Fix unit tests and issue with "chrom.sizes" genomes.

igvteam · Aug 13, 2024 · 1a426ee · 1a426ee
1 parent 8c599b8
commit 1a426ee
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Showing 3 changed files with 9 additions and 9 deletions.
diff --git a/src/main/java/org/broad/igv/feature/genome/Genome.java b/src/main/java/org/broad/igv/feature/genome/Genome.java
@@ -139,7 +139,7 @@ public Genome(GenomeConfig config) throws IOException {
         List<Chromosome> chromosomeList = null;
         if (config.chromSizesURL != null) {
             chromosomeList = ChromSizesParser.parse(config.chromSizesURL);
-        } else if (sequence.hasChromosomes()) {
+        } else if (sequence != null && sequence.hasChromosomes()) {
             chromosomeList = sequence.getChromosomes();
         } else if (config.indexURL != null) {
             FastaIndex index = new FastaIndex(config.indexURL);
@@ -173,7 +173,7 @@ public Genome(GenomeConfig config) throws IOException {
 
         // Whole genome view is enabled by default if we have the chromosome information amd the
         // number of chromosomes is not too large
-        showWholeGenomeView = config.wholeGenomeView  &&
+        showWholeGenomeView = config.wholeGenomeView &&
                 chromosomeList.size() > 1 &&
                 longChromosomeNames.size() <= MAX_WHOLE_GENOME_LONG;
 
@@ -242,6 +242,7 @@ public Genome(String id, List<Chromosome> chromosomes) {
             chromosomeMap.put(chromosome.getName(), chromosome);
         }
         this.longChromosomeNames = computeLongChromosomeNames();
+        this.chromAliasSource = (new ChromAliasDefaults(id, chromosomeNames));
     }
 
     private void addTracks(GenomeConfig config) {
@@ -291,7 +292,9 @@ public String getCanonicalChrName(String str) {
                 ChromAlias aliasRecord = chromAliasSource.search(str);
                 if (aliasRecord != null) {
                     String chr = aliasRecord.getChr();
-                    chrAliasCache.put(str, chr);
+                    for (String a : aliasRecord.values()) {
+                        chrAliasCache.put(a, chr);
+                    }
                     return chr;
                 }
             } catch (IOException e) {
@@ -404,17 +407,16 @@ public Chromosome getChromosome(String name) {
         String chrName = getCanonicalChrName(name);
         if (chromosomeMap.containsKey(chrName)) {
             return chromosomeMap.get(chrName);
-        } else {
+        } else if (sequence != null) {
             int length = this.sequence.getChromosomeLength(chrName);
             if (length > 0) {
                 int idx = this.chromosomeMap.size();
                 Chromosome chromosome = new Chromosome(idx, chrName, length);
                 chromosomeMap.put(chrName, chromosome);
                 return chromosome;
-            } else {
-                return null;
             }
         }
+        return null;
     }
 
 

diff --git a/src/main/java/org/broad/igv/feature/genome/load/DotGenomeLoader.java b/src/main/java/org/broad/igv/feature/genome/load/DotGenomeLoader.java
@@ -102,7 +102,7 @@ public Genome loadGenome() throws IOException {
             config.fastaURL = sequencePath;
             config.indexURL =  sequencePath + ".fai";
             if (sequencePath.endsWith(".gz")) {
-                config.gziIndexURL = sequencePath + "gzi";
+                config.gziIndexURL = sequencePath + ".gzi";
             }
         }
 

diff --git a/src/test/java/org/broad/igv/tools/IGVToolsCountTest.java b/src/test/java/org/broad/igv/tools/IGVToolsCountTest.java
@@ -93,8 +93,6 @@ public void testCountBEDoutWig() throws Exception {
     @Test
     public void testCountBEDoutWigCheckBW() throws Exception {
 
-        GenomeUtils.main(null);
-
         String inputFile = TestUtils.DATA_DIR + "bed/test2.bed";
         String fullout = TestUtils.TMP_OUTPUT_DIR + "twig.wig";
         String input = "count " + inputFile + " " + fullout + " " + genomePath;