Fixed error with javadoc generation

Author: Victor Kirst

src/main/java/com/astrazeneca/vardict/VarDict.java

@@ -4786,7 +4786,7 @@ static boolean ismatch(String seq1, String seq2, int dir, boolean debugLog) {
 
     /**
      * Find the consensus sequence in soft-clipped reads. Consensus is called if
-     * the matched nucleotides are >90% of all softly clipped nucleotides.
+     * the matched nucleotides are >90% of all softly clipped nucleotides.
      * @param scv soft-clipped sequences
      * @param debugLog print debug message if true
      * @return consensus sequence
@@ -5511,7 +5511,7 @@ private static void ampVardictNotParallel(final List<List<Region>> segs, final M
      *            region
      * @param vars
      *            result of {@link #toVars} calling
-     * @param positions map of positon => (list of (region number, region))
+     * @param positions map of positon =&gt; (list of (region number, region))
      * @param sample sample name
      * @param splice set of strings representing spliced regions
      * @param conf configuration
@@ -5787,7 +5787,7 @@ static void adjComplex(Variant vref) {
     }
 
     /**
-     * VARN - array of variants, REF - reference variant, VAR - map of (variant description string => variant)
+     * VARN - array of variants, REF - reference variant, VAR - map of (variant description string =&gt; variant)
      */
     static enum VarsType {
         varn, ref, var,
@@ -5951,7 +5951,6 @@ private static Region buildRegion(String region, final int numberNucleotideToExt
      * @param querySeq Base sequence
      * @param queryQual
      * @param lowqual
-     * @param performLocalRealignment
      * @return Tuple of (adjusted position of first matched base, modified CIGAR string)
      */
     static Tuple2<Integer, String> modifyCigar(int indel, Map<Integer, Character> ref,

src/main/java/com/astrazeneca/vardict/Variant.java

@@ -14,7 +14,7 @@ public class Variant {
      * 4). ... # sequence                  - for insertion/deletion variants followed by short matched sequence
      * 5). ... ^ sequence                  - followed by insertion
      * 6). ... ^ number                    - followed by deletion
-     * 7). ... & sequence                  - for insertion/deletion variants followed by matched sequence
+     * 7). ... & sequence                  - for insertion/deletion variants followed by matched sequence
      */
     String n;
 
@@ -89,7 +89,7 @@ public class Variant {
     int shift3;
 
     /**
-     * msi. > 1 indicates Microsatellite instability
+     * msi. > 1 indicates Microsatellite instability
      */
     double msi;
 
@@ -167,4 +167,4 @@ public class Variant {
      * Debug information
      */
     String DEBUG;
-}
+}