Fixed a bug in pileup mode relating to number of haplotypes #2985

Job	Run time
build and push gatk docker to artifacts	30m 20s
check if the environment has privileges	1s
Validate generated WDLs using womtools	15m 13s
Validate script WDLs using womtools	1m 6s
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell	36m 45s
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell	38m 34s
WDL test RUN_CNV_SOMATIC_WDL on cromwell	47m 51s
WDL test RUN_M2_WDL on cromwell	36m 1s
WDL test RUN_CNN_WDL on cromwell	33m 9s
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell	30m 40s
Java 17.0.6+10 build and test cloud	32m 49s
Java 17.0.6+10 build and test integration	1h 1m 6s
Java 17.0.6+10 build and test unit	33m 15s
Java 17.0.6+10 test on docker integration	49m 50s
Java 17.0.6+10 test on docker unit	31m 13s
Java 17.0.6+10 test on docker variantcalling	54m 34s
Java 17.0.6+10 test on docker conda	46m 33s
	9h 39m 0s

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