umich-brcf-bioinf / Jacquard

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LAST BUILD ON BRANCH EX-92_Fix_normalize

branch: EX-92_Fix_normalize

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• EX-92_Fix_normalize
• EX-64_moveCallerBasedMethodsInMergeToNormalize
• EX-91_distinguish_varscanHC_sources
• JQ-319_update_to_recognize_newer_Mutect_format
• JQ-322_adjust_mutect_translate
• JQ-324_pad_optional_trailing_format_fields
• JQ-329_fix_mutect_AF_FA_tag
• develop
• distinguish_varscanHC_sources
• doc_spike
• ex-102_filterAndSortColumns
• ex-109-dynamic_mocking_framework
• ex-115_addTagsIn
• ex-154_validate_samples
• ex-156_safelyAddToExistingDirectory
• ex-160_fixConsensus
• ex-161_orderVcfHeadersCorrect
• ex-164_high_confidence_file
• ex-166_snpIndels
• ex-167_check_vcf_
• ex-168_extend_filter_command
• ex-171_replace_merge_with_merge2
• ex-173_move_versioning_into_init
• ex-174_consolidate_rounding_in_utils
• ex-176_translated_vcf_objec
• ex-181_downgrade_to_4.1
• ex-185_specifyLogFileLocatoin
• ex-196_consensus_to_summarize
• ex-198_add_docstrings
• ex-199_exampleTestData
• ex-202_simplify_summary_tags
• ex-209_combine_filter_merge_commands
• ex-210_allowPython2.7OrPython3
• ex-217_rearrangeClassesAndPackages
• ex-246_process_unsorted_vcfs
• ex-258_disambiguate_format_tags
• ex-260_Add-Genotype-Tag
• ex-264_modify_jacquard_tags
• ex-266_simplify_merge_implementation
• ex-267_add-documentation
• ex-83_Pip_install
• hotfix_strelka_af
• jq-320_fix_expand_handling_of_name_collisions_between_fixed_and_info
• logging
• master
• merge2
• refactor_merge
• refactor_normalize
• release
• release-0.3
• release-0.31
• spike_expand_filtering
• v0.31
• v0.41
• v0.42
• v0.43
• v1.0.0
• v1.1.1
• v1.1.4
• v1.1.5

EX-92 (cgates): Fix normalize.
Added top-level try catch to fail more gracefully. Fixed merge to fail
gracefully when specified dirs not exist.