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feat(nanno): if snpeff deems a variant to be in multiple genes report them all #400

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6516f60
feat(nanno): if snpeff deems a variant to be in multiple genes report…
holmeso Feb 27, 2026
460c9c4
Initial plan
Copilot Feb 27, 2026
2d606cc
Initial plan
Copilot Feb 27, 2026
283d201
fix: guard against mismatched array lengths in extractFieldsFromRecord
Copilot Feb 27, 2026
0cd751f
Initial plan
Copilot Feb 27, 2026
d431245
fix: preserve user-requested field order in AnnotationSourceTSV by it…
Copilot Feb 27, 2026
79cc951
fix: use LinkedHashMap in getHeaderNameAndPositions to preserve user-…
Copilot Feb 27, 2026
6f724e2
Merge pull request #401 from AdamaJava/copilot/sub-pr-400
holmeso Feb 27, 2026
d646599
fix: remove --enable-preview, fix Executor classpath quoting, update …
Copilot Feb 27, 2026
f3e112a
revert: remove Executor.java changes from this PR
Copilot Mar 3, 2026
cbf60aa
Merge pull request #402 from AdamaJava/copilot/sub-pr-400-again
holmeso Mar 3, 2026
623d911
test: add test verifying user-requested field order is preserved in a…
Copilot Mar 3, 2026
993ffb3
Merge pull request #403 from AdamaJava/copilot/sub-pr-400-another-one
holmeso Mar 3, 2026
fa8743e
Apply suggestion from @Copilot
holmeso Mar 3, 2026
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33 changes: 16 additions & 17 deletions qannotate/src/au/edu/qimr/qannotate/nanno/AnnotationSource.java
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Original file line number Diff line number Diff line change
Expand Up @@ -78,25 +78,24 @@ public String getAnnotation(long requestedCpAsLong, ChrPosition requestedCp) {
* lets see if there are any records that match on ref and alt
*/
return getAnnotationsFromCurrentRecords(requestedCp);
}

} else {
int matchWithNextCP = Long.compare(requestedCpAsLong, nextCPAsLong);
if (nextCPAsLong > -1 && matchWithNextCP < 0) {
/*
* requestedCp is "less than" next CP
* return empty list here
*/
} else {
// logger.debug(reader.getFile().getName() + ": getting next record. requestedCp: " + (null != requestedCp ? requestedCp.toIGVString() : null) + ", currentCP: " + (null != currentCP ? currentCP.toIGVString() : null));
getNextRecord(requestedCpAsLong, matchWithNextCP);
if (requestedCpAsLong == currentCPAsLong) {
return getAnnotationsFromCurrentRecords(requestedCp);
}
/*
* requestedCP and currentCP are not equal
*/
}
int matchWithNextCP = Long.compare(requestedCpAsLong, nextCPAsLong);
if (nextCPAsLong > -1 && matchWithNextCP < 0) {
/*
* requestedCp is "less than" next CP
* return empty list here
*/
return annotationToReturn(null);
}

getNextRecord(requestedCpAsLong, matchWithNextCP);
if (requestedCpAsLong == currentCPAsLong) {
return getAnnotationsFromCurrentRecords(requestedCp);
}
/*
* requestedCP and currentCP are not equal
*/
return annotationToReturn(null);
}

Expand Down
115 changes: 38 additions & 77 deletions qannotate/src/au/edu/qimr/qannotate/nanno/AnnotationSourceSnpEffVCF.java
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Expand Up @@ -62,8 +62,6 @@ public AnnotationSourceSnpEffVCF(RecordReader<String> reader, int chrPositionInR
@Override
public String getAnnotation(long requestedCpAsLong, ChrPosition requestedCp) {

// logger.debug(reader.getFile().getName() + ": requestedCp is " + (null != requestedCp ? requestedCp.toIGVString() : null) + ", currentCP: " + (null != currentCP ? currentCP.toIGVString() : null) + ", nextCP: " + (null != nextCP ? nextCP.toIGVString() : null));

/*
* check to see if the records we currently have stored are a match
*/
Expand All @@ -73,70 +71,21 @@ public String getAnnotation(long requestedCpAsLong, ChrPosition requestedCp) {
* we match on position
* lets see if there are any records that match on ref and alt
*/
// return getAnnotationsFromRecords(requestedCp);
if (requestedCp instanceof ChrPositionRefAlt reqCpRefAlt) {
String reqRef = reqCpRefAlt.getRef();
String reqAlt = reqCpRefAlt.getAlt();
for (String rec : currentRecords) {
String[] recArray = TabTokenizer.tokenize(rec, DEFAULT_DELIMITER);
String recRef = recArray[refPositionInFile];
String recAlt = recArray[altPositionInFile];

if (recAlt.contains(",")) {
String[] recAltArray = recAlt.split(",");
for (String recAltValue : recAltArray) {
if (reqRef.equals(recRef) && reqAlt.equals(recAltValue)) {
return annotationToReturnWithAlt(rec, recAltValue);
}
}
} else {
if (reqRef.equals(recRef) && reqAlt.equals(recAlt)) {
return annotationToReturnWithAlt(rec, recAlt);
}
}
}
}

return getAnnotationsFromRecords(requestedCp);
} else {
int matchWithNextCP = Long.compare(requestedCpAsLong, nextCPAsLong);
if (nextCPAsLong > -1 && matchWithNextCP < 0) {

} else {

// logger.debug(reader.getFile().getName() + ": getting next record. requestedCp: " + (null != requestedCp ? requestedCp.toIGVString() : null) + ", currentCP: " + (null != currentCP ? currentCP.toIGVString() : null));
getNextRecord(requestedCpAsLong, matchWithNextCP);
if (requestedCpAsLong == currentCPAsLong) {
/*
* we match on position
* lets see if there are any records that match on ref and alt
*/
if (requestedCp instanceof ChrPositionRefAlt reqCpRefAlt) {
String reqRef = reqCpRefAlt.getRef();
String reqAlt = reqCpRefAlt.getAlt();
for (String rec : currentRecords) {
String[] recArray = TabTokenizer.tokenize(rec, DEFAULT_DELIMITER);
String recRef = recArray[refPositionInFile];
String recAlt = recArray[altPositionInFile];

if (recAlt.contains(",")) {
String[] recAltArray = recAlt.split(",");
for (String recAltValue : recAltArray) {
if (reqRef.equals(recRef) && reqAlt.equals(recAltValue)) {
return annotationToReturnWithAlt(rec, recAltValue);
}
}
} else {
if (reqRef.equals(recRef) && reqAlt.equals(recAlt)) {
return annotationToReturnWithAlt(rec, recAlt);
}
}
}
}
// return getAnnotationsFromRecords(requestedCp);
return getAnnotationsFromRecords(requestedCp);
}
/*
* requestedCP and currentCP are not equal
*/
}
}
return annotationToReturn(null);
Expand All @@ -151,7 +100,7 @@ private String getAnnotationsFromRecords(ChrPosition requestedCp){
String recRef = recArray[refPositionInFile];
String recAlt = recArray[altPositionInFile];

if (recAlt.contains(",")) {
if (recAlt.indexOf(',') >= 0) {
String[] recAltArray = recAlt.split(",");
for (String recAltValue : recAltArray) {
if (reqRef.equals(recRef) && reqAlt.equals(recAltValue)) {
Expand All @@ -177,7 +126,6 @@ public String annotationToReturn(String[] record) {
* dealing with a vcf file and assuming that the required annotation fields are in the INFO field
* so get that and go from there.
*/
// String[] recordArray = record.split("\t");
String info = record[7];
String alt = record[4];

Expand Down Expand Up @@ -221,32 +169,31 @@ public static String extractFieldsFromInfoField(String info, List<String> fields
if (StringUtils.isNullOrEmpty(worstConsequence)) {
return emptyInfoFieldResult;
}

/*
* we have our consequence
* split by pipe and then get our fields
* we have our consequences (comma-delimited)
* split by comma into consequences, then by pipe into fields
*/
String[] consequenceArray = TabTokenizer.tokenize(worstConsequence, '|');
String[] consequences = worstConsequence.split(",");

for (String af : fields) {
if (!StringUtils.isNullOrEmpty(af)) {

/*
* get position from map
*/
String aflc = af.toLowerCase();
Integer arrayPosition = SNP_EFF_ANNOTATION_FIELDS_AND_POSITIONS.get(aflc);
if (null != arrayPosition && arrayPosition >= 0 && arrayPosition < consequenceArray.length) {
/*
* good
*/
String annotation = consequenceArray[arrayPosition];
dataToReturn.append((!dataToReturn.isEmpty()) ? FIELD_DELIMITER_TAB + af + "=" + annotation : af + "=" + annotation);
} else {
// System.out.println("Could not find field [" + af + "] in SNP_EFF_ANNOTATION_FIELDS_AND_POSITIONS map!");
// System.out.println("arrayPosition.intValue(): " + arrayPosition.intValue() + ", consequenceArray.length: " + consequenceArray.length);
}

if (null != arrayPosition) {
StringBuilder fieldValues = new StringBuilder();
for (String consequence : consequences) {
String[] consequenceArray = TabTokenizer.tokenize(consequence, '|');
if (arrayPosition >= 0 && arrayPosition < consequenceArray.length) {
String annotation = consequenceArray[arrayPosition];
fieldValues.append(fieldValues.isEmpty() ? annotation : "|" + annotation);
}
}
dataToReturn.append((!dataToReturn.isEmpty())
? FIELD_DELIMITER_TAB + af + "=" + fieldValues
: af + "=" + fieldValues);
}
}
}
return (dataToReturn.isEmpty()) ? emptyInfoFieldResult : dataToReturn.toString();
Expand Down Expand Up @@ -283,19 +230,33 @@ public static String getWorstConsequence(String info, String alt) {
* Pick the first one as that is the one with the highest effect as decreed by snpEff
*/
int annoIndex = info.indexOf("ANN=");
if (annoIndex < 0) {
return "";
}
int end = info.indexOf(FIELD_DELIMITER_SEMI_COLON, annoIndex);
String ann = info.substring(annoIndex + 4, end == -1 ? info.length() : end);


String[] annArray = ann.split(",");
String worstConsequence = "";
Map<String, String> worstByGene = new java.util.LinkedHashMap<>();
for (String aa : annArray) {
if (aa.startsWith(alt)) {
worstConsequence = aa;
break;
int pipeIndex = aa.indexOf('|');
if (pipeIndex <= 0) {
// Malformed ANN entry or missing allele token; skip
continue;
}
String alleleToken = aa.substring(0, pipeIndex);
if (alleleToken.equals(alt)) {
String[] parts = TabTokenizer.tokenize(aa, '|');
if (parts.length > 3) {
String gene = parts[3];
if (!StringUtils.isNullOrEmpty(gene) && !worstByGene.containsKey(gene)) {
worstByGene.put(gene, aa);
}
}
}
}
return worstConsequence;
return String.join(",", worstByGene.values());
}

@Override
Expand Down
32 changes: 20 additions & 12 deletions qannotate/src/au/edu/qimr/qannotate/nanno/AnnotationSourceTSV.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
import java.io.IOException;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
Expand All @@ -19,6 +19,9 @@ public class AnnotationSourceTSV extends AnnotationSource {
List<String> headerLines;
Map<String, Integer> headerNameAndPosition;

private String[] fieldNames;
private int[] fieldPositions;

public AnnotationSourceTSV(RecordReader<String> reader, int chrPositionInRecord, int positionPositionInRecord,
int refPositionInFile, int altPositionInFile, String fieldNames, boolean chrStartsWithChr) {
super(reader, chrPositionInRecord, positionPositionInRecord, refPositionInFile, altPositionInFile, chrStartsWithChr);
Expand Down Expand Up @@ -46,6 +49,13 @@ public AnnotationSourceTSV(RecordReader<String> reader, int chrPositionInRecord,
if (headerNameAndPosition.isEmpty()) {
throw new IllegalArgumentException("Could not find requested fields (" + fieldNames + ") in header: " + headerLine);
}
// precompute arrays for fast extraction, preserving user-requested field order
String[] requestedFields = fieldNames.split(",");
this.fieldNames = requestedFields;
this.fieldPositions = new int[requestedFields.length];
for (int i = 0; i < requestedFields.length; i++) {
this.fieldPositions[i] = headerNameAndPosition.get(requestedFields[i]);
}
}

/*
Expand All @@ -72,7 +82,7 @@ public static String getLastHeaderLine(List<String> headerLines) {
* return an empty map if any of the fields are not in the header
*/
public static Map<String, Integer> getHeaderNameAndPositions(String fieldNames, String header) {
Map<String, Integer> namePositions = new HashMap<>();
Map<String, Integer> namePositions = new LinkedHashMap<>();

System.out.println("header: " + header);

Expand All @@ -96,20 +106,18 @@ public String annotationToReturn(String[] record) {
/*
* entries in the INFO field are delimited by ';'
*/
return extractFieldsFromRecord(record, headerNameAndPosition);
return extractFieldsFromRecord(record, fieldNames, fieldPositions);
}

public static String extractFieldsFromRecord(String[] record, Map<String, Integer> fields) {
public static String extractFieldsFromRecord(String[] record, String[] fieldNames, int[] fieldPositions) {
StringBuilder dataToReturn = new StringBuilder();
int recordLength = null != record ? record.length : 0;
if ( recordLength > 0 && null != fields) {
// String [] recordArray = TabTokenizer.tokenize(record);
for (Entry<String, Integer> entry : fields.entrySet()) {
/*
* make sure that array length is not shorter than entry value
*/
if (recordLength > entry.getValue()) {
dataToReturn.append(( ! dataToReturn.isEmpty()) ? FIELD_DELIMITER_TAB : "").append(entry.getKey()).append("=").append(record[entry.getValue()]);
if (recordLength > 0 && null != fieldNames && null != fieldPositions) {
for (int i = 0; i < Math.min(fieldNames.length, fieldPositions.length); i++) {
int pos = fieldPositions[i];
if (recordLength > pos) {
dataToReturn.append((!dataToReturn.isEmpty()) ? FIELD_DELIMITER_TAB : "")
.append(fieldNames[i]).append("=").append(record[pos]);
}
}
}
Expand Down
57 changes: 44 additions & 13 deletions qannotate/src/au/edu/qimr/qannotate/nanno/AnnotationSourceVCF.java
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Expand Up @@ -2,7 +2,9 @@

import java.io.IOException;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;

import org.qcmg.common.string.StringUtils;
Expand All @@ -11,7 +13,8 @@
public class AnnotationSourceVCF extends AnnotationSource {

public static final String FIELD_DELIMITER_SEMI_COLON = ";";

private static final int INFO_LENGTH_PARSE_THRESHOLD = 2000;
private static final int FIELDS_PARSE_THRESHOLD = 3;


List<String> annotationFields;
Expand Down Expand Up @@ -52,24 +55,52 @@ public String annotationToReturn(String [] record) {


public static String extractFieldsFromInfoField(String info, List<String> fields, String emptyInfoFieldResult) {
if (StringUtils.isNullOrEmptyOrMissingData(info)) {
if (StringUtils.isNullOrEmptyOrMissingData(info) || fields == null) {
return emptyInfoFieldResult;
}
StringBuilder dataToReturn = new StringBuilder();
for (String af : fields) {
if ( ! StringUtils.isNullOrEmpty(af)) {
int start = info.indexOf(af + "=");
if (start > -1) {
int end = info.indexOf(FIELD_DELIMITER_SEMI_COLON, start);
if (end == -1) {
dataToReturn.append((!dataToReturn.isEmpty()) ? FIELD_DELIMITER_TAB + info.substring(start) : info.substring(start));
boolean parseOnce = (fields.size() > FIELDS_PARSE_THRESHOLD) || info.length() > INFO_LENGTH_PARSE_THRESHOLD;
if ( ! parseOnce) {
StringBuilder dataToReturn = new StringBuilder();
for (String af : fields) {
if (!StringUtils.isNullOrEmpty(af)) {
int start = info.indexOf(af + "=");
if (start > -1) {
int end = info.indexOf(FIELD_DELIMITER_SEMI_COLON, start);
if (end == -1) {
dataToReturn.append((!dataToReturn.isEmpty()) ? FIELD_DELIMITER_TAB + info.substring(start) : info.substring(start));
} else {
dataToReturn.append((!dataToReturn.isEmpty()) ? FIELD_DELIMITER_TAB + info.substring(start, end) : info.substring(start, end));
}
} else {
dataToReturn.append((!dataToReturn.isEmpty()) ? FIELD_DELIMITER_TAB + info.substring(start, end) : info.substring(start, end));
dataToReturn.append((!dataToReturn.isEmpty()) ? FIELD_DELIMITER_TAB + af + "=" : af + "=");
}
} else {
dataToReturn.append((!dataToReturn.isEmpty()) ? FIELD_DELIMITER_TAB + af + "=" : af + "=");
}
}
return (dataToReturn.isEmpty()) ? emptyInfoFieldResult : dataToReturn.toString();
}
Map<String, String> infoMap = new HashMap<>();
int start = 0;
while (start <= info.length()) {
int end = info.indexOf(FIELD_DELIMITER_SEMI_COLON, start);
if (end == -1) end = info.length();

String token = info.substring(start, end);
int eq = token.indexOf('=');
if (eq > -1) {
infoMap.put(token.substring(0, eq), token.substring(eq + 1));
} else if (!token.isEmpty()) {
infoMap.put(token, "");
}

start = end + 1;
}
StringBuilder dataToReturn = new StringBuilder();
for (String af : fields) {
if (!StringUtils.isNullOrEmpty(af)) {
String value = infoMap.get(af);
String entry = (value != null) ? af + "=" + value : af + "=";
dataToReturn.append((!dataToReturn.isEmpty()) ? FIELD_DELIMITER_TAB : "").append(entry);
}
}
return (dataToReturn.isEmpty()) ? emptyInfoFieldResult : dataToReturn.toString();
}
Expand Down
2 changes: 1 addition & 1 deletion qannotate/test/au/edu/qimr/qannotate/nanno/AnnotateTest.java
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Expand Up @@ -115,7 +115,7 @@ public void jsonInputsTSV() throws IOException {
AnnotateUtils.populateAnnotationSources(ais, sources);
assertEquals(1, sources.size());
String annotation = sources.getFirst().getAnnotation(ChrPositionUtils.convertContigAndPositionToLong("1", 655652), new ChrPositionRefAlt("chr1", 655652, 655652, "A", "T"));
assertEquals("HGVSc_VEP=c.1A>C\tHGVSp_VEP=p.Met1?\taaref=M", annotation);
assertEquals("aaref=M\tHGVSc_VEP=c.1A>C\tHGVSp_VEP=p.Met1?", annotation);
}

@Test
Expand Down
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