fix build failure with Gcc 16 (#498)

Starting with Gcc 16, unused but set variables have become error.
This results in the following build failure in abyss.

	Consensus.cpp:379:18: error: variable ‘numIgnored’ set but not used [-Werror=unused-but-set-variable=]
	  379 |         unsigned numIgnored = 0;

This change drops occurrences of the numIgnored variable, since it is
unused.

Bug-Debian: https://bugs.debian.org/1132058

Signed-off-by: Étienne Mollier <emollier@debian.org>

Author: emollier

Consensus/Consensus.cpp

@@ -376,7 +376,6 @@ static void consensus(const string& outPath, const string& pileupPath)
 		: (pileupFile.open(pileupPath.c_str()), pileupFile);
 	assert_good(pileupOut, pileupPath);
 
-	unsigned numIgnored = 0;
 	for (ContigMap::const_iterator it = g_contigs.begin();
 			it != g_contigs.end(); ++it) {
 		const ContigCount& contig = it->second;
@@ -397,7 +396,6 @@ static void consensus(const string& outPath, const string& pileupPath)
 			float percentAgreement
 				= sumBest / (float)(sumBest + sumSecond);
 			if (isnan(percentAgreement) || percentAgreement < .9) {
-				numIgnored++;
 				if (opt::csToNt) {
 					if (opt::verbose > 0)
 						cerr << "warning: Contig " << it->first

RResolver/BloomFilters.cpp

@@ -141,10 +141,8 @@ loadReads(const std::vector<std::string>& readFilepaths, int r)
 {
 	ReadSize::readsSampleSize = 0;
 	ReadSize::current.sampleCount = 0;
-	int i = 0;
 	for (auto& b : ReadSize::readSizes) {
 		b.sampleCount = 0;
-		i++;
 	}
 
 	for (const auto& path : readFilepaths) {

SimpleGraph/SimpleGraph.cpp

@@ -516,7 +516,7 @@ static void handleEstimate(const Graph& g,
 			= makeDistanceMap(g, origin, *solIter);
 
 		// Remove solutions whose distance estimates are not correct.
-		unsigned validCount = 0, invalidCount = 0, ignoredCount = 0;
+		unsigned validCount = 0, invalidCount = 0;
 		for (Estimates::const_iterator iter
 					= er.estimates[dirIdx].begin();
 				iter != er.estimates[dirIdx].end(); ++iter) {
@@ -528,7 +528,6 @@ static void handleEstimate(const Graph& g,
 				= distanceMap.find(v);
 			if (dmIter == distanceMap.end()) {
 				// This contig is a repeat.
-				ignoredCount++;
 				vout << "ignored\n";
 				continue;
 			}
@@ -541,11 +540,9 @@ static void handleEstimate(const Graph& g,
 			bool invalid = (unsigned)abs(diff) > buffer;
 			bool repeat = repeats.count(v.contigIndex()) > 0;
 			bool ignored = invalid && repeat;
-			if (ignored)
-				ignoredCount++;
-			else if (invalid)
+			if (invalid)
 				invalidCount++;
-			else
+			else if (!ignored)
 				validCount++;
 			vout << "dist: " << actualDistance
 				<< " diff: " << diff