Use helper methods to create IN clauses (#449)

## Rationale
Using helpers to generate SQL IN clauses is more convenient and prevents
broken SQL & injection risks

## Related Pull Requests
- LabKey/platform#8187

Author: labkey-adam

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisManager.java

@@ -436,7 +436,7 @@ else if (doDelete)
 
     public Set<Integer> getAnalysesAssociatedWithOutputFiles(List<Integer> outputFileIds)
     {
-        Set<Integer> possibleDeletes = new HashSet<>(outputFileIds.isEmpty() ? Collections.emptyList() : new SqlSelector(SequenceAnalysisSchema.getInstance().getSchema(), new SQLFragment("SELECT distinct a.rowid FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_OUTPUTFILES + " o JOIN " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_ANALYSES + " a ON (o.dataId = a.alignmentFile) WHERE o.rowid IN (" + StringUtils.join(outputFileIds, ",") + ")")).getArrayList(Integer.class));
+        Set<Integer> possibleDeletes = new HashSet<>(outputFileIds.isEmpty() ? Collections.emptyList() : new SqlSelector(SequenceAnalysisSchema.getInstance().getSchema(), new SQLFragment("SELECT distinct a.rowid FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_OUTPUTFILES + " o JOIN " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_ANALYSES + " a ON (o.dataId = a.alignmentFile) WHERE o.rowid").appendInClause(outputFileIds, SequenceAnalysisSchema.getInstance().getSchema().getSqlDialect())).getArrayList(Integer.class));
 
         //make sure these are not in use by other outputfiles not being deleted
         if (!possibleDeletes.isEmpty())

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java

@@ -7,6 +7,7 @@
 import htsjdk.variant.utils.SAMSequenceDictionaryExtractor;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.Strings;
 import org.apache.commons.lang3.math.NumberUtils;
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.Nullable;
@@ -86,7 +87,7 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
         {
             SAMSequenceDictionary dict = SAMSequenceDictionaryExtractor.extractDictionary(genome.getSequenceDictionary().toPath());
             List<String> toKeep = dict.getSequences().stream().map(SAMSequenceRecord::getSequenceName).filter(sequenceName -> {
-                String name = StringUtils.replaceIgnoreCase(sequenceName, "^chr", "");
+                String name = Strings.CI.replace(sequenceName, "^chr", "");
 
                 return NumberUtils.isCreatable(name) || "X".equalsIgnoreCase(name) || "Y".equalsIgnoreCase(name);
             }).toList();

SequenceAnalysis/src/org/labkey/sequenceanalysis/util/AbstractSequenceMatcher.java

@@ -4,6 +4,7 @@
 import htsjdk.samtools.fastq.FastqRecord;
 import htsjdk.samtools.fastq.FastqWriter;
 import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.text.similarity.LevenshteinDistance;
 import org.apache.logging.log4j.Logger;
 import org.labkey.api.util.Pair;
 import org.labkey.sequenceanalysis.model.SequenceTag;
@@ -82,7 +83,7 @@ protected void processTag5(FastqRecord rec, String sequenceToTest, SequenceTag b
             targetSeq = sequenceToTest.substring(0, barcodeSeq.length());
         }
 
-        int editDist = StringUtils.getLevenshteinDistance(barcodeSeq, targetSeq);
+        int editDist = LevenshteinDistance.getDefaultInstance().apply(barcodeSeq, targetSeq);
         if (editDist <= _editDistance)
         {
             Map<String, SequenceMatch> matchesAtDist = trackingMap.get(editDist);
@@ -117,7 +118,7 @@ protected void processTag3(FastqRecord rec, String sequenceToTest, SequenceTag b
             targetSeq = StringUtils.reverse(sequenceToTest).substring(0, barcodeSeq.length());
         }
 
-        int editDist = StringUtils.getLevenshteinDistance(barcodeSeq, targetSeq);
+        int editDist = LevenshteinDistance.getDefaultInstance().apply(barcodeSeq, targetSeq);
         if (editDist <= _editDistance)
         {
             Map<String, SequenceMatch> matchesAtDist = trackingMap.get(editDist);