Permalink
Browse files

+ gmt-web documentation page update

  - further indent the body of the SYNOPSIS section to get
    the <pre> formatting syntax
  • Loading branch information...
1 parent 7a40e00 commit 7d188bba8a52244873cd68b8cb64f6417112d7d9 @indraniel indraniel committed Jun 30, 2011
Showing with 34 additions and 34 deletions.
  1. +34 −34 gmt-web/content/documentation.md
@@ -4,40 +4,40 @@
# SYNOPSIS
- fqgrep [options] -p <pattern> <fastq_or_fasta_files>
- -h This help message
- -V Program and version information
- -p <STRING> Pattern of interest to grep [REQUIRED]
- -v Invert match - show only sequences that
- DO NOT match the pattern
- -a Show all records irregardless of match status
- Useful in conjunction with the -r option;
- when one would like to do further post-processing
- of the match data
- -c Highlight matching string with color
- -f Output matches in FASTA format
- -r Output matches in detailed stats report format
- -b <STRING> Delimiter string to separate columns
- in detailed stats report [Default: '\t']
- -m <INT> Total number of mismatches to at most allow for
- in search pattern [Default: 0]
- -s <INT> Max threshold of substitution mismatches to allow
- for in search pattern [Default: unlimited]
- -i <INT> Max threshold of insertion mismatches to allow for
- in search pattern [Default: unlimited]
- -d <INT> Max threshold of deletion mismatches to allow for
- in search pattern [Default: unlimited]
- -S <INT> Cost of base substitutions in obtaining
- approximate match [Default: 1]
- -I <INT> Cost of base insertions in obtaining
- approximate match [Default: 1]
- -D <INT> Cost of base deletions in obtaining
- approximate match [Default: 1]
- -e Force tre regexp engine usage
- -C Display only a total count of matches
- (per input FASTQ/FASTA file)
- -o <out_file> Desired output file.
- If not specified, defaults to stdout
+ fqgrep [options] -p <pattern> <fastq_or_fasta_files>
+ -h This help message
+ -V Program and version information
+ -p <STRING> Pattern of interest to grep [REQUIRED]
+ -v Invert match - show only sequences that
+ DO NOT match the pattern
+ -a Show all records irregardless of match status
+ Useful in conjunction with the -r option;
+ when one would like to do further post-processing
+ of the match data
+ -c Highlight matching string with color
+ -f Output matches in FASTA format
+ -r Output matches in detailed stats report format
+ -b <STRING> Delimiter string to separate columns
+ in detailed stats report [Default: '\t']
+ -m <INT> Total number of mismatches to at most allow for
+ in search pattern [Default: 0]
+ -s <INT> Max threshold of substitution mismatches to allow
+ for in search pattern [Default: unlimited]
+ -i <INT> Max threshold of insertion mismatches to allow for
+ in search pattern [Default: unlimited]
+ -d <INT> Max threshold of deletion mismatches to allow for
+ in search pattern [Default: unlimited]
+ -S <INT> Cost of base substitutions in obtaining
+ approximate match [Default: 1]
+ -I <INT> Cost of base insertions in obtaining
+ approximate match [Default: 1]
+ -D <INT> Cost of base deletions in obtaining
+ approximate match [Default: 1]
+ -e Force tre regexp engine usage
+ -C Display only a total count of matches
+ (per input FASTQ/FASTA file)
+ -o <out_file> Desired output file.
+ If not specified, defaults to stdout
# Software Details

0 comments on commit 7d188bb

Please sign in to comment.