Add competitive --bam and --cram CLI options, CRAM output with reference, fallback to BAM if reference missing, update help, enable BAM/CRAM by default

[BenjaminDEMAILLE]

Add competitive --bam and --cram CLI options, CRAM output with reference, fallback to BAM if reference missing, update help, enable BAM/CRAM by default

Summary

• Adds two mutually exclusive CLI flags: --bam and --cram to force output format.
• Adds --cram-reference to specify the reference FASTA for CRAM output (required for CRAM).
• If --cram is specified without --cram-reference, falls back to BAM output with a warning.
• Updates help text to document all new options and clarify usage.
• Enables BAM/CRAM (HTSLIB) support by default in CMake.
• Output CRAM files are fully compatible with samtools and other HTSlib tools.

Usage

• --bam : Force BAM output.
• --cram --cram-reference=ref.fa : Force CRAM output using the provided reference (must be the same as for the index).
• If both --bam and --cram are set, the program exits with an error.
• If --cram is set without --cram-reference, the program falls back to BAM output and prints a warning.

Motivation

• Improves user control over output format.
• Ensures CRAM output is always valid and compatible.
• Makes the CLI more explicit and user-friendly.

Let me know if you need any changes or more details!