From c9ecacf15bcb21c30af79f7fedc186f0cf2ee3a3 Mon Sep 17 00:00:00 2001 From: Laurent Gil Date: Fri, 31 Aug 2018 16:50:53 +0100 Subject: [PATCH] Fix alias discrepancy between the VEP web doc and the scripts --- filter_vep | 2 +- haplo | 8 ++++---- variant_recoder | 2 +- vep | 6 +++--- 4 files changed, 9 insertions(+), 9 deletions(-) diff --git a/filter_vep b/filter_vep index 40018327e..9766c534d 100755 --- 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 index f42f72fca..2962fa3f7 100755 --- 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 index 9ab3f1213..2e55a2bd5 100755 --- 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 index 3582d5828..6e5b6459d 100755 --- 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