Check RNA stats before 3rd gen to detect long-read rna seq. Fixes #1491.

Fix bug interpreting read sequence = "*". Was interpreting as mismatch to reference.
igvteam · Jul 26, 2024 · 0f0b4fb · 0f0b4fb
1 parent e9ccb3b
commit 0f0b4fb
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/src/main/java/org/broad/igv/sam/AlignmentBlockImpl.java b/src/main/java/org/broad/igv/sam/AlignmentBlockImpl.java
@@ -52,7 +52,7 @@ public AlignmentBlockImpl(int start, byte[] bases, byte[] qualities, int offset,
 
         this.start = start;
         this.offset = offset;
-        this.bases = new ByteSubarray(bases, offset, nBases, (byte) '?');
+        this.bases = bases.length == 0 ? EMPTY_ARRAY :new ByteSubarray(bases, offset, nBases, (byte) '?');
         this.basesLength = nBases;
 
         // qualities are optional in a SAMRecord, we might get null or an array of zero

diff --git a/src/main/java/org/broad/igv/sam/ReadStats.java b/src/main/java/org/broad/igv/sam/ReadStats.java
@@ -60,7 +60,7 @@ public class ReadStats {
 
     public void addAlignment(Alignment alignment) {
 
-        if(readCount > MAX_READ_COUNT) return;
+        if (readCount > MAX_READ_COUNT) return;
 
         if (alignment.isMapped()) {
 
@@ -135,10 +135,10 @@ private double[] downsample(DoubleArrayList list, int size) {
     public AlignmentTrack.ExperimentType inferType() {
         compute();
         if (readCount < 20) return AlignmentTrack.ExperimentType.UNKOWN; // Not enough reads
-        if ((readLengthStdDev > 100 || medianReadLength > 1000) && averageCigarLength > 10) { // Cigar length to filter consensus reads
-            return AlignmentTrack.ExperimentType.THIRD_GEN;
-        } else if (medianRefToReadRatio > 5 || fracReadsWithNs > 0.01) {
+        if (medianRefToReadRatio > 5 || fracReadsWithNs > 0.01) {
             return AlignmentTrack.ExperimentType.RNA;
+        } else if ((readLengthStdDev > 100 || medianReadLength > 1000) && averageCigarLength > 10) { // Cigar length to filter consensus reads
+            return AlignmentTrack.ExperimentType.THIRD_GEN;
         } else {
             return AlignmentTrack.ExperimentType.OTHER;
         }