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Add case-insensitive search to chrom aliasing code #1621

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merged 1 commit into from
Nov 19, 2024
Merged

Add case-insensitive search to chrom aliasing code #1621

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26 changes: 0 additions & 26 deletions src/main/java/org/broad/igv/feature/genome/ChromAliasBB.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,6 @@
import org.broad.igv.feature.BasicFeature;
import org.broad.igv.ucsc.bb.BBFile;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;

public class ChromAliasBB extends ChromAliasSource {

Expand All @@ -16,30 +14,6 @@ public ChromAliasBB(String path, Genome genome) throws IOException {
}


/**
* Return the canonical chromosome name for the alias. If none found return the alias
*
* @param alias
* @returns {*}
*/
public String getChromosomeName(String alias) {
if(aliasCache.containsKey(alias)) {
return aliasCache.get(alias).getChr();
} else {
try {
ChromAlias aliasRecord = search(alias);
if(aliasRecord == null) {
aliasRecord.put(alias, null); // Prevents future attempts
} else {
return aliasRecord.getChr();
}
} catch (IOException e) {
// TODO -- log
}
}
return null;
}

/**
* Return an alternate chromosome name (alias).
*
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11 changes: 0 additions & 11 deletions src/main/java/org/broad/igv/feature/genome/ChromAliasDefaults.java
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Expand Up @@ -118,17 +118,6 @@ private void init(String id, List<String> chromosomeNames) {
}
}

/**
* Return the canonical chromosome name for the alias. If none found return the alias
*
* @param alias
* @returns {*}
*/
@Override
public String getChromosomeName(String alias) {
return this.aliasCache.containsKey(alias) ? this.aliasCache.get(alias).getChr() : alias;
}

/**
* Return an alternate chromosome name (alias).
*
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10 changes: 0 additions & 10 deletions src/main/java/org/broad/igv/feature/genome/ChromAliasFile.java
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Expand Up @@ -99,16 +99,6 @@ public ChromAliasFile(List<List<String>> chromAliases, List<String> chromosomeNa
}


/**
* Return the canonical chromosome name for the alias. If none found return the alias
*
* @param alias
* @returns {*}
*/
public String getChromosomeName(String alias) {
return this.aliasCache.containsKey(alias) ? this.aliasCache.get(alias).getChr() : alias;
}

/**
* Return an alternate chromosome name (alias).
*
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2 changes: 0 additions & 2 deletions src/main/java/org/broad/igv/feature/genome/ChromAliasSource.java
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Expand Up @@ -12,8 +12,6 @@ public ChromAliasSource() {
aliasCache = new HashMap<>();
}

public abstract String getChromosomeName(String alias);

public abstract String getChromosomeAlias(String chr, String nameSet);

public abstract ChromAlias search(String alias) throws IOException;
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10 changes: 9 additions & 1 deletion src/main/java/org/broad/igv/feature/genome/Genome.java
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Expand Up @@ -293,16 +293,24 @@ private void addTracks(GenomeConfig config) {
public String getCanonicalChrName(String str) {
if (str == null) {
return str;
} else if (chrAliasCache.containsKey(str)) {
}

if (chrAliasCache.containsKey(str)) {
return chrAliasCache.get(str);
} else if (chromAliasSource != null) {
try {
ChromAlias aliasRecord = chromAliasSource.search(str);

if(aliasRecord == null && !str.equals(str.toLowerCase())) {
aliasRecord = chromAliasSource.search(str.toLowerCase());
}

if (aliasRecord != null) {
String chr = aliasRecord.getChr();
for (String a : aliasRecord.values()) {
chrAliasCache.put(a, chr);
}
chrAliasCache.put(str, chr); // Usually redundant, but will catch lowercase search case
return chr;
}
} catch (IOException e) {
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6 changes: 3 additions & 3 deletions src/test/java/org/broad/igv/feature/genome/ChromAliasBBTest.java
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Expand Up @@ -23,9 +23,9 @@ public static void setup() {
public void getChromosomeName() throws IOException {
String path = "test/data/genomes/GCF_000002655.1.chromAlias.bb";
ChromAliasSource chromAlias = new ChromAliasBB(path, mockGenome);
assertEquals("NC_007194.1", chromAlias.getChromosomeName("CM000169.1")) ;
assertEquals("NC_007194.1", chromAlias.getChromosomeName( "1"));
assertEquals("NC_007194.1", chromAlias.getChromosomeName( "chr1"));
assertEquals("NC_007194.1", chromAlias.search("CM000169.1").getChr());
assertEquals("NC_007194.1", chromAlias.search( "1").getChr());
assertEquals("NC_007194.1", chromAlias.search( "chr1").getChr());
}

@Test
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10 changes: 6 additions & 4 deletions src/test/java/org/broad/igv/feature/genome/ChromAliasDefaultsTest.java
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Expand Up @@ -48,11 +48,13 @@ public static void setup() {
@Test
public void getCanonicalChromosomeName() {

assertEquals(ncibMockGenome.getCanonicalChrName("chrX"), "23");
assertEquals(ncibMockGenome.getCanonicalChrName("chrM"), "MT");
assertEquals("23", ncibMockGenome.getCanonicalChrName("chrX"));
assertEquals("MT", ncibMockGenome.getCanonicalChrName("chrM"));

assertEquals(ucscMockGenome.getCanonicalChrName("23"), "chrX");
assertEquals(ucscMockGenome.getCanonicalChrName("MT"), "chrM");
assertEquals("chrX", ucscMockGenome.getCanonicalChrName("23"));
assertEquals("chrM", ucscMockGenome.getCanonicalChrName("MT"));

assertEquals("chr1", ucscMockGenome.getCanonicalChrName("Chr1"));

}

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6 changes: 3 additions & 3 deletions src/test/java/org/broad/igv/feature/genome/ChromAliasFileTest.java
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Expand Up @@ -25,9 +25,9 @@ public static void setup() {
public void getChromosomeName() throws IOException {
String path = TestUtils.DATA_DIR + "genomes/GCF_000002655.1.chromAlias.txt";
ChromAliasFile chromAlias = new ChromAliasFile(path, mockGenome.getChromosomeNames());
assertEquals("NC_007194.1", chromAlias.getChromosomeName("CM000169.1")) ;
assertEquals("NC_007194.1", chromAlias.getChromosomeName( "1"));
assertEquals("NC_007194.1", chromAlias.getChromosomeName( "chr1"));
assertEquals("NC_007194.1", chromAlias.search("CM000169.1").getChr()) ;
assertEquals("NC_007194.1", chromAlias.search( "1").getChr());
assertEquals("NC_007194.1", chromAlias.search( "chr1").getChr());
}

@Test
Expand Down
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