Merge branch 'develop' into ex-258_disambiguate_format_tags

Conflicts:
	jacquard/jacquard.py

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

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)

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
 ##