Throw ex-info on hgvs->vcf for a variant containing ambiguous coordinates

[totakke]

Current hgvs->vcf throws NPE when a variant containing ambiguous coordinates is supplied.

(require '[varity.hgvs-to-vcf :as h2v]
         '[clj-hgvs.core :as hgvs])

(h2v/hgvs->vcf-variants (hgvs/parse "NM_007294:c.1-?_80+?del")
                        "path/to/fasta.fa"
                        "path/to/refGene.txt")
;; NullPointerException   clojure.lang.Numbers.ops (Numbers.java:1018)

NM_007294:c.1-?_80+?del is totally correct as a coding DNA HGVS, but it
cannot be converted to a VCF variant because genomic positions are underspecified.
I modified cds-coord->genomic-pos to throw ex-info with :ambiguous-coordinate
error type when such a coordinate is passed.

(try
  (h2v/hgvs->vcf-variants (hgvs/parse "NM_007294:c.1-?_80+?del")
                          "path/to/fasta.fa"
                          "path/to/refGene.txt")
  (catch Exception e
    (ex-data e)))
;;=> {:type :varity.hgvs-to-vcf.cdna/ambiguous-coordinate,
;;    :coordinate {:start {:position 80, :offset 1, :region nil}, :end {}}}

This patch is useful for error handling on hgvs->vcf.

And besides, I removed oraclejdk from CI because they cause build failure (Build #229).
That may be resolved if using Trusty instead of Xenial, but I think only tests with OpenJDK are enough for this library.

I confirmed lein test :all passed.

[codecov]

Codecov Report

Merging #27 into master will decrease coverage by 0.16%.
The diff coverage is 2.08%.

@@            Coverage Diff             @@
##           master      #27      +/-   ##
==========================================
- Coverage    38.4%   38.24%   -0.17%     
==========================================
  Files          13       13              
  Lines        1471     1480       +9     
  Branches       31       31              
==========================================
+ Hits          565      566       +1     
- Misses        875      883       +8     
  Partials       31       31

Impacted Files	Coverage Δ
src/varity/hgvs_to_vcf/cdna.clj	7.85% <2.08%> (+0.22%)	⬆️

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[alumi]

LGTM 👍and thank you for fixing the CI config!