Clean up sidecar index files (.tbi, .bai) in refine_assembly

Temp files created by samtools index (.bai) and tabix (.tbi) are not
managed by the tempfname context manager since they are derived from
the parent filename. Add explicit cleanup to prevent accumulation.

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

Author: dpark01

src/viral_ngs/assembly.py

@@ -752,6 +752,9 @@ def refine_assembly(
                 samtools.sort(downsampledUnsortedBam, downsampledBam, threads=threads)
                 samtools.index(downsampledBam, threads=threads)
                 fb.call(downsampledBam, deambigFasta, tmpVcf)
+                # clean up samtools index sidecar
+                if os.path.isfile(downsampledBam + '.bai'):
+                    os.unlink(downsampledBam + '.bai')
         else:
             fb.call(realignBam, deambigFasta, tmpVcf)
 
@@ -778,6 +781,9 @@ def refine_assembly(
             if outVcf.endswith('.gz'):
                 shutil.copyfile(tmpVcf + '.tbi', outVcf + '.tbi')
         shutil.copyfile(tmpFasta, outFasta)
+        # clean up tabix index sidecar created by FreeBayes/tabix
+        if os.path.isfile(tmpVcf + '.tbi'):
+            os.unlink(tmpVcf + '.tbi')
 
     # Index final output FASTA for Picard, Samtools, and Novoalign
     picard_index.execute(outFasta, overwrite=True)