ex-209 (jebene) - removed filter.py

umich-brcf-bioinf · Apr 13, 2015 · b664f00 · b664f00
1 parent 4fd8fff
commit b664f00
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Showing 21 changed files with 321 additions and 579 deletions.
diff --git a/jacquard/commands/filter.py b/jacquard/commands/filter.py
diff --git a/jacquard/commands/merge.py b/jacquard/commands/merge.py
@@ -16,8 +16,11 @@
 * Calls for the same patient/sample are joined into a single column. Each output
     column is the patient name (prefix of the file name) plus the sample name
     from the column header.
-* The merged file will have as many records as the distinct set of
+* By default, the merged file will have as many records as the distinct set of
     (chrom, pos, ref, alt) across all input files.
+    Running Merge with "--include_variants" or "--include_loci" will reduce the
+    number of records in the merged file to include only those which conform
+    with the desired flag.
 * Each variant record will have the minimal set of incoming format tags for
     that variant (i.e. the list of format tags is specific to each record).
 * Incoming QUAL and INFO fields are ignored.

diff --git a/jacquard/jacquard.py b/jacquard/jacquard.py
@@ -51,7 +51,6 @@
 from jacquard import __version__
 import jacquard.command_validator as command_validator
 import jacquard.commands.expand as expand
-import jacquard.commands.filter as filter
 import jacquard.logger as logger
 import jacquard.commands.merge as merge
 import jacquard.commands.summarize as summarize
@@ -61,7 +60,6 @@
 
 
 _SUBCOMMANDS = [translate,
-                filter,
                 merge,
                 summarize,
                 expand]

diff --git a/test/variant_callers/__init__.py → test/commands/__init__.py b/test/variant_callers/__init__.py → test/commands/__init__.py