Esvee: cap frag distribution output by max observer read length, load…

… disc stats file from prep dir
hartwigmedical · Dec 16, 2024 · 79b20be · 79b20be
1 parent a5e7e98
commit 79b20be
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Showing 2 changed files with 5 additions and 1 deletion.
diff --git a/esvee/src/main/java/com/hartwig/hmftools/esvee/assembly/AssemblyApplication.java b/esvee/src/main/java/com/hartwig/hmftools/esvee/assembly/AssemblyApplication.java
@@ -184,7 +184,7 @@ private boolean loadJunctionFiles()
             return true;
         }
 
-        String discStatsFilename = formDiscordantStatsFilename(mConfig.OutputDir, mConfig.sampleId());
+        String discStatsFilename = formDiscordantStatsFilename(mConfig.PrepDir, mConfig.sampleId());
         DiscordantStats discordantStats = loadDiscordantStats(discStatsFilename);
 
         int minJunctionFrags = MIN_JUNCTION_SUPPORT;

diff --git a/esvee/src/main/java/com/hartwig/hmftools/esvee/prep/FragmentSizeDistribution.java b/esvee/src/main/java/com/hartwig/hmftools/esvee/prep/FragmentSizeDistribution.java
@@ -363,6 +363,10 @@ private void writeDistribution()
 
             for(LengthFrequency lengthFrequency : mLengthFrequencies)
             {
+                // cap any fragmemt distribution entry at the observed read length to avoid the use of trimmed fragments impacting it
+                if(mMaxReadLength > 0 && lengthFrequency.Length < mMaxReadLength)
+                    continue;
+
                 writer.write(format("%d\t%d", lengthFrequency.Length, lengthFrequency.Frequency));
                 writer.newLine();
             }