Fixes parsing variant annotations for multi-allelic rows

[majkiw]

When I tried to run the code in master I had java.lang.ArrayIndexOutOfBoundsException exceptions in org.bdgenomics.adam.converters.VariantContextConverter#fromArrayExtractor whenever multi-allelic row was encountered.
It turned out the index was off by 1 when accessing multivalued annotations.

For example in gvcf_dir/gvcf_multiallelic.g.vcf there is a line:
chr22 18030096 . TAAA T,TA,TAA,<NON_REF> 564.73 . BaseQRankSum=-0.133;ClippingRankSum=-1.438;DP=114;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQ=69.72;MQ0=0;MQRankSum=-0.686;ReadPosRankSum=-0.013 GT:AD:DP:GQ:PL 2/3:13,3,17,17,0:50:86:602,508,1628,86,678,553,137,342,0,281,467,744,353,309,659

ALT is T,TA,TAA,<NON_REF> with alt allele indexes (as returned by vc.getAlleleIndex(allele)): 1,2,3,4
When accessing annotation MLEAC=0,1,1,0 it would load indexes 1,2,3 for T,TA,TAA resulting in 1,1,0.
However there is never a value for reference allele here! So instead it should be loading indexes 0,1,2 resulting in values 0,1,1.

Incidentally test using gvcf_dir/gvcf_multiallelic.g.vcf wasn't breaking for you because there was always extra 0 as the last value corresponding to <NON_REF> - which was effecting in silent shift of values.
This becomes much easier to break in "real" VCF where there is no <NON_REF> anymore.

[AmplabJenkins]

Can one of the admins verify this patch?

[heuermh]

Jenkins, test this please

[heuermh]

Thanks for reporting this, @majkiw!

The test looks good; give me a bit to review the fix, to make sure there aren't other cases where we're off. That's probably the only method in VariantContextConverter that wasn't rewritten in the refactor.

If you could extract a test file from a non-gVCF with multiple alts, that would be helpful. Additionally we should probably craft one with some pathological cases.

[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/1726/
Test PASSed.

[fnothaft]

Thanks for the bugfix, @majkiw! @heuermh, I ran out of time today to make a review pass but this is first in line on my docket tomorrow.

[fnothaft]

LGTM! Thank you for the fix, @majkiw! I will merge this manually.

[fnothaft]

Merged manually as 5f0ef28. Thank you for the contribution, @majkiw!

[heuermh]

Thank you, @majkiw!

[majkiw]

Thank you guys for processing this PR so quickly :)