Fix: Added a fix in CLI and fragCounter.R to take reference when cram files are used.

[tanubrata]

Description:

• Updated the CLI to consider reference when mentioned with CRAM format input
• Updated PrepareCov() function to accept reference when CRAM files are provided.

Changes:

• Updated the CLI to add an option for reference when CRAM files are given as input
• Updated PrepareCov() function to take reference
• Updated the DESCRIPTION and NAMESPACE to set the current paths of in-house packages
• Added a typo fix in line 956 ( cramo -> cram)
• Loading the GenomeInfoDb because it was failing for cram files

Impact:

• This should fix the issue for working with cram files

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