Merge pull request #108 from PolinaBevad/unique_mode_by_read_number

Added unique mode by read number (option -UN)

Readme.md

@@ -275,7 +275,10 @@ The VarDictJava program follows the workflow:
      `SILENT`   - Like `LENIENT`, only don't emit warning messages.
     Default: `LENIENT`
 - `-u`  
-    Indicate unique mode, which when mate pairs overlap, the overlapping part will be counted only once using forward read only.
+    Indicate unique mode, which when mate pairs overlap, the overlapping part will be counted only once using **forward** read only.
+    Default: unique mode disabled, all reads are counted.
+- `-UN`  
+    Indicate unique mode, which when mate pairs overlap, the overlapping part will be counted only once using **first** read only.
     Default: unique mode disabled, all reads are counted.
 - `--chimeric`
     Indicate to turn off chimeric reads filtering.  Chimeric reads are artifacts from library construction, 

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

@@ -147,7 +147,13 @@ public class Configuration {
      * Indicate unique mode, which when mate pairs overlap,
      * the overlapping part will be counted only once using forward read only.
      */
-    boolean uniqueModeOn = false; // -u
+    boolean uniqueModeAlignmentEnabled = false; // -u
+
+    /**
+     * Indicate unique mode, which when mate pairs overlap,
+     * the overlapping part will be counted only once using first read only.
+     */
+    boolean uniqueModeSecondInPairEnabled = false; // -UN
 
     /**
      * Threads count

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

@@ -137,9 +137,12 @@ private void run(CommandLine cmd) throws ParseException, IOException {
             conf.chimeric = true;
         }
 
+        if (cmd.hasOption("UN")) {
+            conf.uniqueModeSecondInPairEnabled = true;
+        }
 
         if (cmd.hasOption("u")) {
-            conf.uniqueModeOn = true;
+            conf.uniqueModeAlignmentEnabled = true;
         }
 
         conf.threads = Math.max(readThreadsCount(cmd), 1);
@@ -190,7 +193,8 @@ private static Options buildOptions() {
         options.addOption("t", false, "Indicate to remove duplicated reads.  Only one pair with same start positions will be kept");
         options.addOption("3", false, "Indicate to move indels to 3-prime if alternative alignment can be achieved.");
         options.addOption("K", false, "Include Ns in the total depth calculation");
-        options.addOption("u", false, "Indicate unique mode, which when mate pairs overlap, the overlapping part will be counted only once using forward read only.");
+        options.addOption("u", false, "Indicate unique mode, which when mate pairs overlap, the overlapping part will be counted only once using first read only.");
+        options.addOption("UN", false, "Indicate unique mode, which when mate pairs overlap, the overlapping part will be counted only once using forward read only.");
         options.addOption("chimeric", false, "Indicate to turn off chimeric reads filtering.");
 
         options.addOption(OptionBuilder.withArgName("bit")

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

@@ -1582,12 +1582,10 @@ static Tuple4<Map<Integer, Map<String, Variation>>, Map<Integer, Map<String, Var
 
                     int mateAlignmentStart = record.getMateAlignmentStart();
 
-                    boolean isPairedAndTheSameChromosome = record.getReadPairedFlag()
-                            && record.getMateReferenceName().equals(record.getReferenceName());
-
+                    processCigar:
                     //Loop over CIGAR records
                     for (int ci = 0; ci < cigar.numCigarElements(); ci++) {
-                        if (conf.uniqueModeOn && !dir && isPairedAndTheSameChromosome && start >= mateAlignmentStart) {
+                        if (skipOverlappingReads(conf, record, dir, start, mateAlignmentStart)) {
                             break;
                         }
                         //length of segment in CIGAR
@@ -2474,8 +2472,8 @@ && isNotEquals('N', ref.get(start))) {
                                 p++;
                             }
                             // Skip read if it is overlap
-                            if (conf.uniqueModeOn && !dir && isPairedAndTheSameChromosome && start >= mateAlignmentStart) {
-                                break;
+                            if (skipOverlappingReads(conf, record, dir, start, mateAlignmentStart)) {
+                                break processCigar;
                             }
                         }
                         if (moffset != 0) {
@@ -2500,28 +2498,59 @@ && isNotEquals('N', ref.get(start))) {
         }
 
         if (conf.performLocalRealignment) {
-            if (conf.y)
-                System.err.println("Start Realigndel");
-            realigndel(hash, dels5, cov, sclip5, sclip3, ref, region.chr, chrs, rlen, bams, conf);
-            if (conf.y)
-                System.err.println("Start Realignins");
-            realignins(hash, iHash, ins, cov, sclip5, sclip3, ref, region.chr, chrs, conf);
-            if (conf.y)
-                System.err.println("Start Realignlgdel");
-            realignlgdel(hash, cov, sclip5, sclip3, ref, region.chr, chrs, rlen, bams, conf);
-            if (conf.y)
-                System.err.println("Start Realignlgins");
-            realignlgins(hash, iHash, cov, sclip5, sclip3, ref, region.chr, chrs, rlen, bams, conf);
-            if (conf.y)
-                System.err.println("Start Realignlgins30");
-            realignlgins30(hash, iHash, cov, sclip5, sclip3, ref, region.chr, chrs, rlen, bams, conf);
+            realignIndels(region, chrs, rlen, ref, conf, bams, hash, iHash, cov, sclip3, sclip5, ins, dels5);
         }
 
         adjMNP(hash, mnp, cov, ref, sclip3, sclip5, conf);
 
         return tuple(hash, iHash, cov, rlen);
     }
 
+    private static void realignIndels(Region region, Map<String, Integer> chrs, int rlen, Map<Integer, Character> ref, Configuration conf, String[] bams, Map<Integer, Map<String, Variation>> hash, Map<Integer, Map<String, Variation>> iHash, Map<Integer, Integer> cov, Map<Integer, Sclip> sclip3, Map<Integer, Sclip> sclip5, Map<Integer, Map<String, Integer>> ins, Map<Integer, Map<String, Integer>> dels5) throws IOException {
+        if (conf.y)
+            System.err.println("Start Realigndel");
+        realigndel(hash, dels5, cov, sclip5, sclip3, ref, region.chr, chrs, rlen, bams, conf);
+        if (conf.y)
+            System.err.println("Start Realignins");
+        realignins(hash, iHash, ins, cov, sclip5, sclip3, ref, region.chr, chrs, conf);
+        if (conf.y)
+            System.err.println("Start Realignlgdel");
+        realignlgdel(hash, cov, sclip5, sclip3, ref, region.chr, chrs, rlen, bams, conf);
+        if (conf.y)
+            System.err.println("Start Realignlgins");
+        realignlgins(hash, iHash, cov, sclip5, sclip3, ref, region.chr, chrs, rlen, bams, conf);
+        if (conf.y)
+            System.err.println("Start Realignlgins30");
+        realignlgins30(hash, iHash, cov, sclip5, sclip3, ref, region.chr, chrs, rlen, bams, conf);
+    }
+
+    private static boolean skipOverlappingReads(Configuration conf, SAMRecord record, boolean dir, int start, int mateAlignmentStart) {
+        if (conf.uniqueModeAlignmentEnabled && isPairedAndSameChromosome(record)
+                && !dir && start >= mateAlignmentStart) {
+            return true;
+        }
+        if (conf.uniqueModeSecondInPairEnabled && record.getSecondOfPairFlag() && isPairedAndSameChromosome(record)
+                && isReadsOverlap(record, start, mateAlignmentStart)) {
+            return true;
+        }
+        return false;
+    }
+
+    private static boolean isReadsOverlap(SAMRecord record, int start, int mateAlignmentStart){
+        if (record.getAlignmentStart() >= mateAlignmentStart) {
+            return start >= mateAlignmentStart
+                            && start <= (mateAlignmentStart + record.getCigar().getReferenceLength() - 1);
+        }
+        else {
+            return start >= mateAlignmentStart
+                            && record.getMateAlignmentStart() <= record.getAlignmentEnd();
+        }
+    }
+
+    private static boolean isPairedAndSameChromosome(SAMRecord record) {
+        return record.getReadPairedFlag() && record.getMateReferenceName().equals(record.getReferenceName());
+    }
+
     private static void sclip3HighQualityProcessing(Region region, Configuration conf, Map<Integer, Sclip> sclip3,
                                                     String querySequence, int mappingQuality, String queryQuality,
                                                     int nm, int n, boolean dir, int start, int m, int q,

testdata/integrationtestcases/Simple;hg19.fa;L861Q.bam;chr7;55259400-55259600;-UN.txt

@@ -0,0 +1,4 @@
+Simple,hg19.fa,L861Q.bam,chr7,55259400,55259600,-UN
+L861Q	testbed	chr7	55259504	55259504	A	T	437	8	210	218	0	8	A/T	0.0183	2;0	7.0	0	36.0	0	60.0	16.000	0.0183	0	0	1.000	1	1.0	8	437	CCGCAGCATGTCAAGATCAC	GATTTTGGGCTGGCCAAACT	chr7:55259401-55259600	SNV
+L861Q	testbed	chr7	55259524	55259524	T	A	533	125	198	209	57	68	T/A	0.2345	2;2	21.6	1	35.5	1	60.0	124.000	0.2362	0	0	2.000	3	1.2	124	525	AGATTTTGGGCTGGCCAAAC	GCTGGGTGCGGAAGAGAAAG	chr7:55259401-55259600	SNV
+L861Q	testbed	chr7	55259544	55259544	G	A	371	4	164	202	3	1	G/A	0.0108	2;2	6.8	1	36.0	0	60.0	8.000	0.0110	0	0	2.000	1	1.5	4	365	TGCTGGGTGCGGAAGAGAAA	AATACCATGCAGAAGGAGGC	chr7:55259401-55259600	SNV