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dstreett / Super-Deduper

An application to remove PCR duplicates from high throughput sequencing runs.
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Typo in help #27

Closed samhunter closed 8 years ago

samhunter commented 8 years ago 
    --no-log, N No logfile (outputs to stderr)

Missing a '-' before N.

It would also be nice to support '-?' as a synonym to '-h' and '--help'.

samhunter commented 8 years ago

It would also be nice if super_deduper was more helpful about how to get help,

e.g.

Current: $ ./super_deduper -? ./super_deduper: invalid option -- '?' This argument is no good ? Bad argument :( Exiting <--------- Note leading space

Alternatively: $ ./super_deduper -? ./super_deduper: invalid argument -- '?', try "--help" for a list of arguments

samhunter commented 8 years ago

Usually short-switches are listed first (see for example 'rsync --help', 'bowtie2 --help', etc).

Also additional arguments are traditionally included in "" instead of "(arg)" .

Current: --version, -v Version print
--read1-input, -1 Read 1 input (comma sep for multiple files)
--read2-input, -2 Read 2 input (comma sep for multiple files)
--singleend-input, -U Single end read input (comma sep for multiple files)
--tab-input, -T Tab input (comma sep for multiple files)
--interleaved-input, -I Interleaved input I (comma sep for multiple files)
--stdin-input, -S STDIN input (MUST BE TAB DELIMITED INPUT)
--start, -s start location for unique ID (int)
--length, -l length of unique ID (int)
--quality-check-off, -q Quality Checking Off First Duplicate seen will be kept
--gzip-output, -g Output gzipped
--interleaved-output, -i Output to interleaved
--fastq-output, -f Fastq format outputted (R1 and R2) --force, -F Forces overwrite of files --tab-output, -t Tab-delimited output --to-stdout, -O Prints to STDOUT in Tab Delimited --prefix, -P Prefix for outputted files --log-file, -L Output-Logfile --no-log, N No logfile (outputs to stderr) --help, -h Prints help.

Suggested: -v, --version, Print version -1, --read1-input <fastq1,fastq2,...>, Read 1 input (comma sep for multiple files)
-2, --read2-input <fastq1,fastq2,...>, Read 2 input (comma sep for multiple files)
-U, --singleend-input <fastq1,fastq2,...>, Single end read input (comma sep for multiple files)
-T, --tab-input <tab1,tab2,...>, Tab input (comma sep for multiple files)

... -s --start , 0-based start location for unique ID
...

dstreett commented 8 years ago

Cool! I think I got all that, @samhunter . Let me know if something doesn't look correct.