fix bug of specific init with AAAAA... in sequence and kmer

cobilab · Sep 26, 2023 · 5a592a5 · 5a592a5
1 parent bd5116e
commit 5a592a5
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Showing 2 changed files with 4 additions and 6 deletions.
diff --git a/benchmark/Download_FASTA.sh b/benchmark/Download_FASTA.sh
@@ -25,6 +25,3 @@ cat DNACorpus/* | gto_fasta_from_seq -n "CORPUS" > CORPUS.fa
 #
 # -----------------------------------------------------------------------------
 #
-wget virus.fa
-#
-#
diff --git a/src/repeats.c b/src/repeats.c
@@ -127,8 +127,11 @@ int32_t StartRM(RCLASS *C, uint32_t m, uint64_t i, uint8_t r)
     if(last == 0) return 0;
 
     RM = &C->RM[m];
-    uint64_t idx = rand() % C->T->nPos; 
+    uint64_t idx = rand() % C->T->nPos;
 
+    if(E[idx] <= C->P->ctx+1)
+      return 0;
+
     if(r == 0) // REGULAR REPEAT
       {
       if(E[idx] == 0)
@@ -138,8 +141,6 @@ int32_t StartRM(RCLASS *C, uint32_t m, uint64_t i, uint8_t r)
       }
     else // INVERTED REPEAT
       {
-      if(E[idx] <= C->P->ctx+1) 
-        return 0;
       RM->pos = E[idx] - C->P->ctx - 1;
       }
     }
-Original file line number
+Diff line change
@@ Expand Up / @@ -25,6 +25,3 @@ cat DNACorpus/* | gto_fasta_from_seq -n "CORPUS" > CORPUS.fa @@
     #
     # -----------------------------------------------------------------------------
     #
-    wget virus.fa
-    #
-    #