CVS log for pkgsrc/biology/mummer/distinfo

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biology: Replace RMD160 checksums with BLAKE2s checksums

All checksums have been double-checked against existing RMD160 and
SHA512 hashes

biology: Remove SHA1 hashes for distfiles

Add SHA512 digests for distfiles for biology category.

Existing SHA1 digests verified, all found to be the same on the
machine holding the existing distfiles (morden).  Existing SHA1
digests retained for now as an audit trail.

Remove concurrently created patch.

Fix build with GCC 4.5

biology/mummer: Put sort function in scope

Add <algorithm> header for sort, DragonFly's compiler needs it.
No PKGREVISION bump required.

updated to MUMmer3.20

Updated mummer to 3.19.

Changes since 3.18:
- More documentation.

Fix path to csh in scripts. Bump revision.

Fix build with newer versions of GNU make.

Updated biology/mummer to release 3.18. Changes include:
- MUMmer now resides at Sourceforge
- new tools such as delta-filter
- more extensive html documentation and examples
- bug fixes

Prevent paths to the build directories from being included in the package.
Bump PKGREVISION.

Add RMD160 digests in addition to the SHA1 ones.

Update to version 3.15.  From David Price in PR#28305.

3.05 - Added -k option to show-coords to only display the best frame for
       overlapping PROmer alignments. Added --[no]optimize option to nucmer
       and promer to allow alignment score optimization to be turned off, i.e
       allow alignments to extend to the ends of sequences rather than
       backtracking to optimize the alignment score. Updated docs.
3.06 - Added -F and -h option to mummer. Changed -mumcand option to
       -mumreference, but left deprecated -mumcand option available. Added
       -maxmatch option to mummer, and changed default behavior of all
       applicable programs to -mumreference (nucmer, promer and mummer).
       Added -w (screen width) option to show-aligns. Updated documentation
       with all of these changes.
3.07 - Added the 'mapview' plotting utility and appropriate documentation.
       Fixed origin wrap shadowing bug in show-tiling when using the -c option.
       NUCmer and PROmer now convert to absolute paths to avoid ambiguity.
3.08 - Added MUMmer examples web docs which gives brief walkthroughs
3.10 - Now Mac OSX compatible. Added -R option to show-tiling.
3.11 - Fixed bug show-tiling -R option. Added some mapview changes. Fixed
       the issue with mummerplot being to faint.
3.12 - Added the --nosimplify option to nucmer for repeat searching. Fixed
       a bug in nucmer and promer. Fixed rounding issue in show-coords.
       Updated citations.
3.13 - Added -d, -g, -G and -o options to show-coords and updated documentation.
       Fixed bug in show-tiling -R
3.14 - Fixed gcc3 compilation bug
3.15 - Fixed --nooptimize in nuc/promer.

Initial import of mummer, one of the many packages provided by
brook at biology dot nmsu dot edu and his team at NMSU.

Mummer is a system for aligning whole genome sequences. Using an efficient
data structure called a suffix tree, the system is able rapidly to align
sequences containing millions of nucleotides whether in complete or draft
form. MUMmer can also align incomplete genomes; it handles the 100s or 1000s
of contigs from a shotgun sequencing project with ease, and will align them to
another set of contigs or a genome using the NUCmer program included with the
system. 

Initial revision