Rewrote the getType method to handle all ploidy levels

[NeillGibson]

Hi,

I rewrote the getType method to handle all ploidy levels.

This is inspired by getType / determineType method in HTS-JDK genotype:
https://github.com/samtools/htsjdk/blob/bd92747fd3672635de96473fea6d4b38e8635c8e/src/java/htsjdk/variant/variantcontext/Genotype.java#L197

I am not sure if the code runs trough the tests, I have some difficulty setting up all code dependencies locally in my IDE (IntelliJ) to run the tests. If the code fails tests please see this as the pseudo code of the method.

One open issue for this code is still which genotypeType to return for genotypes that consist of multiple OtherAlt alleles. #897

Currently the method in this pull request returns NoCall for a genotype consisting of just OtherAlt alleles. This is also what the current method does.

[AmplabJenkins]

Can one of the admins verify this patch?

[heuermh]

Jenkins, test this please.

[AmplabJenkins]

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1036/

Build result: FAILURE

GitHub pull request #904 of commit 46803be automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/904/merge^{commit} # timeout=10 > git branch -a --contains 0ce87c3 # timeout=10 > git rev-parse remotes/origin/pr/904/merge^{commit} # timeout=10Checking out Revision 0ce87c3 (origin/pr/904/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 0ce87c3b0d1617248afeb08b889585a0997f5a63First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

[NeillGibson]

Jenkins, test this please.

[heuermh]

Jenkins, retest this please.

[AmplabJenkins]

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1039/
Test PASSed.

[heuermh]

use IllegalStateException instead?

Then the message could just be "Found single distinct allele other than the four possible alleles: Ref, Alt, NoCall and OtherAlt"

[NeillGibson]

Yes thank you for the advice. I'll update this exception in a new commit accordingly.

[NeillGibson]

I've squashed the commits in to a single commit.

[fnothaft]

Thanks @NeillGibson! Committed as 30f937f.