antlr4HGVSParser.Nt_point_locationContext;
import de.charite.compbio.jannovar.hgvs.parser.Antlr4HGVSParser.Nt_rangeContext;
Expand All @@ -73,7 +74,8 @@
*/
class Antlr4HGVSParserListenerImpl extends Antlr4HGVSParserBaseListener {

private static final Logger LOGGER = LoggerFactory.getLogger(Antlr4HGVSParserListenerImpl.class);
private static final Logger LOGGER = LoggerFactory
.getLogger(Antlr4HGVSParserListenerImpl.class);

/** maps nodes to Objects with Map<ParseTree,Object> */
ParseTreeProperty<Object> values = new ParseTreeProperty<>();
Expand Down Expand Up @@ -128,17 +130,21 @@ public void exitNt_single_allele_var(Nt_single_allele_varContext ctx) {
/**
* Leaving of the nt_single_allele_single_change_var rule.
*
* Collect sequence type, sequence ID, and NucleotideChange from the children and label ctx with the resulting
* {@link SingleAlleleNucleotideVariant}.
* Collect sequence type, sequence ID, and NucleotideChange from the children and label ctx with
* the resulting {@link SingleAlleleNucleotideVariant}.
*/
@Override
public void exitNt_single_allele_single_change_var(Nt_single_allele_single_change_varContext ctx) {
public void exitNt_single_allele_single_change_var(
Nt_single_allele_single_change_varContext ctx) {
LOGGER.debug("Leaving nt_single_allele_single_change_var");
final SequenceType seqType = SequenceType.findMatchingForPrefix(ctx.NT_CHANGE_DESCRIPTION().getText());
final SequenceType seqType = SequenceType
.findMatchingForPrefix(ctx.NT_CHANGE_DESCRIPTION().getText());
final ReferenceLabel refLabel = (ReferenceLabel) getValue(ctx.reference());
final NucleotideChange ntChange = (NucleotideChange) getValue(ctx.nt_change());
setValue(ctx, new SingleAlleleNucleotideVariant(seqType, refLabel.getTranscriptID(), refLabel.getProteinID(),
refLabel.getTranscriptVersion(), NucleotideChangeAllele.singleChangeAllele(ntChange)));
setValue(ctx,
new SingleAlleleNucleotideVariant(seqType, refLabel.getTranscriptID(),
refLabel.getProteinID(), refLabel.getTranscriptVersion(),
NucleotideChangeAllele.singleChangeAllele(ntChange)));
}

/**
Expand All @@ -148,13 +154,16 @@ public void exitNt_single_allele_single_change_var(Nt_single_allele_single_chang
* {@link NucleotideChangeAllele} from child label.
*/
@Override
public void exitNt_single_allele_multi_change_var(Nt_single_allele_multi_change_varContext ctx) {
public void exitNt_single_allele_multi_change_var(
Nt_single_allele_multi_change_varContext ctx) {
LOGGER.debug("Leaving nt_single_allele_multi_change_var");
final SequenceType seqType = SequenceType.findMatchingForPrefix(ctx.NT_CHANGE_DESCRIPTION().getText());
final SequenceType seqType = SequenceType
.findMatchingForPrefix(ctx.NT_CHANGE_DESCRIPTION().getText());
final ReferenceLabel refLabel = (ReferenceLabel) getValue(ctx.reference());
final NucleotideChangeAllele allele = (NucleotideChangeAllele) getValue(ctx.nt_multi_change_allele());
setValue(ctx, new SingleAlleleNucleotideVariant(seqType, refLabel.getTranscriptID(), refLabel.getProteinID(),
refLabel.getTranscriptVersion(), allele));
final NucleotideChangeAllele allele = (NucleotideChangeAllele) getValue(
ctx.nt_multi_change_allele());
setValue(ctx, new SingleAlleleNucleotideVariant(seqType, refLabel.getTranscriptID(),
refLabel.getProteinID(), refLabel.getTranscriptVersion(), allele));
}

/**
Expand All @@ -169,10 +178,11 @@ public void exitNt_multi_allele_var(Nt_multi_allele_varContext ctx) {
ArrayList<NucleotideChangeAllele> alleles = new ArrayList<>();
for (Nt_multi_change_alleleContext childCtx : ctx.nt_multi_change_allele())
alleles.add((NucleotideChangeAllele) getValue(childCtx));
final SequenceType seqType = SequenceType.findMatchingForPrefix(ctx.NT_CHANGE_DESCRIPTION().getText());
final SequenceType seqType = SequenceType
.findMatchingForPrefix(ctx.NT_CHANGE_DESCRIPTION().getText());
final ReferenceLabel refLabel = (ReferenceLabel) getValue(ctx.reference());
setValue(ctx, new MultiAlleleNucleotideVariant(seqType, refLabel.getTranscriptID(), refLabel.getProteinID(),
refLabel.getTranscriptVersion(), alleles));
setValue(ctx, new MultiAlleleNucleotideVariant(seqType, refLabel.getTranscriptID(),
refLabel.getProteinID(), refLabel.getTranscriptVersion(), alleles));
}

/**
Expand All @@ -186,7 +196,8 @@ public void exitNt_multi_change_allele(Nt_multi_change_alleleContext ctx) {
if (ctx.NT_PAREN_OPEN() == null) {
setValue(ctx, getValue(ctx.nt_multi_change_allele_inner()));
} else {
NucleotideChangeAllele allele = (NucleotideChangeAllele) getValue(ctx.nt_multi_change_allele_inner());
NucleotideChangeAllele allele = (NucleotideChangeAllele) getValue(
ctx.nt_multi_change_allele_inner());
setValue(ctx, allele.withOnlyPredicted(true));
}
}
Expand All @@ -204,8 +215,8 @@ public void exitNt_multi_change_allele_inner(Nt_multi_change_allele_innerContext
Nt_var_sepContext firstSep = ctx.nt_var_sep().get(0);
for (Nt_var_sepContext otherSep : ctx.nt_var_sep())
if (!firstSep.getText().equals(otherSep.getText()))
throw new RuntimeException("Mismatching variant separators in allele: " + firstSep.getText()
+ " vs. " + otherSep.getText());
throw new RuntimeException("Mismatching variant separators in allele: "
+ firstSep.getText() + " vs. " + otherSep.getText());
varConfig = VariantConfiguration.fromString(firstSep.getText());
}
ArrayList<NucleotideChange> changes = new ArrayList<>();
Expand Down Expand Up @@ -256,19 +267,58 @@ public void exitNt_change_indel(Nt_change_indelContext ctx) {
range = new NucleotideRange((NucleotidePointLocation) getValue(ctx.nt_point_location()),
(NucleotidePointLocation) getValue(ctx.nt_point_location()));

final boolean hasAny = (ctx.nt_number(0) != null || ctx.nt_string(0) != null);
final boolean hasBoth = hasAny && (ctx.nt_number(1) != null || ctx.nt_string(1) != null);
final boolean hasOnlyDelBases;
if (hasAny && !hasBoth) {
final ParserRuleContext singleton = ctx.nt_number(0) != null ? ctx.nt_number(0)
: ctx.nt_string(0);
final int singletonStart = singleton.getSourceInterval().a;
final int insStart = ctx.NT_DEL().getSourceInterval().a;
if (singletonStart < insStart) {
hasOnlyDelBases = true;
} else {
hasOnlyDelBases = false;
}
} else {
hasOnlyDelBases = false;
}

final ParserRuleContext delBases;
if ((hasBoth || hasOnlyDelBases) && ctx.nt_number(0) != null) {
delBases = ctx.nt_number(0);
} else if ((hasBoth || hasOnlyDelBases) && ctx.nt_string(0) != null) {
delBases = ctx.nt_string(0);
} else {
delBases = null;
}

final ParserRuleContext insBases;
if ((hasBoth && ctx.nt_number(1) != null)) {
insBases = ctx.nt_number(1);
} else if (!hasBoth && !hasOnlyDelBases && ctx.nt_number(0) != null) {
insBases = ctx.nt_number(0);
} else if (hasBoth && ctx.nt_string(1) != null) {
insBases = ctx.nt_string(1);
} else if (!hasBoth && !hasOnlyDelBases && ctx.nt_string(0) != null) {
insBases = ctx.nt_string(0);
} else {
insBases = null;
}

final NucleotideSeqDescription seqDesc1;
if (ctx.nt_number(0) != null)
if (delBases != null && delBases == ctx.nt_number(0))
seqDesc1 = new NucleotideSeqDescription(Integer.parseInt(ctx.nt_number(0).getText()));
else if (ctx.nt_string(0) != null)
else if (delBases != null && delBases == ctx.nt_string(0))
seqDesc1 = new NucleotideSeqDescription(ctx.nt_string(0).getText());
else
seqDesc1 = new NucleotideSeqDescription();

final NucleotideSeqDescription seqDesc2;
if (ctx.nt_number(1) != null)
seqDesc2 = new NucleotideSeqDescription(Integer.parseInt(ctx.nt_number(1).getText()));
else if (ctx.nt_string(1) != null)
seqDesc2 = new NucleotideSeqDescription(ctx.nt_string(1).getText());
if (insBases != null && (insBases == ctx.nt_number(0) || insBases == ctx.nt_number(1)))
seqDesc2 = new NucleotideSeqDescription(Integer.parseInt(insBases.getText()));
else if (insBases != null && (insBases == ctx.nt_string(0) || insBases == ctx.nt_string(1)))
seqDesc2 = new NucleotideSeqDescription(insBases.getText());
else
seqDesc2 = new NucleotideSeqDescription();

Expand All @@ -278,7 +328,8 @@ else if (ctx.nt_string(1) != null)
/**
* Leaving of nt_change_deletion rule
*
* Construct {@link NucleotideDeletion} from children's values and labels and label ctx with this.
* Construct {@link NucleotideDeletion} from children's values and labels and label ctx with
* this.
*/
@Override
public void exitNt_change_deletion(Nt_change_deletionContext ctx) {
Expand All @@ -291,10 +342,11 @@ public void exitNt_change_deletion(Nt_change_deletionContext ctx) {
(NucleotidePointLocation) getValue(ctx.nt_point_location()));
final NucleotideDeletion change;
if (ctx.nt_number() != null)
change = new NucleotideDeletion(false, range, new NucleotideSeqDescription(Integer.parseInt(ctx.nt_number()
.getText())));
change = new NucleotideDeletion(false, range,
new NucleotideSeqDescription(Integer.parseInt(ctx.nt_number().getText())));
else if (ctx.nt_string() != null)
change = new NucleotideDeletion(false, range, new NucleotideSeqDescription(ctx.nt_string().getText()));
change = new NucleotideDeletion(false, range,
new NucleotideSeqDescription(ctx.nt_string().getText()));
else
change = new NucleotideDeletion(false, range, new NucleotideSeqDescription());
setValue(ctx, change);
Expand All @@ -303,7 +355,8 @@ else if (ctx.nt_string() != null)
/**
* Leaving of nt_change_duplication rule
*
* Construct {@link NucleotideDuplication} from children's values and labels and label ctx with this.
* Construct {@link NucleotideDuplication} from children's values and labels and label ctx with
* this.
*/
@Override
public void exitNt_change_duplication(Nt_change_duplicationContext ctx) {
Expand All @@ -316,10 +369,11 @@ public void exitNt_change_duplication(Nt_change_duplicationContext ctx) {
(NucleotidePointLocation) getValue(ctx.nt_point_location()));
final NucleotideDuplication change;
if (ctx.nt_number() != null)
change = new NucleotideDuplication(false, range, new NucleotideSeqDescription(Integer.parseInt(ctx
.nt_number().getText())));
change = new NucleotideDuplication(false, range,
new NucleotideSeqDescription(Integer.parseInt(ctx.nt_number().getText())));
else if (ctx.nt_string() != null)
change = new NucleotideDuplication(false, range, new NucleotideSeqDescription(ctx.nt_string().getText()));
change = new NucleotideDuplication(false, range,
new NucleotideSeqDescription(ctx.nt_string().getText()));
else
change = new NucleotideDuplication(false, range, new NucleotideSeqDescription());
setValue(ctx, change);
Expand All @@ -328,18 +382,20 @@ else if (ctx.nt_string() != null)
/**
* Leaving of nt_change_insertion rule
*
* Construct {@link NucleotideInsertion} from children's values and labels and label ctx with this.
* Construct {@link NucleotideInsertion} from children's values and labels and label ctx with
* this.
*/
@Override
public void exitNt_change_insertion(Nt_change_insertionContext ctx) {
LOGGER.debug("Leaving nt_change_insertion");
final NucleotideRange range = (NucleotideRange) getValue(ctx.nt_range());
final NucleotideInsertion change;
if (ctx.nt_number() != null)
change = new NucleotideInsertion(false, range, new NucleotideSeqDescription(Integer.parseInt(ctx
.nt_number().getText())));
change = new NucleotideInsertion(false, range,
new NucleotideSeqDescription(Integer.parseInt(ctx.nt_number().getText())));
else if (ctx.nt_string() != null)
change = new NucleotideInsertion(false, range, new NucleotideSeqDescription(ctx.nt_string().getText()));
change = new NucleotideInsertion(false, range,
new NucleotideSeqDescription(ctx.nt_string().getText()));
else
change = new NucleotideInsertion(false, range, new NucleotideSeqDescription());
setValue(ctx, change);
Expand All @@ -348,18 +404,20 @@ else if (ctx.nt_string() != null)
/**
* Leaving of nt_change_inversion rule
*
* Construct {@link NucleotideInversion} from children's values and labels and label ctx with this.
* Construct {@link NucleotideInversion} from children's values and labels and label ctx with
* this.
*/
@Override
public void exitNt_change_inversion(Nt_change_inversionContext ctx) {
LOGGER.debug("Leaving nt_change_inversion");
final NucleotideRange range = (NucleotideRange) getValue(ctx.nt_range());
final NucleotideInversion change;
if (ctx.nt_number() != null)
change = new NucleotideInversion(false, range, new NucleotideSeqDescription(Integer.parseInt(ctx
.nt_number().getText())));
change = new NucleotideInversion(false, range,
new NucleotideSeqDescription(Integer.parseInt(ctx.nt_number().getText())));
else if (ctx.nt_string() != null)
change = new NucleotideInversion(false, range, new NucleotideSeqDescription(ctx.nt_string().getText()));
change = new NucleotideInversion(false, range,
new NucleotideSeqDescription(ctx.nt_string().getText()));
else
change = new NucleotideInversion(false, range, new NucleotideSeqDescription());
setValue(ctx, change);
Expand All @@ -368,20 +426,23 @@ else if (ctx.nt_string() != null)
/**
* Leaving of nt_change_substitution rule
*
* Construct {@link NucleotideSubstitution} from children's values and labels and label ctx with this.
* Construct {@link NucleotideSubstitution} from children's values and labels and label ctx with
* this.
*/
@Override
public void exitNt_change_substitution(Nt_change_substitutionContext ctx) {
LOGGER.debug("Leaving nt_change_substitution");
NucleotidePointLocation position = (NucleotidePointLocation) getValue(ctx.nt_point_location());
setValue(ctx, new NucleotideSubstitution(false, position, ctx.NT_STRING(0).getText(), ctx.NT_STRING(1)
.getText()));
NucleotidePointLocation position = (NucleotidePointLocation) getValue(
ctx.nt_point_location());
setValue(ctx, new NucleotideSubstitution(false, position, ctx.NT_STRING(0).getText(),
ctx.NT_STRING(1).getText()));
}

/**
* Leaving of nt_change_ssr rule
*
* Construct {@link NucleotideShortSequenceRepeatVariability} from the children's values and label ctx with this.
* Construct {@link NucleotideShortSequenceRepeatVariability} from the children's values and
* label ctx with this.
*/
@Override
public void exitNt_change_ssr(Nt_change_ssrContext ctx) {
Expand All @@ -395,7 +456,8 @@ public void exitNt_change_ssr(Nt_change_ssrContext ctx) {
(NucleotidePointLocation) getValue(ctx.nt_point_location()));
final int minCount = Integer.parseInt(ctx.NT_NUMBER(0).getText());
final int maxCount = Integer.parseInt(ctx.NT_NUMBER(1).getText());
setValue(ctx, new NucleotideShortSequenceRepeatVariability(false, range, minCount, maxCount));
setValue(ctx,
new NucleotideShortSequenceRepeatVariability(false, range, minCount, maxCount));
}

/**
Expand Down Expand Up @@ -424,7 +486,8 @@ public void exitReference(ReferenceContext ctx) {
transcriptID = ctx.REFERENCE(0).getText();
if (transcriptID.contains(".")) {
int pos = transcriptID.lastIndexOf('.');
transcriptVersion = Integer.parseInt(transcriptID.substring(pos + 1, transcriptID.length()));
transcriptVersion = Integer
.parseInt(transcriptID.substring(pos + 1, transcriptID.length()));
transcriptID = transcriptID.substring(0, pos);
}
if (ctx.PAREN_OPEN() != null)
Expand All @@ -439,25 +502,30 @@ public void exitReference(ReferenceContext ctx) {
@Override
public void exitNt_range(Nt_rangeContext ctx) {
LOGGER.debug("Leaving nt_range");
NucleotidePointLocation startPos = (NucleotidePointLocation) getValue(ctx.nt_point_location(0));
NucleotidePointLocation stopPos = (NucleotidePointLocation) getValue(ctx.nt_point_location(1));
NucleotidePointLocation startPos = (NucleotidePointLocation) getValue(
ctx.nt_point_location(0));
NucleotidePointLocation stopPos = (NucleotidePointLocation) getValue(
ctx.nt_point_location(1));
setValue(ctx, new NucleotideRange(startPos, stopPos));
}

/**
* Leaving of nt_point_location rule
*
* Construction {@link NucleotidePointLocation} from the children's values and label ctx with this.
* Construction {@link NucleotidePointLocation} from the children's values and label ctx with
* this.
*/
@Override
public void exitNt_point_location(Nt_point_locationContext ctx) {
LOGGER.debug("Leaving nt_point_location");
if (ctx.nt_offset() == null) {
setValue(ctx, getValue(ctx.nt_base_location()));
} else {
NucleotidePointLocation baseLoc = (NucleotidePointLocation) getValue(ctx.nt_base_location());
NucleotidePointLocation baseLoc = (NucleotidePointLocation) getValue(
ctx.nt_base_location());
Integer offset = (Integer) getValue(ctx.nt_offset());
setValue(ctx, new NucleotidePointLocation(baseLoc.getBasePos(), offset, baseLoc.isDownstreamOfCDS()));
setValue(ctx, new NucleotidePointLocation(baseLoc.getBasePos(), offset,
baseLoc.isDownstreamOfCDS()));
}
}

Expand Down Expand Up @@ -495,10 +563,10 @@ public void exitNt_offset(Nt_offsetContext ctx) {
@Override
public void exitLegacy_variant(Legacy_variantContext ctx) {
LOGGER.debug("Leaving legacy_variant");

String ref = ctx.reference().REFERENCE(0).getText();
LegacyChange change = (LegacyChange) getValue(ctx.getChild(1));
this.legacyVariant = new LegacyVariant(ref, change);
this.legacyVariant = new LegacyVariant(ref, change);
}

/**
Expand Down Expand Up @@ -611,7 +679,7 @@ public void exitLegacy_point_location(Legacy_point_locationContext ctx) {
int offset = Integer.parseInt(ctx.nt_number(1).getText());
if (ctx.NT_MINUS() != null)
offset = -offset;

if (ctx.LEGACY_IVS_OR_EX().getText().equals("IVS"))
setValue(ctx, LegacyLocation.buildIntronicLocation(featureNo, offset));
else
Expand Down
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