Merge pull request #230 from PolinaBevad/fix_javadoc_warnings

Fixed javadoc warnings

Author: pcingola

src/main/java/com/astrazeneca/vardict/data/scopedata/Scope.java

@@ -9,7 +9,7 @@
 
 /**
  * Common scope of data must be storing between steps of VarDict pipeline.
- * @param <T>
+ * @param <T> data of current step of pipeline
  */
 public class Scope<T> {
 

src/main/java/com/astrazeneca/vardict/modules/ToVarsBuilder.java

@@ -287,6 +287,13 @@ public int compare(Variant o1, Variant o2) {
 
     /**
      * Creates insertion variant from each variation on this position and adds it to the list of aligned variants.
+     * @param duprate duplication rate of insertion
+     * @param position position of the insertion start
+     * @param totalPosCoverage current total position coverage (total depth) that can be updated by extra counts
+     * @param var list of variants at the position to be updated
+     * @param debugLines list of debug lines to be updated
+     * @param hicov position coverage by high quality reads
+     * @return updated total position coverage
      */
     int createInsertion(double duprate, int position, int totalPosCoverage,
                         List<Variant> var, List<String> debugLines, int hicov) {
@@ -371,9 +378,19 @@ int createInsertion(double duprate, int position, int totalPosCoverage,
 
     /**
      * Creates non-insertion variant from each variation on this position and adds it to the list of aligned variants.
+     * @param duprate duplication rate of non-insertion variant
+     * @param alignedVars map of variants for position to get SV info
+     * @param position position of the non-insertion variant start
+     * @param nonInsertionVariations map of description strings and intermediate variations
+     * @param totalPosCoverage current total position coverage (total depth) that can be updated by extra counts
+     * @param var list of variants at the position to be updated
+     * @param debugLines list of debug lines to be updated
+     * @param keys sorted list of variant description strings
+     * @param hicov position coverage by high quality reads
      */
-    void createVariant(double duprate, Map<Integer, Vars> alignedVars, int position, VariationMap<String, Variation> nonInsertionVariations,
-                       int tcov, List<Variant> var, List<String> debugLines, List<String> keys, int hicov) {
+    void createVariant(double duprate, Map<Integer, Vars> alignedVars, int position,
+                       VariationMap<String, Variation> nonInsertionVariations, int totalPosCoverage, List<Variant> var,
+                       List<String> debugLines, List<String> keys, int hicov) {
         //Loop over all variants found for the position except insertions
         for (String descriptionString : keys) {
             if (descriptionString.equals("SV")) {
@@ -404,8 +421,8 @@ void createVariant(double duprate, Map<Integer, Vars> alignedVars, int position,
              # 1). cnt.cnt > tcov                         - variant count is more than position coverage
              # 2). cnt.cnt - tcov < cnt.extracnt          - variant count is no more than position coverage + extracnt
              */
-            int ttcov = tcov;
-            if (cnt.varsCount > tcov && cnt.extracnt > 0 && cnt.varsCount - tcov < cnt.extracnt) { //adjust position coverage if condition holds
+            int ttcov = totalPosCoverage;
+            if (cnt.varsCount > totalPosCoverage && cnt.extracnt > 0 && cnt.varsCount - totalPosCoverage < cnt.extracnt) { //adjust position coverage if condition holds
                 ttcov = cnt.varsCount;
             }
 

src/main/java/com/astrazeneca/vardict/postprocessmodules/SomaticPostProcessModule.java

@@ -97,6 +97,8 @@ public void accept(Scope<AlignedVarsData> scopeFromBam2,
      * @param variants variations from one BAM
      * @param isFirstCover if the first calling
      * @param varLabel type of variation (LikelyLOH, LikelySomatic, Germline, AFDiff, StrongSomatic)
+     * @param region region from BED file
+     * @param splice set of strings representing introns in splice
      * */
     void callingForOneSample(Vars variants, boolean isFirstCover, String varLabel, Region region, Set<String> splice) {
         if (variants.variants.isEmpty()) {
@@ -125,6 +127,14 @@ void callingForOneSample(Vars variants, boolean isFirstCover, String varLabel, R
         }
     }
 
+    /**
+     * Run analysis of variations from BAM1 and BAM2.
+     * @param position position on which analysis is processed
+     * @param v1 variations from BAM1 on target position
+     * @param v2 variations from BAM2 on target position
+     * @param region region from BED file
+     * @param splice set of strings representing introns in splice
+     */
     void callingForBothSamples(Integer position, Vars v1, Vars v2, Region region, Set<String> splice)  {
         if (v1.variants.isEmpty() && v2.variants.isEmpty()) {
             return;
@@ -136,10 +146,12 @@ void callingForBothSamples(Integer position, Vars v1, Vars v2, Region region, Se
         }
     }
     /**
-     * Analyse variations from BAM1 based on variations from BAM2.
+     * Analyse and print variations from BAM1 based on variations from BAM2.
      * @param position position on which analysis is processed
      * @param v1 variations from BAM1 on target position
      * @param v2 variations from BAM2 on target position
+     * @param region region from BED file
+     * @param splice set of strings representing introns in splice
      */
     private void printVariationsFromFirstSample(Integer position, Vars v1, Vars v2, Region region, Set<String> splice){
         int numberOfProcessedVariation = 0;
@@ -263,11 +275,13 @@ private void printVariationsFromFirstSample(Integer position, Vars v1, Vars v2,
     }
 
     /**
-     * Analyse variations from BAM2 based on variations from BAM1.
+     * Analyse and print variations from BAM2 based on variations from BAM1.
      * @param position position on which analysis is processed
      * @param v1 variations from BAM1 on target position
      * @param v2 variations from BAM2 on target position
-     * */
+     * @param region region from BED file
+     * @param splice set of strings representing introns in splice
+     */
     private void printVariationsFromSecondSample(Integer position, Vars v1, Vars v2, Region region, Set<String> splice){
         for (Variant v2var : v2.variants) {
             if (v2var.refallele.equals(v2var.varallele)) {
@@ -326,6 +340,7 @@ private void printVariationsFromSecondSample(Integer position, Vars v1, Vars v2,
      * @param variants variations from BAM2
      * @param standardVariant a variation to compare with
      * @param variantToCompare a variation to be compared
+     * @param splice set of strings representing introns in splice
      * @return type of variation (LikelyLOH, LikelySomatic, Germline, AFDiff, StrongSomatic)
      * */
      String determinateType(Vars variants, Variant standardVariant, Variant variantToCompare, Set<String> splice) {
@@ -358,13 +373,11 @@ String determinateType(Vars variants, Variant standardVariant, Variant variantTo
      * Taken a likely somatic indels and see whether combine two bam files still support somatic status. This is mainly for Indels
      * that softclipping overhang is too short to positively being called in one bam file, but can be called in the other bam file,
      * thus creating false positives
-     *
      * @param variant1 variant 1
      * @param variant2 variant 2
      * @param chrName chromosome
      * @param position position
      * @param descriptionString description string of variant
-     *
      * @param splice set of strings representing introns in splice
      * @param maxReadLength max read length
      * @return (new <code>maxReadLength</code>, "FALSE" | "")