chore(deps): update CPM packages

.github/workflows/ci_linux.yml

@@ -29,7 +29,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        compiler: ["clang-latest", "clang-second-latest", "gcc-latest", "gcc-second-latest", "gcc-third-latest", "intel"]
+        compiler: ["clang-latest", "clang-second-latest", "gcc-latest", "gcc-second-latest", "intel"]
         include:
           - compiler: "intel"
             cxx_flags: "-fp-model=strict -Wno-overriding-option"

.github/workflows/ci_macos.yml

@@ -25,11 +25,11 @@ defaults:
 jobs:
   build:
     name: ${{ matrix.compiler }}
-    runs-on: macos-14
+    runs-on: macos-latest
     strategy:
       fail-fast: false
       matrix:
-        compiler: ["clang-latest", "clang-second-latest", "gcc-latest", "gcc-second-latest", "gcc-third-latest"]
+        compiler: ["clang-latest", "clang-second-latest", "gcc-latest", "gcc-second-latest"]
     steps:
       - name: Checkout
         uses: actions/checkout@v6

.github/workflows/lint.yml

@@ -17,7 +17,7 @@ defaults:
 jobs:
   lint:
     name: Lint
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     timeout-minutes: 30
     permissions:
       contents: write

cmake/CPM.cmake

@@ -2,8 +2,8 @@
 #
 # SPDX-FileCopyrightText: Copyright (c) 2019-2023 Lars Melchior and contributors
 
-set (CPM_DOWNLOAD_VERSION 0.42.0)
-set (CPM_HASH_SUM "2020b4fc42dba44817983e06342e682ecfc3d2f484a581f11cc5731fbe4dce8a")
+set (CPM_DOWNLOAD_VERSION 0.42.1)
+set (CPM_HASH_SUM "f3a6dcc6a04ce9e7f51a127307fa4f699fb2bade357a8eb4c5b45df76e1dc6a5")
 
 if (CPM_SOURCE_CACHE)
     set (CPM_DOWNLOAD_LOCATION "${CPM_SOURCE_CACHE}/cpm/CPM_${CPM_DOWNLOAD_VERSION}.cmake")

cmake/package-lock.cmake

@@ -8,7 +8,7 @@
 # cmake-format: off
 
 # hibf
-set (HIBF_VERSION 7cc3e7119e203b8b65fb6f2ea92cfe3e7645a106 CACHE STRING "")
+set (HIBF_VERSION 37108885a53eec0a0d64251ffc60d43bcf9f9b49 CACHE STRING "")
 CPMDeclarePackage (hibf
                    NAME hibf
                    GIT_TAG ${HIBF_VERSION} # main
@@ -19,18 +19,19 @@ CPMDeclarePackage (hibf
 )
 
 # sharg
-set (SHARG_VERSION cafa602ced86f3a347064c5b8188316db09ade72 CACHE STRING "")
+set (SHARG_VERSION 1.2.2 CACHE STRING "")
 CPMDeclarePackage (sharg
                    NAME sharg
-                   GIT_TAG ${SHARG_VERSION} # main
+                   VERSION ${SHARG_VERSION}
+                   GIT_TAG ${SHARG_VERSION}
                    GITHUB_REPOSITORY seqan/sharg-parser
                    SYSTEM TRUE
                    EXCLUDE_FROM_ALL TRUE
                    OPTIONS "INSTALL_SHARG OFF" "INSTALL_TDL OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING" "SHARG_NO_TDL ON"
 )
 
 # seqan3
-set (SEQAN3_VERSION 3.4.0 CACHE STRING "")
+set (SEQAN3_VERSION 3.4.2 CACHE STRING "")
 CPMDeclarePackage (seqan3
                    NAME seqan3
                    VERSION ${SEQAN3_VERSION}
@@ -54,10 +55,11 @@ CPMDeclarePackage (fmt
 )
 
 # fmindex
-set (FMINDEX_VERSION e35626ba983dde88107709345f1efe49f1ac02e1 CACHE STRING "")
+set (FMINDEX_VERSION 1.6.2 CACHE STRING "")
 CPMDeclarePackage (fmindex
                    NAME fmindex
-                   GIT_TAG ${FMINDEX_VERSION} # main
+                   VERSION ${FMINDEX_VERSION} # latest
+                   GIT_TAG v${FMINDEX_VERSION}
                    GITHUB_REPOSITORY SGSSGene/fmindex-collection
                    SYSTEM TRUE
                    EXCLUDE_FROM_ALL TRUE

include/fpgalign/utility/compat.hpp

@@ -0,0 +1,43 @@
+// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
+// SPDX-License-Identifier: BSD-3-Clause
+
+#pragma once
+
+#include <fmindex-collection/search/SearchNg26.h>
+
+namespace fmc::search_ng26
+{
+
+template <bool Edit = true, typename index_t, Sequence query_t, typename delegate_t>
+void search(index_t const & index,
+            query_t && query,
+            size_t maxErrors,
+            delegate_t && delegate,
+            size_t n = std::numeric_limits<size_t>::max())
+{
+    auto selectSearchScheme = [&]([[maybe_unused]] size_t length) -> auto
+    {
+        auto const & search_scheme = getCachedSearchScheme<Edit>(0, maxErrors, /*.shortLen=*/(length == 2));
+        auto const & partition = getCachedPartition(search_scheme[0].pi.size(), length);
+        return std::tie(search_scheme, partition);
+    };
+    size_t ct{};
+    auto const & [search_scheme, partition] = selectSearchScheme(query.size());
+    search_impl<Edit>(index,
+                      query,
+                      search_scheme,
+                      partition,
+                      [&](auto cur, size_t e)
+                      {
+                          if (cur.count() + ct > n)
+                          {
+                              cur.len = n - ct;
+                          }
+                          ct += cur.count();
+                          delegate(cur, e);
+                          return ct == n;
+                      });
+}
+
+} // namespace fmc::search_ng26

src/argument_parsing.cpp

@@ -3,7 +3,6 @@
 // SPDX-License-Identifier: BSD-3-Clause
 
 #include <algorithm>   // for find_if
-#include <charconv>    // for from_chars
 #include <cstddef>     // for size_t
 #include <filesystem>  // for operator<<, operator>>
 #include <iomanip>     // for operator<<, quoted
@@ -18,6 +17,7 @@
 #include <sharg/detail/to_string.hpp> // for to_string
 #include <sharg/exceptions.hpp>       // for validation_error
 #include <sharg/parser.hpp>           // for parser
+#include <sharg/std/charconv>         // for from_chars
 #include <sharg/validators.hpp>       // for arithmetic_range_validator, input_file_validator, output_file_open_...
 
 #include <fpgalign/argument_parsing.hpp> // for parse_result, subcommand, parse_arguments

src/search/do_alignment.cpp

@@ -3,7 +3,6 @@
 // SPDX-License-Identifier: BSD-3-Clause
 
 #include <algorithm>  // for find_if
-#include <charconv>   // for to_chars
 #include <cstddef>    // for size_t
 #include <cstdint>    // for uint8_t
 #include <filesystem> // for path
@@ -14,6 +13,8 @@
 #include <utility>    // for pair
 #include <vector>     // for vector
 
+#include <sharg/std/charconv> // for to_chars
+
 #include <seqan3/alignment/cigar_conversion/cigar_from_alignment.hpp>              // for cigar_from_alignment
 #include <seqan3/alignment/configuration/align_config_edit.hpp>                    // for edit_scheme
 #include <seqan3/alignment/configuration/align_config_gap_cost_affine.hpp>         // for gap_cost_affine

src/search/fmindex.cpp

@@ -12,6 +12,10 @@
 #include <seqan3/alphabet/nucleotide/dna4.hpp> // for dna4
 #include <seqan3/io/sequence_file/record.hpp>  // for sequence_record
 
+// clang-format: off
+#include <fpgalign/utility/compat.hpp> // IWYU pragma: keep
+// clang-format: on
+
 #include <fmindex-collection/fmindex/BiFMIndex.h> // for BiFMIndex
 #include <fmindex-collection/search/search.h>     // for search
 
@@ -45,8 +49,7 @@ void fmindex(config const & config,
                 {
                     for (auto j : cursor)
                     {
-                        auto [entry, offset] = index.locate(j);
-                        auto [seqId, pos] = entry;
+                        auto [seqId, pos, offset] = index.locate(j);
                         alignment_queue.enqueue(slot,
                                                 alignment_info{.query_idx = idx,
                                                                .reference_number = seqId,