From 31dcc31369c09e0f5abeb4f96774397bae6a7004 Mon Sep 17 00:00:00 2001
From: Evelin <evelin.aasna@fu-berlin.de>
Date: Wed, 11 Sep 2024 16:25:07 +0200
Subject: [PATCH] Fix compiler warnings

Fix include
---
 include/dream_stellar/options/dream_options.hpp            | 1 +
 include/dream_stellar/stellar_launcher.hpp                 | 3 +--
 .../verification/detail/all_or_best_local.hpp              | 2 +-
 include/valik/search/search_local.hpp                      | 7 -------
 4 files changed, 3 insertions(+), 10 deletions(-)

diff --git a/include/dream_stellar/options/dream_options.hpp b/include/dream_stellar/options/dream_options.hpp
index 78bdaa04..8769750a 100644
--- a/include/dream_stellar/options/dream_options.hpp
+++ b/include/dream_stellar/options/dream_options.hpp
@@ -2,6 +2,7 @@
 
 #include <set>
 #include <cstdint>
+#include <cstddef>
 #include <vector>
 
 namespace dream_stellar
diff --git a/include/dream_stellar/stellar_launcher.hpp b/include/dream_stellar/stellar_launcher.hpp
index 4a59fe32..32b951fb 100644
--- a/include/dream_stellar/stellar_launcher.hpp
+++ b/include/dream_stellar/stellar_launcher.hpp
@@ -53,7 +53,6 @@ struct StellarLauncher
     search_and_verify(
         StellarDatabaseSegment<TAlphabet> const databaseSegment,
         TId const & databaseID,
-        QueryIDMap<TAlphabet> const & queryIDMap,
         bool const databaseStrand,
         StellarOptions & localOptions, // localOptions.compactThresh is out-param
         StellarSwiftPattern<TAlphabet> & localSwiftPattern,
@@ -99,7 +98,7 @@ struct StellarLauncher
 
         StellarComputeStatistics statistics = _verificationMethodVisit(
             localOptions.verificationMethod,
-            [&]<typename TTag>(TTag tag) -> StellarComputeStatistics
+            [&]<typename TTag>(TTag) -> StellarComputeStatistics
             {
                 SwiftHitVerifier<TTag> swiftVerifier
                 {
diff --git a/include/dream_stellar/verification/detail/all_or_best_local.hpp b/include/dream_stellar/verification/detail/all_or_best_local.hpp
index 240bc9a2..0c797c55 100644
--- a/include/dream_stellar/verification/detail/all_or_best_local.hpp
+++ b/include/dream_stellar/verification/detail/all_or_best_local.hpp
@@ -217,7 +217,7 @@ allOrBestLocal(Segment<Segment<TSequence const, InfixSegment>, InfixSegment> con
     TEpsilon e = floor(eps*minLength);
     TSize minLength1 = _max(0, (TSize)ceil((e+1) / eps));
     TEpsilon e1 = floor(eps*minLength1);
-    TSize minScore = _min((TSize)ceil((minLength-e) / (e+1)), (TSize)ceil((minLength1-e1) / (e1+1)));
+    TScore minScore = _min((TSize)ceil((minLength-e) / (e+1)), (TSize)ceil((minLength1-e1) / (e1+1)));
 
     // diagonals for banded local alignment
     int64_t upperDiag = 0;
diff --git a/include/valik/search/search_local.hpp b/include/valik/search/search_local.hpp
index d2588bcd..c5470cfd 100644
--- a/include/valik/search/search_local.hpp
+++ b/include/valik/search/search_local.hpp
@@ -266,13 +266,10 @@ bool search_local(search_arguments & arguments, search_time_statistics & time_st
                         seqan2::resize(forwardMatches, length(queries));
 
                         constexpr bool databaseStrand = true;
-                        auto queryIDMap = dream_stellar::QueryIDMap<TAlphabet>(queries);
-
                         dream_stellar::StellarComputeStatistics statistics = dream_stellar::StellarLauncher<TAlphabet>::search_and_verify
                         (
                             databaseSegment,
                             databaseID,
-                            queryIDMap,
                             databaseStrand,
                             threadOptions,
                             swiftPattern,
@@ -328,14 +325,10 @@ bool search_local(search_arguments & arguments, search_time_statistics & time_st
                         seqan2::resize(reverseMatches, length(queries));
 
                         constexpr bool databaseStrand = false;
-
-                        dream_stellar::QueryIDMap<TAlphabet> queryIDMap{queries};
-
                         dream_stellar::StellarComputeStatistics statistics = dream_stellar::StellarLauncher<TAlphabet>::search_and_verify
                         (
                             databaseSegment,
                             databaseID,
-                            queryIDMap,
                             databaseStrand,
                             threadOptions,
                             swiftPattern,