Merge pull request #73 from griffithlab/expose-options

Expose options - update docs

docs/commands/cis-splice-effects-identify.md

@@ -23,6 +23,11 @@ The `cis-splice-effects identify` command is used to identify splicing misregula
 | -v      | Output file containing variants annotated as splice relevant (VCF format). |
 | -w      | Window around the variant file (in basepairs) to identify splicing events in. If specified the tool looks at +/- n b.p around the variant start position. For example -w 500 will look at a 1kb window around the variant. If this option is not specified, the default option is to look at a window that ranges from the start co-ordinate of the previous exon and ends at the end co-ordinate of the next exon i.e by treating the current exon as a cassette exon. |
 | -j      | Optional file containing the aberrant junctions in BED12 format. |
+| -e      | Maximum distance from the start/end of an exon to annotate a variant as relevant to splicing, the variant is in exonic space, i.e a coding variant. [default = 3] |
+| -i      | Maximum distance from the start/end of an exon to annotate a variant as relevant to splicing, the variant is in intronic space. [default = 2] |
+| -I      | Annotate variants in intronic space within a transcript (not to be used with -i).
+| -E      | Annotate variants in exonic space within a transcript (not to be used with -e).
+| -S      | Dont skip single exon transcripts. The default is to skip the single exon transcripts. |
 
 ###Output
 For an explanation of the annotated junctions that are identified by this command please refer to the output of the `junctions annotate` command [here](junctions-annotate.md#output)