06:19 pi 

biology/seqtools: update 4.43.0 -> 4.44.1

- Blixem: Features can now be added to multiple different groups/filters.
- Belvu: Fix a problem where column highlighting can get out of sync
  with the text.

 

14:19 pi 

biology/seqtools: 4.42.1 -> 4.43.0

 
ftp://ftp.sanger.ac.uk/pub4/resources/software/seqtools/PRODUCTION/release_notes.html

- Mark broken on 9.x: Fails to build due to C++ std issues

 

16:27 pi 

biology/seqtools: 4.41.1 -> 4.42.1

- fixes build on 9.x
- Added a feedback box to show the read depth at the selected coord.
  Hover over this box to see the specific base support (i.e. the
  number of A/C/G/Ts).

 

19:40 pi 

biology/seqtools: 4.40.0 -> 4.41.1

- mostly internal changes, some build fixes

 

10:17 pi 

biology/seqtools: 4.39.3 -> 4.40.0

- Blixem can now accept a 'command' tag in a gff line for a region
  feature. The given command should return gff and will be run by
  blixem on the given region.
- Blixem now supports fetching sequence data over https.

 

13:20 pi 

biology/seqtools: 4.39.2 -> 4.39.3

- Blixem
  Further improve the display of features in the detail view
  when they have transparent fill, making sure that they have a
  visible border.

 

20:50 pi 

biology/seqtools: 4.39.1 -> 4.39.2

- Blixem:
  Improve the display of features in the detail view when they
  have transparent fill.

 

10:53 pi 

biology/seqtools: Fix distinfo, WWW

- Side effect of the seqtools automated build system

Submitted by:	pkg-fallout

 

18:46 pi 

biology/seqtools: 4.39.0 -> 4.39.1

- Fix a bug in Belvu where the display was being initialised in
  command-line-only modes.

 

16:39 pi 

biology/seqtools: 4.36 -> 4.39.0

- Blixem
  o There is now an optional setting to highlight "maybe-canonical"
    splice sites in Blixem. This can be used to help identify
    problems where the strand is incorrect in the input data - it
    highlights splice sites in a different colour if they would be
    canonical were they on the other strand.
  o Fixed a bug with colinearity lines when an alignment's cigar
    string contains introns.
  o There are now separate feedback boxes for the selected sequence
    name coordinates. Hover over each box to see a tooltip describing
    its contents.

 

11:22 pi 

biology/seqtools: 4.35 -> 4.36

Minor under-the-hood changes

 

14:17 pi 

biology/seqtools: 4.34.1 -> 4.35

- Blixem bug fix in sorting features, RT 473624
- Compilation of the seqtools in parallel, RT 467905
- Fix bug with sorting by similarity/identity to first sequence (RT:473624)
- Fix an error compiling with multiple threads (RT:467905)

 

20:30 pi 

biology/seqtools: 4.33 -> 4.34.1

Blixem
- Added functionality to shift-select a range of coordinates,
  and copy the reference/match sequence for that range.
- DNA search now highlights the resultant range of coordinates.
- Added a splitter bar to allow the variations track to be resized.
- Dotter
  Fix a crash pressing Esc on an undocked alignment or greyramp tool.
- All
  Code reorganisation: the codebase is now in C++ rather than C,
  and a new module 'gbtools' has been created for generic
  utility functions.

 

18:04 pi 

biology/seqtools: 4.32 -> 4.33

- Blixem/Dotter
  Multi-dotter support; may now start multiple dotters from blixem

 

12:04 pi 

biology/seqtools: 4.31 -> 4.32

- Blixem
  o Previously-unsupported GFF feature types can now be displayed
    as a new 'basic feature' type.
  o Styles are now applied to the detail view as well as the big
    picture, so feature display is more consistent across the two
    views.
  o Fix a bug where styles were not being applied to
    dynamically-loaded features.
- Dotter
  o Added a 'maximise' button for the greyramp tool.
  o Small fixes to inconsistencies in context-sensitive menus and
    keyboard shortcuts.

 

18:10 pi 

biology/seqtools: 4.30 -> 4.31

Some changes to sqlite dependencies

 

13:19 pi 

biology/seqtools: 4.29 -> 4.30

- Blixem
  o Fix potential crash with internal processing
  o Fix two bugs in data input

 

18:46 pi 

biology/seqtools: 4.28 -> 4.29

- Blixem
  o Added the facility to run Dotter on an ad-hoc sequence (RT:408836).
  o Added the facility to run Dotter against a transcript.
- Dotter
  Minimise the greyramp tool to a simple contrast slider. Use
  Ctrl-G to toggle between this and the full greyramp tool.
- Belvu
  Fix a bug with tree bootstrapping in Belvu.

 

03:17 pi 

biology/seqtools: 4.27 -> 4.28

 

18:56 pi 

biology/seqtools: 4.26 -> 4.27

 

19:00 pi 

biology/seqtools: 4.25 -> 4.26, fix broken distinfo by upgrading

Submitted by:   pi (myself)
Approved by:    jadawin (mentor)

 

16:50 pi 

biology/seqtools: 4.24 -> 4.25

PR:             ports/186299
Submitted by:   pi (myself)
Approved by:    jadawin (mentor)

 

17:23 wg 

biology/seqtools: update to 4.24

PR:		ports/185162
Submitted by:	maintainer

 

20:09 wg 

biology/seqtools: update to 4.23

PR:		ports/183960
Submitted by:	maintainer

 

11:01 wg 

biology/seqtools: Tools for visualising sequence alignments

Blixem is an interactive browser of pairwise alignments that have
been stacked up in a "master-slave" multiple alignment; it is not
a 'true' multiple alignment but a 'one-to-many' alignment.

Belvu is a multiple sequence alignment viewer and phylogenetic tool.

Dotter is a graphical dot-matrix program for detailed comparison
of two sequences.

WWW: http://www.sanger.ac.uk/resources/software/seqtools/

PR:		ports/183801
Submitted by:	Kurt Jaeger <fbsd-ports opsec.eu>