Fix 173 cram support

[jamesli124]

Fix for Issue #173 delfi claims CRAM support

Summary

• Add CRAM support for delfi using existing reference_file argument, which now accepts FASTA file format.
• Threads reference_file (FASTA) through all frag module functions
  (coverage, frag_length, frag_length_bins, frag_length_intervals,
  wps, multi_wps, cleavage_profile, multi_cleavage_profile) so CRAM
  files can be decoded correctly. Previously frag_generator was never passed
  the reference needed by htslib.
• Adds --reference-file CLI flags to frag-length-bins,
  frag-length-intervals, wps, and cleavage-profile subcommands.
• ReferenceWrapper now auto-creates a missing .fai index and recognises
  .fna/.fna.gz extensions, so FASTA files work out of the box for DELFI
  GC correction without manual indexing.
• Corrects CLI help text for delfi, end-motifs, interval-end-motifs,
  breakpoint-motifs, and interval-breakpoint-motifs to reflect that FASTA
  is accepted alongside .2bit.
• Adds tests/test_cram.py with equality tests (CRAM matches BAM) for
  single_coverage, frag_length_bins, wps, and delfi, plus smoke tests
  for all remaining functions. All tests skip automatically when samtools is
  not on PATH.

Notes

CRAM input requires a FASTA reference_file. .2bit cannot be used since
htslib requires FASTA for CRAM decoding.

[ravibandaru-lab]

gr8!