adjust threshold for number of solid kmers

bcgsc · Dec 24, 2022 · 4743d22 · 4743d22
1 parent a3f10ea
commit 4743d22
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Showing 2 changed files with 9 additions and 5 deletions.
diff --git a/src/rnabloom/RNABloom.java b/src/rnabloom/RNABloom.java
@@ -3960,7 +3960,9 @@ public ArrayList<BitSequence> correctLongReadsMultithreaded(String[] inputFastxP
                                                 boolean trimArtifact,
                                                 boolean storeReads) throws InterruptedException, IOException, Exception {
 
-        int minNumSolidKmers = Math.max(0, (int) Math.floor((minSeqLen-k+1) * percentIdentity / k));
+        int minNumSolidKmers = Math.max(0, (int) Math.floor(minSeqLen/100.0));
+        //int minNumSolidKmers = Math.max(0, (int) Math.floor((minSeqLen-k+1) * percentIdentity / k));
+
         long numReads = 0;
         ArrayBlockingQueue<Sequence2> outputQueue = new ArrayBlockingQueue<>(maxSampleSize);
 

diff --git a/src/rnabloom/util/GraphUtils.java b/src/rnabloom/util/GraphUtils.java
@@ -3097,10 +3097,12 @@ public static ArrayList<Kmer> correctLongSequenceWindowed(ArrayList<Kmer> kmers,
                                                     int windowSize) {
 
         int numNeeded = minNumSolidKmers;
-        for (Kmer kmer : kmers) {
-            if (kmer.count >= minKmerCov) {
-                if (--numNeeded <= 0) {
-                    break;
+        if (numNeeded > 0) {
+            for (Kmer kmer : kmers) {
+                if (kmer.count >= minKmerCov) {
+                    if (--numNeeded <= 0) {
+                        break;
+                    }
                 }
             }
         }