Number of intervals edge case gCNV fix

src/main/python/org/broadinstitute/hellbender/gcnvkernel/models/model_denoising_calling.py

@@ -1235,6 +1235,10 @@ def _get_update_log_class_emission_tk_theano_func(self) -> th.compile.function_m
                                                   self.calling_config.num_copy_number_classes),
                                                  dtype=types.floatX)
 
+        # this converts TensorType from row to matrix when number in the edge case when number of intervals is equal to 2
+        # (to avoid type mismatch later on)
+        log_class_emission_cum_sum_tk = tt.unbroadcast(log_class_emission_cum_sum_tk, 0)
+
         def inc_log_class_emission_tk_except_for_first_interval(pi_jkc, q_c_tc, cum_sum_tk):
             """Adds the contribution of a given sample to the log class emission (symbolically).
 

src/test/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCallerIntegrationTest.java

@@ -78,6 +78,24 @@ public void testCohortWithoutIntervalAnnotations() {
         runCommandLine(argsBuilder);
     }
 
+    /**
+     * Run the tool in the COHORT mode for a case when number of provided intervals is two (minimum number allowed).
+     */
+    @Test(groups = {"python"})
+    public void testCohortWithTwoIntervals() {
+        final ArgumentsBuilder argsBuilder = new ArgumentsBuilder();
+        Arrays.stream(TEST_COUNT_FILES, 0, 5).forEach(argsBuilder::addInput);
+        argsBuilder.add(GermlineCNVCaller.RUN_MODE_LONG_NAME, GermlineCNVCaller.RunMode.COHORT.name())
+                .add("L", "1:620998-622131")
+                .add("L", "1:877712-877902")
+                .add(GermlineCNVCaller.CONTIG_PLOIDY_CALLS_DIRECTORY_LONG_NAME,
+                        CONTIG_PLOIDY_CALLS_OUTPUT_DIR.getAbsolutePath())
+                .add(StandardArgumentDefinitions.OUTPUT_LONG_NAME, OUTPUT_DIR.getAbsolutePath())
+                .add(CopyNumberStandardArgument.OUTPUT_PREFIX_LONG_NAME, "test-germline-cnv-cohort-two-targets")
+                .add(IntervalArgumentCollection.INTERVAL_MERGING_RULE_LONG_NAME, IntervalMergingRule.OVERLAPPING_ONLY.toString());
+        runCommandLine(argsBuilder);
+    }
+
     /**
      * Run the tool in CASE mode for the first 5 samples using the model generated by
      * {@link #testCohortWithoutIntervalAnnotations()}