filter damaged variants: clean output + VCF filtering

- flag C>T/G>A at read ends (end<=10) as FFPE-suspect, strand bias as supporting evidence
- outputs: candidate_variants.tsv [is_ffpe_suspect,ffpe_reason], clean_variants.tsv,
  ffpe_suspect_variants.tsv, candidate_CtoT/GtoA_clean.bed
- optional --vcf: produce .clean.vcf (without damaged) and .ffpe_flagged.vcf;
  with --keep-damaged mark FILTER=FFPE instead of removing
- auto-create BAM/FASTA index if missing, improved error messages

.gitignore

@@ -3,3 +3,14 @@ __pycache__/
 *.pyc
 test_data/
 FFPE_QC/
+FFPE_sample/
+*.bam
+*.bai
+*.fai
+hg38.fa
+hg38.fa.gz
+*.vcf.gz
+*.tbi
+*.zip
+README.html
+124/