Removing quote symbols on both sides of value in parameter overriding…

… mechanism.

CHANGELOG_CURRENT

@@ -4,4 +4,5 @@ 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
 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`
+Two new filtering options in `exportAlignmentsPretty`: `--cdr3-contains` and `--read-contains`
+Correct handling of quotes in paramters overriding

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

@@ -68,6 +68,7 @@ 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);
     }
 

src/test/java/com/milaboratory/mixcr/cli/JsonOverriderTest.java

@@ -54,6 +54,19 @@ public void test1() throws Exception {
         Assert.assertEquals(expected, override);
     }
 
+    @Test
+    public void test1a() throws Exception {
+        KAlignerParameters parameters = KAlignerParameters.getByName("default");
+        KAlignerParameters override = JsonOverrider.override(
+                parameters,
+                KAlignerParameters.class,
+                "floatingLeftBound=true",
+                "scoring.subsMatrix='simple(match=4,mismatch=-9)'");
+        KAlignerParameters expected = parameters.clone().setFloatingLeftBound(true)
+                .setScoring(new LinearGapAlignmentScoring(NucleotideSequence.ALPHABET, 4, -9, parameters.getScoring().getGapPenalty()));
+        Assert.assertEquals(expected, override);
+    }
+
     @Test
     public void test2() throws Exception {
         KAlignerParameters parameters = KAlignerParameters.getByName("default");