bug fixes

igvteam · Nov 27, 2023 · 5c6decd · 5c6decd
1 parent 835ea84
commit 5c6decd
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Showing 39 changed files with 617 additions and 815 deletions.
diff --git a/src/main/java/org/broad/igv/bbfile/BBDataSource.java b/src/main/java/org/broad/igv/bbfile/BBDataSource.java
@@ -326,7 +326,7 @@ private List<LocusScore> getWholeGenomeScores() {
 
             if (wholeGenomeScores.get(windowFunction) == null) {
 
-                double scale = genome.getNominalLength() / screenWidth;
+                double scale = genome.getWGLength() / screenWidth;
 
                 int maxChromId = reader.getChromosomeNames().size() - 1;
                 String firstChr = reader.getChromsomeFromId(0);

diff --git a/src/main/java/org/broad/igv/data/AbstractDataSource.java b/src/main/java/org/broad/igv/data/AbstractDataSource.java
@@ -96,7 +96,7 @@ public AbstractDataSource(Genome genome) {
 
     public int getChrLength(String chr) {
         if (chr.equals(Globals.CHR_ALL)) {
-            return (int) (genome.getNominalLength() / 1000);
+            return (int) (genome.getWGLength() / 1000);
         } else {
             Chromosome c = genome.getChromosome(chr);
             return c == null ? 0 : c.getLength();

diff --git a/src/main/java/org/broad/igv/data/GenomeSummaryData.java b/src/main/java/org/broad/igv/data/GenomeSummaryData.java
@@ -93,7 +93,7 @@ public class GenomeSummaryData {
     public GenomeSummaryData(Genome genome, String[] samples) {
         this.genome = genome;
         this.samples = samples;
-        scale = (genome.getNominalLength() / locationUnit) / nPixels;
+        scale = (genome.getWGLength() / locationUnit) / nPixels;
 
         List<String> chrNames = genome.getLongChromosomeNames();
         locationMap = new HashMap<String, IntArrayList>();
@@ -115,7 +115,7 @@ public GenomeSummaryData(Genome genome, String[] samples) {
     void setScale(double scale){
         if(nDataPts > 0) throw new IllegalStateException("Can't alter scale after adding data");
         this.scale = scale;
-        nPixels = (int) (((double) this.genome.getNominalLength() / locationUnit) / scale);
+        nPixels = (int) (((double) this.genome.getWGLength() / locationUnit) / scale);
     }
 
 

diff --git a/src/main/java/org/broad/igv/data/seg/FreqData.java b/src/main/java/org/broad/igv/data/seg/FreqData.java
@@ -76,7 +76,7 @@ public void compute(float ampThreshold, float delThreshold) {
         amp.clear();
         del.clear();
 
-        int sizeInKB = (int) (genome.getNominalLength() / 1000);
+        int sizeInKB = (int) (genome.getWGLength() / 1000);
         int wgBinSize = sizeInKB / 700;
         int wgBinCount = sizeInKB / wgBinSize + 1;
 

diff --git a/src/main/java/org/broad/igv/feature/genome/ChromAlias.java b/src/main/java/org/broad/igv/feature/genome/ChromAlias.java
@@ -12,7 +12,7 @@ public class ChromAlias {
     public ChromAlias(String chr) {
         this.chr = chr;
         this.aliases = new HashMap<>();
-        this.aliases.put("chr", chr);
+        this.aliases.put("chr", chr);            // "chr" is the name set
     }
 
     public String getChr() {

diff --git a/src/main/java/org/broad/igv/feature/genome/ChromAliasDefaults.java b/src/main/java/org/broad/igv/feature/genome/ChromAliasDefaults.java
@@ -38,10 +38,12 @@ private void init(String id, List<String> chromosomeNames) {
                     switch (name) {
                         case "chrX":
                             record.put("ncbi", "23");
+                            record.put("?", "X");
                             skipRest = true;
                             break;
                         case "chrY":
                             record.put("ncbi", "24");
+                            record.put("?", "Y");
                             skipRest = true;
                             break;
                     }

diff --git a/src/main/java/org/broad/igv/feature/genome/ChromAliasFile.java b/src/main/java/org/broad/igv/feature/genome/ChromAliasFile.java
@@ -14,69 +14,91 @@ public class ChromAliasFile extends ChromAliasSource {
     private String[] nameSets;
 
 
-    public ChromAliasFile(String path, Genome genome) throws IOException {
+    public ChromAliasFile(String path, List<String> chromosomeNames) throws IOException {
         try (BufferedReader br = ParsingUtils.openBufferedReader(path)) {
-            init(br, genome.getAllChromosomeNames());
+
+            this.aliasCache = new HashMap<>();
+
+            Set<String> chromosomeNameSet = chromosomeNames != null ? new HashSet<>(chromosomeNames) : Collections.EMPTY_SET;
+
+            // First line
+            boolean firstLine = true;
+            String line;
+            while ((line = br.readLine()) != null) {
+                if (firstLine && line.startsWith("#")) {
+                    String[] tokens = line.substring(1).split("\t");
+                    this.nameSets = new String[tokens.length];
+                    for (int i = 0; i < tokens.length; i++) {
+                        this.nameSets[i] = tokens[i].trim();
+                    }
+                } else {
+                    String[] tokens = line.split("\t");
+                    if (tokens.length > 1) {
+
+                        // Find the canonical chromosome
+                        String chr = null;
+                        for (String c : tokens) {
+                            if (chromosomeNameSet.contains(c)) {
+                                chr = c;
+                                break;
+                            }
+                        }
+                        if (chr == null) {
+                            chr = tokens[0];
+                        }
+
+                        ChromAlias aliasRecord = new ChromAlias(chr);
+                        this.aliasCache.put(chr, aliasRecord);
+                        for (int i = 0; i < tokens.length; i++) {
+                            String key = this.nameSets != null ? this.nameSets[i] : String.valueOf(i);
+                            aliasRecord.put(key, tokens[i]);
+                            this.aliasCache.put(tokens[i], aliasRecord);
+                        }
+                    }
+                }
+                firstLine = false;
+            }
+
         }
     }
 
     /**
      * Constructor for legacy  .genome files
-     * @param br
-     * @param genome
+     *
      * @throws IOException
      */
-    public ChromAliasFile(BufferedReader br, Genome genome) throws IOException {
-            init(br, genome.getAllChromosomeNames());
-
-    }
-
-    private void init(BufferedReader br, List<String> chromosomeNames) throws IOException {
-
-        this.aliasCache = new HashMap<>();
+    public ChromAliasFile(List<List<String>> chromAliases, List<String> chromosomeNames) throws IOException {
 
         Set<String> chromosomeNameSet = chromosomeNames != null ? new HashSet<>(chromosomeNames) : Collections.EMPTY_SET;
 
-        // First line
-        boolean firstLine = true;
-        String line;
-        while ((line = br.readLine()) != null) {
-            if (firstLine && line.startsWith("#")) {
-                String[] tokens = line.substring(1).split("\t");
-                this.nameSets = new String[tokens.length];
-                for (int i = 0; i < tokens.length; i++) {
-                    this.nameSets[i] = tokens[i].trim();
-                }
-            } else {
-                String[] tokens = line.split("\t");
-                if (tokens.length > 1) {
-
-                    // Find the canonical chromosome
-                    String chr = null;
-                    for (String c : tokens) {
-                        if (chromosomeNameSet.contains(c)) {
-                            chr = c;
-                            break;
-                        }
-                    }
-                    if (chr == null) {
-                        chr = tokens[0];
-                    }
+        for (List<String> aliases : chromAliases) {
+            if (aliases.size() > 1) {
 
-                    ChromAlias aliasRecord = new ChromAlias(chr);
-                    this.aliasCache.put(chr, aliasRecord);
-                    for (int i = 0; i < tokens.length; i++) {
-                        String key = this.nameSets != null ? this.nameSets[i] : String.valueOf(i);
-                        aliasRecord.put(key, tokens[i]);
-                        this.aliasCache.put(tokens[i], aliasRecord);
+                // Find the canonical chromosome
+                String chr = null;
+                for (String c : aliases) {
+                    if (chromosomeNameSet.contains(c)) {
+                        chr = c;
+                        break;
                     }
                 }
+                if (chr == null) {
+                    chr = aliases.get(0);
+                }
+
+                ChromAlias aliasRecord = new ChromAlias(chr);
+                this.aliasCache.put(chr, aliasRecord);
+                int idx = 0;
+                for (String a : aliases) {
+                    String key = String.valueOf(idx++);
+                    aliasRecord.put(key, a);
+                    this.aliasCache.put(a, aliasRecord);
+                }
             }
-            firstLine = false;
         }
-
     }
 
+
     /**
      * Return the canonical chromosome name for the alias.  If none found return the alias
      *

diff --git a/src/main/java/org/broad/igv/feature/genome/ChromAliasManager.java b/src/main/java/org/broad/igv/feature/genome/ChromAliasManager.java
@@ -3,37 +3,49 @@
 import java.io.IOException;
 import java.util.*;
 
+/**
+ * A data/feature source helper class for managing chromosome aliasing.  Maps reference sequence names to aliases
+ * used by the feature source (e.g. chr20 -> 20).
+ */
 public class ChromAliasManager {
 
-    Set<String> sequenceNames;
-
-    Genome genome;
-
-    Map<String, String> aliasCache;
+    private Set<String> sequenceNames;
 
+    private Genome genome;
+
+    private Map<String, String> aliasCache;
+
+    /**
+     * @param sequenceNames - Sequence names defined by the data source (e.g. bam or feature file)
+     * @param genome        - Reference genome object.
+     */
     public ChromAliasManager(Collection<String> sequenceNames, Genome genome) {
         this.sequenceNames = new HashSet<>(sequenceNames);
         this.aliasCache = new HashMap<>();
         this.genome = genome;
     }
 
-    public String getAliasName(String chr) {
-        if(genome == null) {
-            return chr;   // A no-op manager, used mostly in testing.
+    public String getAliasName(String seqName) {
+        if (genome == null) {
+            return seqName;   // A no-op manager, used in testing.
         }
         try {
-            if(!aliasCache.containsKey(chr)) {
-                ChromAlias aliasRecord = genome.getAliasRecord(chr);
-                for(String alias : aliasRecord.values()) {
-                    if(sequenceNames.contains(alias));
-                    aliasCache.put(chr, alias);
-                    return alias;
+            if (!aliasCache.containsKey(seqName)) {
+                ChromAlias aliasRecord = genome.getAliasRecord(seqName);
+                if (aliasRecord == null) {
+                    aliasCache.put(seqName, null);  // No know alias, record to prevent searching again
+                } else {
+                    for (String alias : aliasRecord.values()) {
+                        if (sequenceNames.contains(alias)) {
+                            aliasCache.put(seqName, alias);
+                        }
+                    }
                 }
             }
-            return aliasCache.get(chr);
+            return aliasCache.get(seqName);
         } catch (IOException e) {
             throw new RuntimeException(e);
         }
     }
-    
+
 }
diff --git a/src/main/java/org/broad/igv/feature/genome/ChromAliasSource.java b/src/main/java/org/broad/igv/feature/genome/ChromAliasSource.java
@@ -18,6 +18,12 @@ public ChromAliasSource() {
 
     public abstract ChromAlias search(String alias) throws IOException;
 
+    /**
+     * Add a ChromAlias record directly to the cache, overriding any existing alias.  This is primarily used for
+     * user-defined overrides.
+     *
+     * @param chromAlias
+     */
     public void add(ChromAlias chromAlias) {
         aliasCache.put(chromAlias.getChr(), chromAlias);
     }

diff --git a/src/main/java/org/broad/igv/feature/genome/ChromosomeComparator.java b/src/main/java/org/broad/igv/feature/genome/ChromosomeComparator.java
@@ -36,7 +36,7 @@
  * For comparing chromosomes. We order by "important" vs "unimportant".
  * The idea being there are main chromosomes (chr1...chrX, chrM) and
  * sometimes many smaller contigs.
- *
+ * <p>
  * Date: 2012-Aug-16
  */
 public class ChromosomeComparator implements Comparator<Chromosome> {
@@ -62,6 +62,10 @@ public int compare(Chromosome o1, Chromosome o2) {
             return -1;
         } else if (isMyto(o2.getName())) {
             return 1;
+        } else if (o1.getName().startsWith("chr") && !o2.getName().startsWith("chr")) {
+            return -1;
+        } else if (o2.getName().startsWith("chr") && !o1.getName().startsWith("chr")) {
+            return 1;
         } else {
             return o2.getLength() - o1.getLength();
         }