add support for unmmapped bams

[zhuchcn]

Description

Command line argument -u/--unmapped-bam was added to avoid the error of pysam.quickcheck for unmapped bam files because of missing reference files in the BAM header.

I'm not very familiar with the unittest set up in this repo, so not sure how to add a test case. If anyone could help me with this it would be fantastic.

Closes #97

---

Test Results

Validation Test

BAM

Case 1 - test type:

• input file(s):

  path/to/input
  

• command:

  <command used>
  

• output:

  path/to/output OR output-message
  

VCF

Case 1 - test:

• input file(s):

  path/to/input
  

• command:

  <command used>
  

• output:

  path/to/output OR output-message
  

Case 2 - test:

• input file(s):

  path/to/input
  

• command:

  <command used>
  

• output:

  path/to/output OR output-message
  

---

Checksum Test

Case 1 - test:

• input file(s):

  path/to/input
  

• command:

  <command used>
  

• output:

  path/to/output OR output-message
  

---

Checklist

File Commits

• This PR does NOT contain Protected Health Information (PHI). A repo may need to be deleted if such data is uploaded.
  Disclosing PHI is a major problem¹ - Even a small leak can be costly².

• This PR does NOT contain germline genetic data³, RNA-Seq, DNA methylation, microbiome or other molecular data⁴.

• This PR does NOT contain other non-plain text files, such as: compressed files, images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other output files.

  To automatically exclude such files using a .gitignore file, see here for example.

Code Review Best Practices

• I have read the code review guidelines and the code review best practice on GitHub check-list.

• I have set up or verified the main branch protection rule following the github standards before opening this pull request.

• The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].

• I have added the major changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

Testing

• I have added unit tests for the new feature(s).

• I modified the integration test(s) to include the new feature.

• All new and previously existing tests passed locally and/or on the cluster.

• The docker image built successfully on the cluster.

Footnotes

1. UCLA Health reaches $7.5m settlement over 2015 breach of 4.5m patient records ↩

2. The average healthcare data breach costs $2.2 million, despite the majority of breaches releasing fewer than 500 records. ↩

3. Genetic information is considered PHI.
   Forensic assays can identify patients with as few as 21 SNPs ↩

4. RNA-Seq, DNA methylation, microbiome, or other molecular data can be used to predict genotypes (PHI) and reveal a patient's identity. ↩

[nwiltsie]

I'll get to this today!

[nwiltsie]

Looks good to me!

I ran pytest locally to confirm that @yashpatel6's changes still work. We should set up an Action to do so automatically as well.

[yashpatel6]

Looks good to me!

I ran pytest locally to confirm that @yashpatel6's changes still work. We should set up an Action to do so automatically as well.

Agreed, I think we want to set up a pytest action, we've had some discussion in the software WG around this with running and also generating coverage reports and such