VS-883 - Add tests for extract cohort lite

[gbggrant]

WIP

[gbggrant]

Think I'm going to need some avro help on one of these tests

[codecov]

Codecov Report

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Additional details and impacted files

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##             ah_var_store     #8284   +/-   ##
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  Coverage                ?   86.098%           
  Complexity              ?     35610           
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  Branches                ?     18006           
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  Hits                    ?    143886           
  Misses                  ?     16799           
  Partials                ?      6434           

[gatk-bot]

Github actions tests reported job failures from actions build 4671388568
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	11	4671388568.13	logs
unit	8	4671388568.1	logs

[mcovarr]

The ExtractCohortLiteFilterRecordUnitTest appears to be blowing up b/c it's looking for a "calibration_sensitivity" field in the src/test/resources/org/broadinstitute/hellbender/tools/gvs/extract/ExtractCohortLiteFilterRecord/test_input.avro file that's not there. Unexpectedly (for VQSR Lite) there is a "vqslod" field.

$ avro-tools getschema ~/gitrepos/gatk/src/test/resources/org/broadinstitute/hellbender/tools/gvs/extract/ExtractCohortLiteFilterRecord/test_input.avro         
23/04/11 16:22:10 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
{
  "type" : "record",
  "name" : "Root",
  "fields" : [ {
    "name" : "location",
    "type" : [ "null", "long" ]
  }, {
    "name" : "alt",
    "type" : [ "null", "string" ]
  }, {
    "name" : "ref",
    "type" : [ "null", "string" ]
  }, {
    "name" : "vqslod",
    "type" : [ "null", "double" ]
  }, {
    "name" : "yng_status",
    "type" : [ "null", "string" ]
  } ]
}

[gbggrant]

Yeah - I need to add that field to the ExtractCohortLiteRecord avro_file.

[mcovarr]

LGTM, thanks for taking this on!