Fixed wrong sequenceHistory tracking in case of sequence-based merge …

…events. Minor fix for exportAlignmentsPretty translation mechanism.
milaboratory · Apr 6, 2018 · a25ba11 · a25ba11
1 parent 39cea2e
commit a25ba11
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Showing 2 changed files with 13 additions and 5 deletions.
diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatter.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatter.java
@@ -137,15 +137,16 @@ public static void drawAASequence(MultiAlignmentHelper helper, SequencePartition
                 ++aaPosition;
             }
             while (aaPosition < aa.size() &&
-                    aa.codeAt(aaPosition) != AminoAcidAlphabet.INCOMPLETE_CODON) {
+                    (aaPosition < aa.size() - 1 || aa.codeAt(aaPosition) != AminoAcidAlphabet.INCOMPLETE_CODON)) {
                 ntPosition = trParam.range.getFrom()
                         + AminoAcidSequence.convertAAPositionToNt(aaPosition, mainSequence.size(),
                         trParam.translationParameters);
                 line[helper.subjectToAlignmentPosition(ntPosition + 1)] =
                         AminoAcidSequence.ALPHABET.codeToSymbol(aa.codeAt(aaPosition));
                 ++aaPosition;
             }
-            if (aaPosition < aa.size() && aa.codeAt(aaPosition) == AminoAcidAlphabet.INCOMPLETE_CODON) {
+            if (aaPosition < aa.size() &&
+                    (aaPosition < aa.size() - 1 || aa.codeAt(aaPosition) != AminoAcidAlphabet.INCOMPLETE_CODON)) {
                 ntPosition = trParam.range.getFrom()
                         + AminoAcidSequence.convertAAPositionToNt(aaPosition, mainSequence.size(),
                         trParam.translationParameters);

diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMerge.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMerge.java
@@ -90,9 +90,16 @@ protected VDJCAlignmentResult<PairedRead> process0(final PairedRead read) {
                         new SequenceHistory[]{
                                 new SequenceHistory.Merge(
                                         SequenceHistory.OverlapType.SequenceOverlap,
-                                        new SequenceHistory.RawSequence(read.getId(), (byte) (isRC ? 1 : 0), false, read.getR1().getData().size()),
-                                        new SequenceHistory.RawSequence(read.getId(), (byte) (isRC ? 0 : 1), merged.isReversed(), read.getR2().getData().size()),
-                                        merged.getOffset(), merged.getErrors())
+                                        new SequenceHistory.RawSequence(read.getId(),
+                                                (byte) (isRC ? 1 : 0), false,
+                                                (isRC ? read.getR2().getData().size() : read.getR1().getData().size())),
+                                        new SequenceHistory.RawSequence(read.getId(),
+                                                (byte) (isRC ? 0 : 1), merged.isReversed(),
+                                                (isRC ? read.getR1().getData().size() : read.getR2().getData().size())),
+                                        isRC
+                                                ? merged.getOffset() + read.getR2().getData().size() - read.getR1().getData().size()
+                                                : merged.getOffset(),
+                                        merged.getErrors())
                         },
                         new SequenceRead[]{read});
             }