From 1ce81a749cf9cc29ff28775a3cd6e40e59c63292 Mon Sep 17 00:00:00 2001
From: nrizzo <nrizzo@users.noreply.github.com>
Date: Tue, 14 Jul 2026 16:54:46 +0300
Subject: [PATCH 1/2] .gitignore. Ignore generated files in local build

---
 .gitignore | 63 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)

diff --git a/.gitignore b/.gitignore
index 3ba52be..53fbea4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -16,3 +16,66 @@ compile
 test-driver
 compile_commands.json
 .deps
+Makefile
+libtool
+mummer.pc
+stamp-h1
+*.o
+*.lo
+.libs
+annotate
+combineMUMs
+delta-filter
+delta2vcf
+dnadiff
+exact-tandems
+libumdmummer.la
+mgaps
+mummer
+mummerplot
+nucmer
+nucmer_ori
+postnuc
+postpro
+prenuc
+prepro
+promer
+repeat-match
+show-aligns
+show-coords
+show-diff
+show-snps
+show-tiling
+*.dirstamp
+src/umd/nucmer_cmdline.hpp
+*.log
+*.trs
+tests/batch
+tests/check_LCP
+tests/check_LCP_cmdline.hpp
+tests/check_cigar
+tests/check_cigar_cmdline.hpp
+tests/data/
+tests/generate_sequences
+tests/generate_sequences_cmdline.hpp
+tests/genome/
+tests/sam/
+tests/save_load/
+tests/testsh
+tests/ufasta
+tests/ufasta_src/dsort_cmdline.hpp
+tests/ufasta_src/extract_cmdline.hpp
+tests/ufasta_src/format_cmdline.hpp
+tests/ufasta_src/head_cmdline.hpp
+tests/ufasta_src/n50_cmdline.hpp
+tests/ufasta_src/one_cmdline.hpp
+tests/ufasta_src/rc_cmdline.hpp
+tests/ufasta_src/rsort_cmdline.hpp
+tests/ufasta_src/sizes_cmdline.hpp
+tests/ufasta_src/sort_cmdline.hpp
+tests/ufasta_src/split_cmdline.hpp
+tests/ufasta_src/tail_cmdline.hpp
+unittests/libgtest.la
+unittests/libgtest_main.la
+unittests/test_all
+unittests/tmp/

From d1a7d0db301a47a6a25538ee4a4a1f49052b8082 Mon Sep 17 00:00:00 2001
From: nrizzo <nrizzo@users.noreply.github.com>
Date: Tue, 14 Jul 2026 17:07:06 +0300
Subject: [PATCH 2/2] fixed bug mummer (issue #235)

---
 include/mummer/sparseSA.hpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/mummer/sparseSA.hpp b/include/mummer/sparseSA.hpp
index 4cceeeb..61bb921 100644
--- a/include/mummer/sparseSA.hpp
+++ b/include/mummer/sparseSA.hpp
@@ -653,7 +653,7 @@ void sparseSA::findMEM_k_each(const char* P, size_t Plen, long k, int min_len, b
         int i = 0;
         bool succes  = true;
         while(i < sparseMult && (succes = suffixlink(mli))){
-          suffixlink(xmi);
+          if( !suffixlink(xmi) ){ xmi = mli; }
           i++;
         }
         if(!succes){