Neo: removed redundant wildtype match field

JTpath · Nov 2, 2021 · 5148840 · 5148840
1 parent 4df24d4
commit 5148840
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Showing 8 changed files with 17 additions and 414 deletions.
diff --git a/hmf-common/src/main/java/com/hartwig/hmftools/common/neo/NeoEpitopeFile.java b/hmf-common/src/main/java/com/hartwig/hmftools/common/neo/NeoEpitopeFile.java
@@ -52,7 +52,6 @@ public class NeoEpitopeFile
     public final String[] CodingBaseCigars;
     public final double[] CancerTpmTotal;
     public final double[] CohortTpmTotal;
-    public final boolean WildtypeNovelAAMatch;
 
     public static final String FLD_NE_ID = "NeId";
     public static final String FLD_NE_VAR_TYPE = "VariantType";
@@ -74,7 +73,7 @@ public NeoEpitopeFile(
             final String transcriptsUp, final String transcriptsDown, final String wildtypeAAs,
             int codingBaseUpPosStart, int codingBaseUpPosEnd, final String codingBasesUp, final String codingBaseCigarUp,
             int codingBaseDownPosStart, int codingBaseDownPosEnd, final String codingBasesDown, final String codingBaseCigarDown,
-            double tmpCancerUp, double tmpCohortUp, double tmpCancerDown, double tmpCohortDown, boolean wildtypeNovelAAMatch)
+            double tmpCancerUp, double tmpCohortUp, double tmpCancerDown, double tmpCohortDown)
     {
         Id = id;
         VariantType = varType;
@@ -101,7 +100,6 @@ public NeoEpitopeFile(
         CodingBasePositions[FS_DOWN] = new int[] {codingBaseDownPosStart, codingBaseDownPosEnd};
         CancerTpmTotal = new double[] { tmpCancerUp, tmpCohortUp };
         CohortTpmTotal = new double[] { tmpCancerDown, tmpCohortDown };
-        WildtypeNovelAAMatch = wildtypeNovelAAMatch;
     }
 
     private static final String FILE_EXTENSION = ".neo.neoepitopes.csv";
@@ -190,7 +188,6 @@ private static List<NeoEpitopeFile> fromLines(@NotNull List<String> lines)
         int tpmCohUpIndex = fieldsIndexMap.get("TpmCohortUp");
         int tpmCanDownIndex = fieldsIndexMap.get("TpmCancerDown");
         int tpmCohDownIndex = fieldsIndexMap.get("TpmCohortDown");
-        int wtNovelAaIndex = fieldsIndexMap.get("WildtypeNovelAAMatch");
 
         for(String line : lines)
         {
@@ -209,7 +206,7 @@ private static List<NeoEpitopeFile> fromLines(@NotNull List<String> lines)
                         Integer.parseInt(values[cbUpPosStartIndex]), Integer.parseInt(values[cbUpPosEndIndex]), values[cbUpIndex], values[cbCigUpIndex],
                         Integer.parseInt(values[cbDownPosStartIndex]), Integer.parseInt(values[cbDownPosEndIndex]), values[cbDownIndex], values[cbCigDownIndex],
                         Double.parseDouble(values[tpmCanUpIndex]), Double.parseDouble(values[tpmCohUpIndex]),
-                        Double.parseDouble(values[tpmCanDownIndex]), Double.parseDouble(values[tpmCohDownIndex]), Boolean.parseBoolean(values[wtNovelAaIndex])));
+                        Double.parseDouble(values[tpmCanDownIndex]), Double.parseDouble(values[tpmCohDownIndex])));
             }
             catch(Exception e)
             {
@@ -261,7 +258,6 @@ public static String header()
                 .add("TpmCohortUp")
                 .add("TpmCancerDown")
                 .add("TpmCohortDown")
-                .add("WildtypeNovelAAMatch")
                 .toString();
     }
 
@@ -307,11 +303,11 @@ public static String toString(@NotNull final NeoEpitopeFile neo)
         sj.add(String.format("%6.3e", neo.CohortTpmTotal[FS_UP]));
         sj.add(String.format("%6.3e", neo.CancerTpmTotal[FS_DOWN]));
         sj.add(String.format("%6.3e", neo.CohortTpmTotal[FS_DOWN]));
-        sj.add(String.valueOf(neo.WildtypeNovelAAMatch));
 
         return sj.toString();
     }
 
+    /*
     @NotNull
     public static NeoEpitopeFile fromString(@NotNull final String data, boolean skipSampleId)
     {
@@ -333,8 +329,9 @@ public static NeoEpitopeFile fromString(@NotNull final String data, boolean skip
                 Integer.parseInt(values[index++]), Integer.parseInt(values[index++]), values[index++], values[index++],
                 Integer.parseInt(values[index++]), Integer.parseInt(values[index++]), values[index++], values[index++],
                 Double.parseDouble(values[index++]), Double.parseDouble(values[index++]),
-                Double.parseDouble(values[index++]), Double.parseDouble(values[index++]), Boolean.parseBoolean(values[index++]));
+                Double.parseDouble(values[index++]), Double.parseDouble(values[index++]));
     }
+    */
 
     public static String pointMutationInfo(final String chromosome, int position, final String ref, final String alt)
     {

diff --git a/neo/src/main/java/com/hartwig/hmftools/neo/cohort/NeoEpitopeCohort.java b/neo/src/main/java/com/hartwig/hmftools/neo/cohort/NeoEpitopeCohort.java
diff --git a/neo/src/main/java/com/hartwig/hmftools/neo/cohort/NeoScorer.java b/neo/src/main/java/com/hartwig/hmftools/neo/cohort/NeoScorer.java
@@ -22,6 +22,7 @@
 import org.apache.commons.cli.ParseException;
 import org.jetbrains.annotations.NotNull;
 
+//
 public class NeoScorer
 {
     private final NeoScorerConfig mConfig;

diff --git a/neo/src/main/java/com/hartwig/hmftools/neo/epitope/NeoConfig.java b/neo/src/main/java/com/hartwig/hmftools/neo/epitope/NeoConfig.java
@@ -64,7 +64,6 @@ public class NeoConfig
     public static final String WRITE_PEPTIDES = "write_peptides";
     public static final String WRITE_TRANS_DATA = "write_trans_data";
 
-    public static final String NEO_EPITOPE_FILE_ID = ".neo.neoepitopes.csv";
     public static final String HLA_PEPTIDE_FILE_ID = ".neo.hla_peptides.csv";
 
     public static final int DEFAULT_AMINO_ACID_REF_COUNT = 18;

diff --git a/neo/src/main/java/com/hartwig/hmftools/neo/epitope/NeoEpitope.java b/neo/src/main/java/com/hartwig/hmftools/neo/epitope/NeoEpitope.java
@@ -240,11 +240,6 @@ refGenome, TransData[FS_UP], chromosome(FS_UP), upstreamAAPosStart, wtOrient,
 
     public abstract void setSkippedSpliceSites(final EnsemblDataCache geneTransCache);
 
-    public boolean matchesAminoAcids(final NeoEpitope other)
-    {
-        return UpstreamAcids.equals(other.UpstreamAcids) && DownstreamAcids.equals(other.DownstreamAcids) && NovelAcid.equals(other.NovelAcid);
-    }
-
     public String aminoAcidString() { return UpstreamAcids + NovelAcid + DownstreamAcids; }
 
     public boolean hasWildtypeAminoAcidMatch()
@@ -286,6 +281,6 @@ TransData[FS_UP].GeneId, TransData[FS_DOWN].GeneId, geneName(FS_UP), geneName(FS
                 ExtPositions[FS_UP][SE_START], ExtPositions[FS_UP][SE_END], ExtCodingBases[FS_UP], ExtCigars[FS_UP].toString(),
                 ExtPositions[FS_DOWN][SE_START], ExtPositions[FS_DOWN][SE_END], ExtCodingBases[FS_DOWN],
                 ExtCigars[FS_DOWN] != null ? ExtCigars[FS_DOWN].toString() : "",
-                tpmCancer[FS_UP], tpmCohort[FS_UP], tpmCancer[FS_DOWN], tpmCohort[FS_DOWN], hasWildtypeAminoAcidMatch());
+                tpmCancer[FS_UP], tpmCohort[FS_UP], tpmCancer[FS_DOWN], tpmCohort[FS_DOWN]);
     }
 }