Add support for LinkSeq XML

[hinerm]

Referenced here.

XML Sections to parse

It looks like the XML has an labAssignmentSection block at the top which includes the assigned typings. These can be read and passed to a ValidationModelBuilder to populate the core typing data.

For haplotype information, there is a testResultsSection that has all the possible alleles for each locus, which will be used to populate haplotype information.

Implementation Notes

• You can use the Score6 XML parser as a reference for how to read the desired XML sections.
• For reference, the XML parsing is done with JSoup. You're given the Document, so building the parser is all about finding the appropriate XML Elements, getting their text contents, and passing them appropriately to the builder.

Goals

• Assigned typing parsing works
• Haplotype parsing works

[hinerm]

• @kaitlinrenee I think a good first step is to try out the JSoup API to get all the elements of the labAssignmentSection

[hinerm]

The XML hierarchy of the haplotype allele storage for a single locus is:

• testResult (e.g. HLA-A)
  • hlaCallList (result combinations)
    • hlaTestCall (a specific strand 1 + strand 2 allele combination)
      • hlaTestCallGroup (results for a single strand in the combination)

The hlaCallList can contain multiple hlaTestCalls:

When there are multiple entries like this, we should look for a this was MANUALLY chosen flag in the footnote list:

and that is the hlaTestCall we should pull allele information from.

If a testCallList contains multiple hlaTestCalls and none have that footnote, just skip the check including that locus (e.g. if there are multiple C calls and none were manually selected, we wouldn't compute any B-C haplotype probabilities)