Additionally "per-read" collapse immunoseq dataset, probably fixes a reported bug

Author: mikessh

src/main/groovy/com/antigenomics/vdjtools/misc/CommonUtil.groovy

@@ -385,6 +385,11 @@ public class CommonUtil {
 
     final static String OOF_SYMBOLS_POSSIBLE = /([atgc#~_\?])+/, OOF_CHAR = "_", STOP_CHAR = "*"
 
+    /**
+     * Translates CDR3 sequence in V><J directions simultaneously, supports non-coding sequences
+     * @param seq sequence to translate
+     * @return amino acid sequence, as String object
+     */
     static String translate(String seq) {
         if (seq.length() == 0)
             return ""

src/main/groovy/com/antigenomics/vdjtools/misc/Software.groovy

@@ -49,13 +49,13 @@ enum Software {
                                         "cdr1nt", "cdr2nt", "cdr3nt", "cdr1aa", "cdr2aa", "cdr3aa",
                                         "inFrame", "noStop", "complete",
                                         4.times { _ }].flatten()),
-    ImmunoSeq("\t", null, 1, true, false, ["cdr3nt", "cdr3aa", "count", "freq", "cdr3Length",
+    ImmunoSeq("\t", null, 1, true, true, ["cdr3nt", "cdr3aa", "count", "freq", "cdr3Length",
                                            _, "v", 5.times { _ },
                                            _, "d", 5.times { _ },
                                            _, "j", 5.times { _ },
                                            6.times { _ },
                                            _, "VEnd", "DStart", "DEnd", "JStart"].flatten()),
-    ImmunoSeqV3("\t", null, 1, true, false, ["cdr3nt", "cdr3aa", "count", "freq", "cdr3Length",
+    ImmunoSeqV3("\t", null, 1, true, true, ["cdr3nt", "cdr3aa", "count", "freq", "cdr3Length",
                                            _, "v", 5.times { _ },
                                            _, "d", 5.times { _ },
                                            _, "j", 5.times { _ },