Fix issues in masksequence

soedinglab · Dec 8, 2024 · b80ce10 · b80ce10
1 parent a2d01d0
commit b80ce10
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Showing 3 changed files with 5 additions and 2 deletions.
diff --git a/src/commons/Masker.cpp b/src/commons/Masker.cpp
@@ -20,7 +20,7 @@ int Masker::maskSequence(Sequence & seq, bool maskTantan, double maskProb,
     if(maskTantan){
         // 1. Apply tantan masking without influencing by repeat mask
         maskedResidues += tantan::maskSequences(seq.numSequence,
-                                            (seq.numSequence + seq.L),
+                                            seq.numSequence + seq.L,
                                             50 /*maxCycleLength*/,
                                             probMatrix.probMatrixPointers,
                                             0.005 /*repeatProb*/,

diff --git a/src/commons/Parameters.cpp b/src/commons/Parameters.cpp
@@ -768,6 +768,7 @@ Parameters::Parameters():
 
     // mask sequence
     masksequence.push_back(&PARAM_MASK_PROBABILTY);
+    masksequence.push_back(&PARAM_MASK_N_REPEAT);
     masksequence.push_back(&PARAM_THREADS);
     masksequence.push_back(&PARAM_COMPRESSED);
     masksequence.push_back(&PARAM_V);

diff --git a/src/util/masksequence.cpp b/src/util/masksequence.cpp
@@ -46,8 +46,10 @@ int masksequence(int argc, const char **argv, const Command& command) {
         for (size_t id = 0; id < reader.getSize(); ++id) {
             seq.mapSequence(id, reader.getDbKey(id), reader.getData(id, thread_idx), reader.getSeqLen(id));
             masker.maskSequence(seq, true, par.maskProb, par.maskLowerCaseMode, par.maskNrepeats);
+            memcpy(charSequence, seq.getSeqData(), seq.L * sizeof(char));
             masker.applySoftmasking(charSequence, seq.numSequence, seq.L);
-            writer.writeData((char*)charSequence, seq.L,  thread_idx);
+            charSequence[seq.L] = '\n';
+            writer.writeData((const char *)charSequence, seq.L + 1,  seq.getDbKey(), thread_idx);
         }
         delete[] charSequence;
     }