Rebased and updated submodule. Updated docs.

Author: PolinaBevad

VarDict

@@ -38,7 +38,6 @@ public VarDict(Configuration conf, ReferenceResource referenceResource) {
     }
     /**
      * The main method to start Vardict in any mode.
-     * @param conf prepared configuration object from arguments
      * @throws IOException if BAM file can't be read
      */
     public void start() throws IOException {
@@ -517,6 +516,7 @@ private static Tuple2<String, String> getSampleNames(String sample,
      * @param splice set of strings representing introns in splice
      * @param ampliconBasedCalling string of maximum_distance:minimum_overlap for amplicon based calling
      * @param rlen max read length
+     * @param referenceResource object for access to reference map
      * @param conf Configuration
      * @param out output stream
      * @return maximum read length
@@ -782,7 +782,7 @@ && isGoodVar(v1.var.get(n), v1.ref, v1.var.get(n).varType(), splice, conf)) {
      * @param chr chromosome
      * @param p position
      * @param nt nucleotide
-     *
+     * @param referenceResource object for access to reference map
      * @param chrs map of chromosome lengths
      * @param sample sample name
      * @param splice set of strings representing introns in splice

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

@@ -67,6 +67,7 @@ static String getBaseQualityString(SAMRecord record) {
      * @param sclip3 map of soft clips 3' on positions
      * @param sclip5 map of soft clips 5' on positions
      * @param svflag true if BAM file is re-parsed due to structural variants analysis on extended region of interest
+     * @param referenceResource object for access to reference map
      * @return Tuple of (noninsertion variant  structure, insertion variant structure, coverage, maxmimum read length)
      * @throws IOException if BAM file can't be read
      */

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

@@ -367,6 +367,7 @@ private static Sclip getLastSVStructure(List<Sclip> svStructure) {
      * @param sclip5 map of soft clips 5' on positions
      * @param svStructures Contains all structural variants ends for deletions, duplications, inversions, insertions
     and structures for structural variant analysis
+     * @param referenceResource object for access to reference map
      * @throws IOException if BAM file can't be read
      */
     static void findAllSVs(Region region, String bam, Map<String, Integer> chrs, String sample,
@@ -1102,6 +1103,7 @@ && isHasAndEquals(complement(ref.get(bp + 1)), ref, p3 - 1)) {
      * @param svrinv3 list of INV SVs in reverse direction of 3'
      * @param svrinv5 list of INV SVs in reverse direction of 5'
      * @param conf Configuration
+     * @param referenceResource object for access to reference map
      * @param RLEN max read length
      * @param chrs map of chromosome lengths
      */
@@ -1308,6 +1310,7 @@ static void findINVdisc (Map<Integer, VariationMap<String, Variation>> hash,
      * @param svrdup list of DUP SVs in discordant pairs in reverse direction
      * @param conf Configuration
      * @param RLEN max read length
+     * @param referenceResource object for access to reference map
      * @param chrs map of chromosome lengths
      * @throws IOException if BAM file can't be read
      */
@@ -1824,6 +1827,7 @@ static Tuple.Tuple2<Integer, String> findMatch(Configuration conf,
      * @param svfdel list of DEL SVs in discordant pairs in forward direction
      * @param svrdel list of DEL SVs in discordant pairs in reverse direction
      * @param conf Configuration
+     * @param referenceResource object for access to reference map
      * @param rlen max read length
      * @param chrs map of chromosome lengths
      */
@@ -1975,6 +1979,7 @@ static void findDELdisc(Configuration conf,
      * @param rlen max read length
      * @param chrs map of chromosome lengths
      * @param sample sample name
+     * @param referenceResource object for access to reference map
      * @param splice set of strings representing spliced regions
      * @param ampliconBasedCalling string of maximum_distance:minimum_overlap for amplicon based calling
      * @throws IOException if BAM file can't be read
@@ -2333,6 +2338,7 @@ static void findDEL(Configuration conf,
      * @param svrinv5 list of INV SVs in reverse direction in 5'
      * @param rlen max read length
      * @param chrs map of chromosome lengths
+     * @param referenceResource object for access to reference map
      * @param sample sample name
      * @param splice set of strings representing spliced regions
      * @param ampliconBasedCalling string of maximum_distance:minimum_overlap for amplicon based calling
@@ -2380,6 +2386,7 @@ static void findINV(Configuration conf,
      * @param side 3 or 5 end
      * @param rlen max read length
      * @param chrs map of chromosome lengths
+     * @param referenceResource object for access to reference map
      * @param sample sample name
      * @param splice set of strings representing spliced regions
      * @param ampliconBasedCalling string of maximum_distance:minimum_overlap for amplicon based calling

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

@@ -42,6 +42,7 @@ public class ToVarsBuilder {
      * @param SPLICE set of strings representing spliced regions
      * @param ampliconBasedCalling string of maximum_distance:minimum_overlap for amplicon based calling
      * @param Rlen maximum read length
+     * @param referenceResource object for access to reference map
      * @param conf VarDict configuration
      * @return Tuple of (maximum read length, variant structure)
      * @throws IOException if BAM file can't be read

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

@@ -676,6 +676,7 @@ && noPassingReads(chr, p, pe, bams, conf)
      * @param bam BAM file list
      * @param svfdel list of DEL SVs in forward strand
      * @param svrdel list of DEL SVs in reverse strand
+     * @param referenceResource object for access to reference map
      * @param conf configuration
      * @throws IOException if BAM file can't be read
      */
@@ -1094,6 +1095,7 @@ && isEquals(ref.get(bp - 1), ref.get(bp + dellen - 1))) {
      * @param bam BAM file list
      * @param svfdup list of DUP SVs in forward strand
      * @param svrdup list of DUP SVs in reverse strand
+     * @param referenceResource object for access to reference map
      * @param conf configuration
      * @throws IOException if BAM file can't be read
      */