Address PR review comments: cleanup stale GATK references and temp files

- Rename '# ========= GATK ==========' section header to 'align_and_fix'
- Remove unused IS_ARM import from test_assembly_integration.py
- Clean up .tbi temp file after FreeBayes VCF processing
- Fix stale 'deambiguated genome for GATK' comment

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: dpark01

src/viral_ngs/assembly.py

@@ -704,7 +704,7 @@ def refine_assembly(
     if not already_realigned_bam:
         novoalign = viral_ngs.core.novoalign.NovoalignTool(license_path=novoalign_license_path)
 
-    # Sanitize fasta header & create deambiguated genome for GATK
+    # Sanitize fasta header & create deambiguated genome for variant calling
     deambigFasta = viral_ngs.core.file.mkstempfname('.deambig.fasta')
     with viral_ngs.core.file.fastas_with_sanitized_ids(inFasta, use_tmp=True) as sanitized_fastas:
         deambig_fasta(sanitized_fastas[0], deambigFasta)
@@ -763,6 +763,8 @@ def refine_assembly(
         if outVcf.endswith('.gz'):
             shutil.copyfile(tmpVcf + '.tbi', outVcf + '.tbi')
     os.unlink(tmpVcf)
+    if os.path.exists(tmpVcf + '.tbi'):
+        os.unlink(tmpVcf + '.tbi')
     shutil.copyfile(tmpFasta, outFasta)
     os.unlink(tmpFasta)
 

src/viral_ngs/read_utils.py

@@ -1233,7 +1233,7 @@ def main_novoindex(args):
 
 __commands__.append(('novoindex', parser_novoindex))
 
-# ========= GATK ==========
+# ========= align_and_fix ==========
 
 
 def align_and_fix(

tests/unit/assemble/test_assembly_integration.py

@@ -17,7 +17,7 @@
 import viral_ngs.core.minimap2
 import viral_ngs.core.picard
 import viral_ngs.core.samtools
-from tests import TestCaseWithTmp, _CPUS, IS_ARM
+from tests import TestCaseWithTmp, _CPUS
 
 
 def _align_with_minimap2(refFasta, inBam):