Minor bug fix in case of readsLayout=Unknown.

Also minor addition to previous commit.

CHANGELOG_CURRENT

@@ -1,8 +1,9 @@
-Correct progress reporting with `-n` option in align action.
-Additional micro filtration step for paired-end read aligner (work in very rear cases)
-Added export options -vHitsWithoutScores (same for J and D genes)
-Added support for optional compression of .vdjca and .clns files (when specifying additional `.gz` extension: e.g. `mixcr align inut.fastq output.vdjca.gz` etc.)
-Possible set of D genes is limited by loci of V and J genes in current rearrengement
+Possible set of D genes is limited by loci of V and J genes in current rearrangement
 Default output format for `exportAlignmentsPretty` changed for the new one which is more compact and vivid
 Two new filtering options in `exportAlignmentsPretty`: `--cdr3-contains` and `--read-contains`
-Correct handling of quotes in paramters overriding
+m: Additional micro filtration step for paired-end read aligner (work in very rear cases)
+m: Fixed bug leading to incorrect behaviour if `readsLayout=Unknown`
+m: Correct progress reporting with `-n` option in align action.
+m: Added export options -vHitsWithoutScores (same for J and D genes)
+m: Added support for optional compression of .vdjca and .clns files (when specifying additional `.gz` extension: e.g. `mixcr align inut.fastq output.vdjca.gz` etc.)
+m: Correct handling of quotes in parameters overriding

src/main/java/com/milaboratory/mixcr/cli/JsonOverrider.java

@@ -68,7 +68,6 @@ public static boolean override(JsonNode node, String command) {
         String[] split = command.split("=", 2);
         String path = split[0];
         String value = split[1];
-        value = value.replaceAll("^[\'\"]", "").replaceAll("[\'\"]$", "");
         return override(node, path, value);
     }
 
@@ -77,6 +76,7 @@ public static boolean override(JsonNode node, String path, String value) {
     }
 
     private static boolean override1(JsonNode node, String path, String value, boolean v) {
+        value = value.replaceAll("^[\'\"]", "").replaceAll("[\'\"]$", "");
         if (node == null)
             return false;
         boolean b = false;

src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java

@@ -127,10 +127,10 @@ PairedTarget[] getTargets(PairedRead read) {
     }
 
     PAlignmentHelper[] createInitialHelpers(PairedTarget[] target) {
-        return new PAlignmentHelper[]{
-                createInitialHelper(target[0]),
-                createInitialHelper(target[1])
-        };
+        PAlignmentHelper[] result = new PAlignmentHelper[target.length];
+        for (int i = 0; i < target.length; i++)
+            result[i] = createInitialHelper(target[i]);
+        return result;
     }
 
     PAlignmentHelper createInitialHelper(PairedTarget target) {
@@ -289,7 +289,7 @@ VDJCAlignments createResult(long readId, VDJCAlignerPVFirst aligner) {
                     if (from > to)
                         continue;
                     List<PreVDJCHit> temp = singleDAligner.align0(target.targets[i].getSequence(),
-                            getPossibleDLoci(vHits,jHits), from, to);
+                            getPossibleDLoci(vHits, jHits), from, to);
                     preDHits[i] = temp.toArray(new PreVDJCHit[temp.size()]);
                 }