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Pre-filter saturating sequences only. Retaining singletons seems to improve matching accuracy in high sample rate test (well populations 10% of total cell sample size)

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eugenefischer
2022-09-25 15:19:56 -05:00
parent 1971a96467
commit 4f2fa4cbbe
1 changed files with 3 additions and 3 deletions
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6
src/main/java/Simulator.java
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@@ -48,9 +48,9 @@ public class Simulator implements GraphModificationFunctions {
if(verbose){System.out.println("Well maps made");}
//if(verbose){System.out.println("Removing singleton sequences and sequences present in all wells.");}
//filterByOccupancyThresholds(allAlphas, 2, numWells - 1);
//filterByOccupancyThresholds(allBetas, 2, numWells - 1);
if(verbose){System.out.println("Removing sequences present in all wells.");}
filterByOccupancyThresholds(allAlphas, 1, numWells - 1);
filterByOccupancyThresholds(allBetas, 1, numWells - 1);
if(verbose){System.out.println("Sequences removed");}
int pairableAlphaCount = allAlphas.size();
if(verbose){System.out.println("Remaining alphas count: " + pairableAlphaCount);}