Fix some bugs in LeftAlignAndTrimVariants #5989

Job	Run time
build and push gatk docker to artifacts	13m 4s
Validate generated WDLs using womtools	15m 12s
Validate script WDLs using womtools	1m 26s
check if the environment has privileges	4s
WDL test RUN_M2_WDL on cromwell	19m 9s
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell	10m 50s
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell	11m 5s
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell	10m 59s
WDL test RUN_CNV_SOMATIC_WDL on cromwell	10m 36s
integration build and test Java 17.0.6+10	28m 52s
cloud build and test Java 17.0.6+10	14m 30s
unit build and test Java 17.0.6+10	18m 43s
conda test on docker Java 17.0.6+10	26m 29s
integration test on docker Java 17.0.6+10	35m 6s
unit test on docker Java 17.0.6+10	19m 44s
variantcalling test on docker Java 17.0.6+10	27m 48s
	4h 23m 37s

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