Merge pull request #271 from ens-lgil/postreleasefix/94

Fix alias discrepancy between the VEP web doc and the scripts
Ensembl · Sep 4, 2018 · 97046c7 · 97046c7
2 parents 98e6a6d + c9ecacf
commit 97046c7
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Showing 4 changed files with 9 additions and 9 deletions.
diff --git a/filter_vep b/filter_vep
@@ -94,7 +94,7 @@ sub configure {
     'registry=s',
 
     'start|s=i',               # skip first N results
-    'limit|l=i',               # return max N results
+    'limit=i',                 # return max N results
 
     'filter|f=s@',             # filter
   ) or throw("ERROR: Failed to parse command-line flags\n");

diff --git a/haplo b/haplo
@@ -44,8 +44,8 @@ GetOptions(
   'registry=s',              # registry file
   'host=s',                  # database host
   'port=s',                  # database port
-  'user|u=s',                  # database user name
-  'password=s',              # database password
+  'user|u=s',                # database user name
+  'password|pass=s',         # database password
   'db_version=i',            # Ensembl database version to use e.g. 62
   'assembly|a=s',            # assembly version to use
   'genomes',                 # automatically sets DB params for e!Genomes
@@ -63,12 +63,12 @@ GetOptions(
 
   # verbosity options
   'verbose|v',               # print out a bit more info while running
-  'quiet',                   # print nothing to STDOUT (unless using -o stdout)
+  'quiet|q',                 # print nothing to STDOUT (unless using -o stdout)
 
   # output options
   'output_file|o=s',         # output file name
   'warning_file=s',          # file to write warnings to
-  'force_overwrite',         # force overwrite of output file if already exists
+  'force_overwrite|force',   # force overwrite of output file if already exists
   'json',                    # create JSON output
   'dont_export=s',           # list of JSON keys to exclude
 

diff --git a/variant_recoder b/variant_recoder
@@ -51,7 +51,7 @@ GetOptions(
   'host=s',                  # database host
   'port=s',                  # database port
   'user|u=s',                # database user name
-  'password=s',              # database password
+  'password|pass=s',         # database password
   'db_version=i',            # Ensembl database version to use e.g. 62
   'assembly|a=s',            # assembly version to use
   'grch37',                  # set for using GRCh37

diff --git a/vep b/vep
@@ -43,7 +43,7 @@ GetOptions(
   'host=s',                  # database host
   'port=s',                  # database port
   'user|u=s',                # database user name
-  'password=s',              # database password
+  'password|pass=s',         # database password
   'db_version=i',            # Ensembl database version to use e.g. 62
   'assembly|a=s',            # assembly version to use
   'grch37',                  # set for using GRCh37
@@ -108,7 +108,7 @@ GetOptions(
 
   # verbosity options
   'verbose|v',               # print out a bit more info while running
-  'quiet',                   # print nothing to STDOUT (unless using -o stdout)
+  'quiet|q',                 # print nothing to STDOUT (unless using -o stdout)
   'no_progress',             # don't display progress bars
 
   # output options
@@ -122,7 +122,7 @@ GetOptions(
   'stats_html',              # write stats as html
   'no_stats',                # don't write stats file
   'warning_file=s',          # file to write warnings to
-  'force_overwrite',         # force overwrite of output file if already exists
+  'force_overwrite|force',   # force overwrite of output file if already exists
   'terms|t=s',               # consequence terms to use e.g. NCBI, SO
   'coding_only',             # only return results for consequences in coding regions
   'canonical',               # indicates if transcript is canonical