Recent changes to feature-requests

improved command-line usage

Martin A Hansen — Wed, 04 Oct 2006 13:32:24 -0000

Hello Mummers

I would like to suggest a more friendly way of allowing
mummer to interact with scripts.

First of all, I am frustrated because mummer needs to
read imput from files and that you cannot pipe
sequences directly to mummer. Could that be fixed
somehow, so that if you pipe fasta files to mummer, the
suffix tree is build from the first sequence, and that
subsequent sequences are used for matching? (I am dying
to get this functionality).

Alternatively, some sort of API may be worth considering.

Cheers

Martin

improved command-line usage

Martin A Hansen — Wed, 04 Oct 2006 12:56:18 -0000

Hello Mummers

I would like to suggest a more friendly way of allowing
mummer to interact with scripts.

Alternatively, some sort of API may be worth considering.

Cheers

Martin

verbose/silent command-line usage

Martin A Hansen — Wed, 04 Oct 2006 12:28:14 -0000

Hello Mummers

I would like a command-line switch to either run Mummer
silently or that mummer only displays lines:

# reading input file "../test.fna" of length 9312
# construct suffix tree for sequence of length 9312
# (maximum input length is 536870908)
# CONSTRUCTIONTIME mummer ../test.fna 0.00
# reading input file "../test.fna" of length 9312
# matching query-file "../test.fna"
# against subject-file "../test.fna"

when a verbose switch is enabled.

Cheers

Martin

plot title

Michael Schatz — Thu, 23 Jun 2005 21:28:49 -0000

Please add a --title option to mummerplot instead of
hacking the gp file.

Specification:

Option:
--title <titlevalue>

Result:
set title "<titlevalue>"
is written to the out.gp file

a more conventional install

Dick Repasky — Mon, 13 Jun 2005 13:47:18 -0000

It would be terrific if "make install" produced results
that were a little more typical of unix systems. That
is, it installs necessary files somewhere other than in
the source tree. My hope is that this will come with
the --prefix with the move to autoconf.

Also, it would be nice to have all executables
installed into a single bin directory rather than
having many programs in the basal directory, a scripts
directory and an aux_bin directory. How about just a
single directory of executables?

I think that many sys admins would thank you for these
changes.

inexact matching

Adam Phillippy — Wed, 01 Jun 2005 21:06:04 -0000

Some sort of inexact matching (match a complete string
within some given edit distance) would be nice. See
vmatch -e option.

synteny browser

Adam Phillippy — Wed, 01 Jun 2005 21:04:18 -0000

Some sort of (visual) synteny browser should be added
to MUMmer. This ticket is intentionally vague.

nucmer/promer do not check for FastA header uniqueness

Adam Phillippy — Wed, 01 Jun 2005 20:57:16 -0000

obscure errors arise if the fasta input headers are not
unique, this problem should be fixed... loading the
entire file into memory and hashing by the ID is one
option that would speed up nucmer and present a
solution to this problem.

switch to autoconf/automake build system

Adam Phillippy — Wed, 01 Jun 2005 20:52:05 -0000

replace the current minimalist build system with
autoconf/automake equivalent