Fix some bugs in LeftAlignAndTrimVariants #5988

Job	Run time
Validate generated WDLs using womtools	14m 39s
check if the environment has privileges	2s
build and push gatk docker to artifacts	14m 31s
Validate script WDLs using womtools	1m 39s
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell	11m 43s
WDL test RUN_M2_WDL on cromwell	18m 33s
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell	25m 58s
WDL test RUN_CNV_SOMATIC_WDL on cromwell	25m 57s
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell	11m 31s
integration build and test Java 17.0.6+10	29m 17s
unit build and test Java 17.0.6+10	19m 30s
cloud build and test Java 17.0.6+10	23m 2s
conda test on docker Java 17.0.6+10	26m 19s
variantcalling test on docker Java 17.0.6+10	27m 37s
integration test on docker Java 17.0.6+10	33m 45s
unit test on docker Java 17.0.6+10	20m 42s
	5h 4m 45s

Provide feedback