From ecea89f31d741bdac25b30965decd952cbbd9226 Mon Sep 17 00:00:00 2001
From: Joey Lee <leejoey0921@gmail.com>
Date: Fri, 30 Aug 2024 02:30:29 +0900
Subject: [PATCH] fix: disable feature by default

---
 src/commons/Parameters.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/commons/Parameters.cpp b/src/commons/Parameters.cpp
index 072a16a5..0cb81e9b 100644
--- a/src/commons/Parameters.cpp
+++ b/src/commons/Parameters.cpp
@@ -152,7 +152,6 @@ Parameters::Parameters():
         PARAM_IGNORE_MULTI_KMER(PARAM_IGNORE_MULTI_KMER_ID, "--ignore-multi-kmer", "Skip repeating k-mers", "Skip k-mers occurring multiple times (>=2)", typeid(bool), (void *) &ignoreMultiKmer, "", MMseqsParameter::COMMAND_CLUSTLINEAR | MMseqsParameter::COMMAND_EXPERT),
         PARAM_HASH_SHIFT(PARAM_HASH_SHIFT_ID, "--hash-shift", "Shift hash", "Shift k-mer hash initialization", typeid(int), (void *) &hashShift, "^[1-9]{1}[0-9]*$", MMseqsParameter::COMMAND_CLUSTLINEAR | MMseqsParameter::COMMAND_EXPERT),
         PARAM_PICK_N_SIMILAR(PARAM_PICK_N_SIMILAR_ID, "--pick-n-sim-kmer", "Add N similar to search", "Add N similar k-mers to search", typeid(int), (void *) &pickNbest, "^[1-9]{1}[0-9]*$", MMseqsParameter::COMMAND_CLUSTLINEAR | MMseqsParameter::COMMAND_EXPERT),
-        // TODO: qualify as COMMAND_EXPERT?
         PARAM_MATCH_ADJACENT_SEQ(PARAM_MATCH_ADJACENT_SEQ_ID, "--match-adjacent-seq", "Compare adjacent sequences to k-mers", "Compare sequence information adjacent to k-mers and elect multiple representative sequences per cluster", typeid(bool), (void *) &matchAdjacentSeq, "", MMseqsParameter::COMMAND_CLUSTLINEAR),
         PARAM_ADJUST_KMER_LEN(PARAM_ADJUST_KMER_LEN_ID, "--adjust-kmer-len", "Adjust k-mer length", "Adjust k-mer length based on specificity (only for nucleotides)", typeid(bool), (void *) &adjustKmerLength, "", MMseqsParameter::COMMAND_CLUSTLINEAR | MMseqsParameter::COMMAND_EXPERT),
         PARAM_RESULT_DIRECTION(PARAM_RESULT_DIRECTION_ID, "--result-direction", "Result direction", "result is 0: query, 1: target centric", typeid(int), (void *) &resultDirection, "^[0-1]{1}$", MMseqsParameter::COMMAND_CLUSTLINEAR | MMseqsParameter::COMMAND_EXPERT),
@@ -2515,7 +2514,8 @@ void Parameters::setDefaults() {
     resultDirection = Parameters::PARAM_RESULT_DIRECTION_TARGET;
     weightThr = 0.9;
     weightFile = "";
-    matchAdjacentSeq = true;
+    // TODO: change to true after fixing regression tests
+    matchAdjacentSeq = false;
     hashSeqBuffer = 1.05;
 
     // result2stats