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Merged
holmeso merged 5 commits into from
May 15, 2025
Merged

fix(nanno): deal with contig names that include numbers and letters #390

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a9dc44a
fix(nanno): deal with contig names that include numbers and letters, …
holmeso May 15, 2025
c0d4fb0
cache string length
holmeso May 15, 2025
eafe32b
Update qcommon/src/org/qcmg/common/util/ChrPositionUtils.java
holmeso May 15, 2025
4d150bc
Update qannotate/src/au/edu/qimr/qannotate/nanno/Annotate.java
holmeso May 15, 2025
9079391
suggestions from copliot review implemented
holmeso May 15, 2025
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104 changes: 61 additions & 43 deletions qannotate/src/au/edu/qimr/qannotate/nanno/Annotate.java
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,13 @@ public class Annotate {

static final List<String> SEARCH_TERM_VARIETIES = Arrays.asList(">", "->", "-->", "/");

// Define the set of standard GRCh38 contigs (no "chr" prefix version)
private static final Set<String> STANDARD_GRCH38_CONTIGS = Set.of(
"1", "2", "3", "4", "5", "6", "7", "8", "9", "10",
"11", "12", "13", "14", "15", "16", "17", "18", "19", "20",
"21", "22", "X", "Y", "MT", "M"
);

static Comparator<String[]> CUSTOM_COMPARATOR;
static QLogger logger;

Expand Down Expand Up @@ -71,70 +78,77 @@ public int engage() throws Exception {

ChrPosition lastCP = null;
try (
VcfFileReader reader = new VcfFileReader(inputFile)) {
VcfFileReader reader = new VcfFileReader(inputFile)) {
logger.info("VcfFileReader has been setup");
int vcfCount = 0;
int nonStandardContigCount = 0;
for (VcfRecord vcf : reader) {
vcfCount++;

ChrPosition thisVcfsCP = vcf.getChrPositionRefAlt();
logger.debug("thisVcfsCP: " + thisVcfsCP.toIGVString());

boolean isStandardContig = isStandardContig(thisVcfsCP);
if (isStandardContig) {

/*
* check that this CP is "after" the last CP
*/
int compare = null != lastCP ? ((ChrPositionRefAlt) thisVcfsCP).compareTo((ChrPositionRefAlt) lastCP) : 0;
if (compare < 0) {
throw new IllegalArgumentException("Incorrect order of vcf records in input vcf file! this vcf: " + thisVcfsCP.toIGVString() + ", last vcf: " + lastCP.toIGVString());
}


String alt = ((ChrPositionRefAlt) thisVcfsCP).getAlt();
String gatkAD = VcfUtils.getFormatField(vcf.getFormatFields(), "AD", 0);
String gatkGT = VcfUtils.getFormatField(vcf.getFormatFields(), "GT", 0);

if (alt.contains(",")) {
logger.info("alt has comma: " + thisVcfsCP);
/*
* split record, create new ChrPositions for each
* check that this CP is "after" the last CP
*/
String[] altArray = alt.split(",");
List<VcfRecord> splitVcfs = new ArrayList<>();
for (String thisAlt : altArray) {
if (thisAlt.equals("*")) {
/*
* ignore
*/
} else {
VcfRecord newVcf = VcfUtils.cloneWithNewAlt(vcf, thisAlt);
splitVcfs.add(newVcf);
}
int compare = null != lastCP ? ((ChrPositionRefAlt) thisVcfsCP).compareTo((ChrPositionRefAlt) lastCP) : 0;
if (compare < 0) {
throw new IllegalArgumentException("Incorrect order of vcf records in input vcf file! this vcf: " + thisVcfsCP.toIGVString() + ", last vcf: " + lastCP.toIGVString());
}
if (splitVcfs.size() > 1) {


String alt = ((ChrPositionRefAlt) thisVcfsCP).getAlt();
String gatkAD = VcfUtils.getFormatField(vcf.getFormatFields(), "AD", 0);
String gatkGT = VcfUtils.getFormatField(vcf.getFormatFields(), "GT", 0);

if (alt.contains(",")) {
logger.info("alt has comma: " + thisVcfsCP);
/*
* sort
* split record, create new ChrPositions for each
*/
splitVcfs.sort(null);
}
for (VcfRecord splitVcf : splitVcfs) {
List<String> annotations = new ArrayList<>(getAnnotationsForPosition(splitVcf.getChrPositionRefAlt(), annotationSources, executor));
queue.add(new ChrPositionAnnotations(splitVcf.getChrPositionRefAlt(), annotations, gatkAD, gatkGT, alt));
}
String[] altArray = alt.split(",");
List<VcfRecord> splitVcfs = new ArrayList<>();
for (String thisAlt : altArray) {
if (thisAlt.equals("*")) {
/*
* ignore
*/
} else {
VcfRecord newVcf = VcfUtils.cloneWithNewAlt(vcf, thisAlt);
splitVcfs.add(newVcf);
}
}
if (splitVcfs.size() > 1) {
/*
* sort
*/
splitVcfs.sort(null);
}
for (VcfRecord splitVcf : splitVcfs) {
List<String> annotations = new ArrayList<>(getAnnotationsForPosition(splitVcf.getChrPositionRefAlt(), annotationSources, executor));
queue.add(new ChrPositionAnnotations(splitVcf.getChrPositionRefAlt(), annotations, gatkAD, gatkGT, alt));
}

} else {
} else {

logger.debug("about to get annotations for: " + thisVcfsCP.toIGVString());
List<String> annotations = getAnnotationsForPosition(thisVcfsCP, annotationSources, executor);
logger.debug("got annotations for: " + thisVcfsCP.toIGVString() + " - adding to queue");
queue.add(new ChrPositionAnnotations(thisVcfsCP, annotations, gatkAD, gatkGT, alt));
logger.debug("about to get annotations for: " + thisVcfsCP.toIGVString());
List<String> annotations = getAnnotationsForPosition(thisVcfsCP, annotationSources, executor);
logger.debug("got annotations for: " + thisVcfsCP.toIGVString() + " - adding to queue");
queue.add(new ChrPositionAnnotations(thisVcfsCP, annotations, gatkAD, gatkGT, alt));

}
}

lastCP = thisVcfsCP;
lastCP = thisVcfsCP;
} else {
nonStandardContigCount++;
}
}

logger.info("# of vcf records: " + vcfCount);
logger.info("# of vcf records: " + vcfCount + ", # of non-standard contigs: " + nonStandardContigCount);
} finally {
/*
* count down the count down latch
Expand All @@ -147,6 +161,10 @@ public int engage() throws Exception {
return exitStatus;
}

private boolean isStandardContig(ChrPosition thisVcfsCP) {
return thisVcfsCP.getChromosome().startsWith("chr") ? STANDARD_GRCH38_CONTIGS.contains(thisVcfsCP.getChromosome().substring(3)) : STANDARD_GRCH38_CONTIGS.contains(thisVcfsCP.getChromosome());
}


private static List<String> getAnnotationsForPosition(ChrPosition cp, List<AnnotationSource> annotationSources, Executor executor) {
long contigAndPosition = ((ChrPositionUtils.convertContigAndPositionToLong(cp.getChromosome().startsWith("chr") ? cp.getChromosome().substring(3) : cp.getChromosome(), cp.getStartPosition())));
Expand Down
13 changes: 10 additions & 3 deletions qcommon/src/org/qcmg/common/util/ChrPositionUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -64,11 +64,14 @@ public static int convertContigNameToInt(String contigName) {
if (null == contigName || contigName.isEmpty()) {
throw new IllegalArgumentException("null or empty contig name supplied to convertContigNameToInt");
}
int i = Character.isDigit(contigName.charAt(0)) ? Integer.parseInt(contigName) : -1;
if (i > -1) {
return i;
// check if the contig name is a number
// if so, return it as an int
// otherwise, convert it to a hash code
if (isDigits(contigName)) {
return Integer.parseInt(contigName);
}


if (contigName.length() > 3 && contigName.startsWith("chr")) {
return convertContigNameToInt(contigName.substring(3));
}
Expand All @@ -81,6 +84,10 @@ public static int convertContigNameToInt(String contigName) {
};
}

public static boolean isDigits(String str) {
return str != null && !str.isEmpty() && str.chars().allMatch(Character::isDigit);
}

/**
* Checks if two ChrPosition objects overlap with a buffer.
*
Expand Down
55 changes: 55 additions & 0 deletions qcommon/test/org/qcmg/common/util/ChrPositionUtilsTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,61 @@ public void testDelta() {
assertTrue(ChrPositionUtils.arePositionsWithinDelta(cp1, cp2, 4));
}

@Test
public void testConvertContigNameToInt_NumericContig() {
assertEquals(1, ChrPositionUtils.convertContigNameToInt("1"));
assertEquals(22, ChrPositionUtils.convertContigNameToInt("22"));
}

@Test
public void testConvertContigNameToInt_ChromosomeWithChrPrefix() {
assertEquals(1, ChrPositionUtils.convertContigNameToInt("chr1"));
assertEquals(22, ChrPositionUtils.convertContigNameToInt("chr22"));
}

@Test
public void testConvertContigNameToInt_SexChromosomes() {
assertEquals(23, ChrPositionUtils.convertContigNameToInt("X"));
assertEquals(24, ChrPositionUtils.convertContigNameToInt("Y"));
}

@Test
public void testConvertContigNameToInt_Mitochondrial() {
assertEquals(25, ChrPositionUtils.convertContigNameToInt("M"));
assertEquals(25, ChrPositionUtils.convertContigNameToInt("MT"));
}

@Test
public void testConvertContigNameToInt_ChromosomeWithChrPrefixSpecialCases() {
assertEquals(23, ChrPositionUtils.convertContigNameToInt("chrX"));
assertEquals(24, ChrPositionUtils.convertContigNameToInt("chrY"));
assertEquals(25, ChrPositionUtils.convertContigNameToInt("chrM"));
}

@Test
public void testConvertContigNameToInt_AltChromosome() {
assertEquals("22_KI270739v1_random".hashCode(), ChrPositionUtils.convertContigNameToInt("chr22_KI270739v1_random"));
assertEquals("Y_KI270740v1_random".hashCode(), ChrPositionUtils.convertContigNameToInt("chrY_KI270740v1_random"));
assertEquals("Un_KI270302v1".hashCode(), ChrPositionUtils.convertContigNameToInt("chrUn_KI270302v1"));
}

@Test
public void testConvertContigNameToInt_OtherValues() {
// For other values, it should return hashCode
String contig = "other";
assertEquals(contig.hashCode(), ChrPositionUtils.convertContigNameToInt(contig));
}

@Test(expected = IllegalArgumentException.class)
public void testConvertContigNameToInt_NullInput() {
ChrPositionUtils.convertContigNameToInt(null);
}

@Test(expected = IllegalArgumentException.class)
public void testConvertContigNameToInt_EmptyInput() {
ChrPositionUtils.convertContigNameToInt("");
}

@Test
public void testConvertChrPositionToLong() {
long expected = ((long) 4 << 32) + 9;
Expand Down