From 5a592a553b8b0162ae142a45da95042108d103a5 Mon Sep 17 00:00:00 2001
From: pratas <6882743+pratas@users.noreply.github.com>
Date: Tue, 26 Sep 2023 15:34:05 +0100
Subject: [PATCH] fix bug of specific init with AAAAA... in sequence and kmer

---
 benchmark/Download_FASTA.sh | 3 ---
 src/repeats.c               | 7 ++++---
 2 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/benchmark/Download_FASTA.sh b/benchmark/Download_FASTA.sh
index 9d9ca0c..98d5fda 100755
--- 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
index c6f864d..1cb93e8 100644
--- 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;
       }
     }