diff --git a/TODO.rst b/TODO.rst index a8c7d09..f10b7e6 100644 --- a/TODO.rst +++ b/TODO.rst @@ -1,8 +1,9 @@ TODO ==== - Improved workflow documentation with example data -- Extend [translate] to support more tags (e.g. GT) - Extend [merge] to filter and disambiguate tag collisions +- Extend [translate/summarize] to support more tags (e.g. GT) +- Parallelize [translate] - Add [weave] command to combine [translate, merge, summarize] - Extend [expand] to parse SnpEff/Annovar annotated results - Extend [expand] to generate formatted results diff --git a/jacquard/expand.py b/jacquard/expand.py index b089118..0c1df13 100644 --- a/jacquard/expand.py +++ b/jacquard/expand.py @@ -174,7 +174,7 @@ def validate_args(args): def _get_actual_columns(vcf_reader, col_spec): columns = _create_potential_column_list(vcf_reader) glossary_fields = [] - for glossary_field in sorted([x for x in columns.values() if x], + for glossary_field in sorted([x for x in columns.values() if x], key=lambda x: x.upper()): if glossary_field and glossary_field not in glossary_fields: glossary_fields.append(glossary_field) diff --git a/jacquard/jacquard.py b/jacquard/jacquard.py index 1a2a7ad..44b9c66 100644 --- a/jacquard/jacquard.py +++ b/jacquard/jacquard.py @@ -12,16 +12,16 @@ Then architecture of Jacquard modules can be divided into: * commands : These transform files or directories (e.g. translate.py) and are - indirectly executable through the jacquard module. Each command must + indirectly executed through the jacquard module. Each command must implement an execute method that does the heavy lifting along with some - simpler methods that expedite command validation - * callers : These transform VcfRecords (e.g. mutect.py). They typically have + simpler methods that expedite command validation. + * transforms : These transform VcfRecords (e.g. mutect.py). They typically have a collection of tag classes; where each tag holds the metaheader and code to transform a single VcfRecord. Note that a caller could manipulate any aspect of a VcfRecord, but (by strong convention) typically only adds information, for example add a sample-format tag, add an info field, or add a filter field. - * helpers : Common functionality (e.g. command_validator, vcf, logger, etc.) + * utils : Common functionality (e.g. command_validator, vcf, logger, etc.) """ ## Copyright 2014 Bioinformatics Core, University of Michigan ##