[EMBOSS] EMBOSS 6.1.0 patch 1.3

[Charles Plessy]

Le Thu, Dec 10, 2009 at 01:36:14PM +0000, Peter Rice a écrit :
> A patch for EMBOSS 6.1.0 is on the FTP server. This fixes problems with
> extractfeat, using format names with dashes (fastq-sanger) in USAs,
> scaling issues in plot outputs, and some minor bugs.
>
> The files are on our FTP server ftp://emboss.open-bio.org/pub/EMBOSS/fixes
> with a patch file and instructions in the patches subdirectory.
>
> Fix 3. EMBOSS-6.1.0/ajax/ajfeat.c
>        EMBOSS-6.1.0/ajax/ajfeat.h
>        EMBOSS-6.1.0/ajax/ajgraph.c
>        EMBOSS-6.1.0/ajax/ajmath.c
>        EMBOSS-6.1.0/ajax/ajseq.c
>        EMBOSS-6.1.0/ajax/ajseqread.c
>        EMBOSS-6.1.0/ajax/ajseqwrite.c
>        EMBOSS-6.1.0/nucleus/embmisc.c
>        EMBOSS-6.1.0/nucleus/embmisc.h
>        EMBOSS-6.1.0/nucleus/embpat.c
>        EMBOSS-6.1.0/emboss/coderet.c
>        EMBOSS-6.1.0/emboss/extractfeat.c
>        EMBOSS-6.1.0/emboss/notseq.c
>        EMBOSS-6.1.0/emboss/prettyplot.c
>        EMBOSS-6.1.0/emboss/seqmatchall.c
>        EMBOSS-6.1.0/emboss/showfeat.c
>        EMBOSS-6.1.0/emboss/showpep.c
>        EMBOSS-6.1.0/emboss/showseq.c
>        EMBOSS-6.1.0/emboss/twofeat.c
>        EMBOSS-6.1.0/jemboss/utils/install-jemboss-server.sh

Dear Peter and all EMBOSS developers,

There were two issues that were discussed previously on the EMBOSS user list or
on the sourceforge tracker, that I do not see fixed in this patch. The EMBOSS
package distributed by Debian contains a patch for each of them.

1) To prevent vectorstrip to discard FASTQ qualities.
http://git.debian.org/?p=debian-med/emboss.git;a=blob;f=debian/patches/transient-vectorstrip.patch;h=c4d8fd1e6c6d223ec8664b1aa08171407f9ace55;hb=HEAD
https://sourceforge.net/tracker/index.php?func=detail&aid=2886368&group_id=93650&atid=605034

2) To help tfm to find the HTML documentation.
http://git.debian.org/?p=debian-med/emboss.git;a=blob;f=debian/patches/tfm-html.patch;h=c0595eb5008f53fec27e0ba4ff144c6385c6acdd;hb=HEAD
https://sourceforge.net/tracker/?func=detail&aid=2877960&group_id=93650&atid=605031

I would welcome in particular comments on the second patch. If it is not
suitable, then I will remove it from the Debian package.

Best regards,

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan