* Catch errors in sampling alignments to determine experiment type.

* Null check in IGVReferenceSource -- can occur when alignments in CRAM files reference sequences no present in loaded genome. * Revert name change to menu item for downloading hosted genomes
igvteam · Sep 30, 2024 · 5629b43 · 5629b43
1 parent 2838c30
commit 5629b43
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Showing 4 changed files with 36 additions and 29 deletions.
diff --git a/src/main/java/org/broad/igv/sam/AlignmentDataManager.java b/src/main/java/org/broad/igv/sam/AlignmentDataManager.java
@@ -378,29 +378,36 @@ private void updateBaseModfications(List<Alignment> alignments) {
     }
 
     public AlignmentTrack.ExperimentType inferType() {
-        if (this.inferredType != null) {
-            return this.inferredType;
-        }
-
-        ReadStats readStats = new ReadStats();
-        List<Alignment> sample = AlignmentUtils.firstAlignments(reader, 100);
-        for (Alignment a : sample) {
-            readStats.addAlignment(a);
-        }
-        inferredType = readStats.inferType();
 
-        if (inferredType == AlignmentTrack.ExperimentType.THIRD_GEN) {
-            return inferredType;
-        } else {
-            // Get a larger sample to distinguish RNA-Seq
-            readStats = new ReadStats();
-            sample = AlignmentUtils.firstAlignments(reader, 2000);
-            for (Alignment a : sample) {
-                readStats.addAlignment(a);
+        if (this.inferredType == null) {
+            try {
+                ReadStats readStats = new ReadStats();
+                List<Alignment> sample = AlignmentUtils.firstAlignments(reader, 100);
+                for (Alignment a : sample) {
+                    readStats.addAlignment(a);
+                }
+                inferredType = readStats.inferType();
+
+                if (inferredType == AlignmentTrack.ExperimentType.THIRD_GEN) {
+                    return inferredType;
+                } else {
+                    // Get a larger sample to distinguish RNA-Seq
+                    readStats = new ReadStats();
+                    sample = AlignmentUtils.firstAlignments(reader, 2000);
+                    for (Alignment a : sample) {
+                        readStats.addAlignment(a);
+                    }
+                    inferredType = readStats.inferType();
+                    return inferredType;
+                }
+            } catch (Exception e) {
+                // Ignore errors, inferring alignment type is not essential.
+                log.error("Error inferring alignment type", e);
+                inferredType = AlignmentTrack.ExperimentType.UNKOWN;
             }
-            inferredType = readStats.inferType();
-            return inferredType;
         }
+
+        return inferredType;
     }
 
     private AlignmentTrack.ExperimentType getExperimentType() {

diff --git a/src/main/java/org/broad/igv/sam/AlignmentUtils.java b/src/main/java/org/broad/igv/sam/AlignmentUtils.java
@@ -233,7 +233,7 @@ public static AlignmentBlockImpl buildAlignmentBlock(char operator,
     }
 
 
-    public static List<Alignment> firstAlignments(AlignmentReader reader, int count) {
+    public static List<Alignment> firstAlignments(AlignmentReader reader, int count) throws IOException {
 
         List<Alignment> alignments = new ArrayList<>();
         CloseableIterator<Alignment> iter = null;
@@ -244,12 +244,9 @@ public static List<Alignment> firstAlignments(AlignmentReader reader, int count)
                 alignments.add(iter.next());
             }
             return alignments;
-        } catch (IOException e) {
-
         } finally {
             iter.close();
         }
-        return alignments;
     }
 
 

diff --git a/src/main/java/org/broad/igv/sam/cram/IGVReferenceSource.java b/src/main/java/org/broad/igv/sam/cram/IGVReferenceSource.java
@@ -39,6 +39,7 @@
 import org.broad.igv.ui.IGV;
 import org.broad.igv.util.ObjectCache;
 
+import java.util.Arrays;
 import java.util.HashMap;
 
 /**
@@ -52,7 +53,7 @@ public class IGVReferenceSource implements CRAMReferenceSource {
 
     @Override
     public byte[] getReferenceBases(SAMSequenceRecord record, boolean tryNameVariants) {
-        return getReferenceBasesByRegion(record, 0,  record.getSequenceLength());
+        return getReferenceBasesByRegion(record, 0, record.getSequenceLength());
     }
 
     @Override
@@ -62,9 +63,11 @@ public byte[] getReferenceBasesByRegion(final SAMSequenceRecord sequenceRecord,
         String chrName = currentGenome.getCanonicalChrName(name);
         byte[] bases = currentGenome.getSequence(chrName, zeroBasedStart, zeroBasedStart + requestedRegionLength, true);
 
-        // CRAM spec requires upper case
-        for (int i = 0; i < bases.length; i++) {
-            if (bases[i] >= 97) bases[i] -= 32;
+        if (bases != null) {
+            // CRAM spec requires upper case
+            for (int i = 0; i < bases.length; i++) {
+                if (bases[i] >= 97) bases[i] -= 32;
+            }
         }
         return bases;
     }

diff --git a/src/main/java/org/broad/igv/ui/IGVMenuBar.java b/src/main/java/org/broad/igv/ui/IGVMenuBar.java
@@ -433,7 +433,7 @@ private JMenu createGenomesMenu() {
 
         JMenu menu = new JMenu("Genomes");
 
-        loadGenomeFromServerMenuItem = new JMenuItem("Download Hosted Genome...");
+        loadGenomeFromServerMenuItem = new JMenuItem("Select Hosted Genome...");
         loadGenomeFromServerMenuItem.addActionListener(e -> GenomeSelectionDialog.selectGenomesFromServer());
         loadGenomeFromServerMenuItem.setToolTipText(LOAD_GENOME_SERVER_TOOLTIP);
         menu.add(loadGenomeFromServerMenuItem);