Add slightly modified version of GATK3 github issue template

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,56 @@
+### Instructions
+
+The github issue tracker is for bug reports, feature requests, and API documentation requests. General questions about how to use the GATK, how to interpret the output, etc should be asked on the [official support forum](http://gatkforums.broadinstitute.org/gatk).
+- Search the existing github issues to see if your issue (or something similar) has already been reported.  If the issue already exists, you may comment there to inquire about the progress.;
+- Determine whether your issue is a **bug report**, a **feature request**, or a **documentation request** (for tool gatkdocs only; for forum docs see [the support issues repo](https://github.com/broadinstitute/dsde-docs/issues));
+- Consider if your "issue" is better addressed on the GATK forum: http://gatkforums.broadinstitute.org/gatk  Post there if you have questions about expected tool behavior, output format, unexpected results or generally any question that does not fit the categories above;
+- Use a **concise** yet **descriptive** title;
+- Choose the corresponding template block below and fill it in, replacing or deleting text in italics (surrounded by `_`) as appropriate;
+- Delete the other template blocks and this header.
+
+----
+
+## Bug Report
+
+### Affected tool(s)
+_Tool name(s), special parameters?_
+
+### Affected version(s)
+- [ ] Latest public release version [version?]
+- [ ] Latest development/master branch as of [date of test?]
+
+### Description 
+_Describe the problem below. Provide **screenshots** , **stacktrace** , **logs** where appropriate._
+
+#### Steps to reproduce
+_Tell us how to reproduce this issue. If possible, include command lines that reproduce the problem. (The support team may follow up to ask you to upload data to reproduce the issue.)_
+
+#### Expected behavior
+_Tell us what should happen_
+
+#### Actual behavior
+_Tell us what happens instead_
+
+----
+
+## Feature request
+
+### Tool(s) involved
+_Tool name(s), special parameters?_
+
+### Description
+_Specify whether you want a modification of an existing behavior or addition of a new capability._
+_Provide **examples**, **screenshots**, where appropriate._
+
+----
+
+## Documentation request
+
+### Tool(s) involved
+_Tool name(s), parameters?_
+
+### Description 
+_Describe what needs to be added or modified._
+
+----
+

src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/afcalc/AlleleFrequencyCalculatorUnitTest.java

@@ -170,6 +170,25 @@ public void testManyRefSamplesDontKillGoodVariant() {
         }
     }
 
+    @Test
+    public void testPresenceOfUnlikelySpanningDeletionDoesntAffectResults() {
+        final int ploidy = 2;
+        final AlleleFrequencyCalculator afCalc = new AlleleFrequencyCalculator(1, 0.1, 0.1, ploidy);
+        final List<Allele> allelesWithoutSpanDel = Arrays.asList(A, B);
+        final List<Allele> allelesWithSpanDel = Arrays.asList(A, B, Allele.SPAN_DEL);
+
+        // make PLs that support an A/B genotype
+        final int[] plsWithoutSpanDel = new int[] {50, 0, 50};
+        final int[] plsWithSpanDel = new int[] {50, 0, 50, 100, 100, 100};
+        final Genotype genotypeWithoutSpanDel = makeGenotype(ploidy, plsWithoutSpanDel);
+        final Genotype genotypeWithSpanDel = makeGenotype(ploidy, plsWithSpanDel);
+        final VariantContext vcWithoutSpanDel = makeVC(allelesWithoutSpanDel, Arrays.asList(genotypeWithoutSpanDel));
+        final VariantContext vcWithSpanDel = makeVC(allelesWithSpanDel, Arrays.asList(genotypeWithSpanDel));
+        final double log10PVariantWithoutSpanDel = afCalc.getLog10PNonRef(vcWithoutSpanDel).getLog10LikelihoodOfAFGT0();
+        final double log10PVariantWithSpanDel = afCalc.getLog10PNonRef(vcWithSpanDel).getLog10LikelihoodOfAFGT0();
+        Assert.assertEquals(log10PVariantWithoutSpanDel, log10PVariantWithSpanDel, 0.0001);
+    }
+
     // make PLs that correspond to an obvious call i.e. one PL is relatively big and the rest are zero
     // alleleCounts is the GenotypeAlleleCounts format for the obvious genotype, with repeats but in no particular order
     private static int[] PLsForObviousCall(final int ploidy, final int numAlleles, final int[] alleleCounts, final int PL)   {