-h/--help

[Jelinek-J]

Both bowtie2-build --help and bowtie2-build -h prints default

Bowtie 2 version 2.4.4 by Ben Langmead ([email protected], www.cs.jhu.edu/~langmea)
Usage: bowtie2-build [options]* <reference_in> <bt2_index_base>
    reference_in            comma-separated list of files with ref sequences
    bt2_index_base          write bt2 data to files with this dir/basename
*** Bowtie 2 indexes work only with v2 (not v1).  Likewise for v1 indexes. ***
Options:
    -f                      reference files are Fasta (default)
    -c                      reference sequences given on cmd line (as
                            <reference_in>)
    --large-index           force generated index to be 'large', even if ref
                            has fewer than 4 billion nucleotides
    --debug                 use the debug binary; slower, assertions enabled
    --sanitized             use sanitized binary; slower, uses ASan and/or UBSan
    --verbose               log the issued command
    -a/--noauto             disable automatic -p/--bmax/--dcv memory-fitting
    -p/--packed             use packed strings internally; slower, less memory
    --bmax <int>            max bucket sz for blockwise suffix-array builder
    --bmaxdivn <int>        max bucket sz as divisor of ref len (default: 4)
    --dcv <int>             diff-cover period for blockwise (default: 1024)
    --nodc                  disable diff-cover (algorithm becomes quadratic)
    -r/--noref              don't build .3/.4 index files
    -3/--justref            just build .3/.4 index files
    -o/--offrate <int>      SA is sampled every 2^<int> BWT chars (default: 5)
    -t/--ftabchars <int>    # of chars consumed in initial lookup (default: 10)
    --threads <int>         # of threads
    --seed <int>            seed for random number generator
    -q/--quiet              verbose output (for debugging)
    -h/--help               print detailed description of tool and its options
    --usage                 print this usage message
    --version               print version information and quit

instead of "detailed description of tool and its options" as it is claimed.

[ch4rr0]

I can understand your confusion. I may change things up so that --help/-h prints a brief synopsis of the options, --usage prints the output pasted with an additional message directing the user to the Bowtie 2 manual for additional details. What are your thoughts on this?

[mmokrejs]

I think I saw few times that other tools show short help text with -h and verbose help text with --help. But I am definitely puzzled why --usage print this usage message show the supposedly the text to be printed by -h and --help (this usage message)

[ch4rr0]

So no --usage just -h/--help, got it.

[Jelinek-J]

Hi, I'm sorry I wrote it awkwardly/ too briefly. My complaint was (as @mmokrejs written) that all of

bowtie2-build
bowtie2-build --usage
bowtie2-build -h
bowtie2-build --help

print the same message (well, except No input sequence or sequence file specified! for the first one), while the message

...
    -h/--help               print detailed description of tool and its options
    --usage                 print this usage message
...

seems like their outputs should differ. So the easiest repair is to merge it into

...
    -h/--help               print this usage message
...

and discard --usage option. However what you suggested in the first comment sounds great (although more laborious for you:).