JoinMap 5 Release Notes
=========================
=== 19 January 2024 ===
Maintenance release of JoinMap 5
(Build: 19jan2024.28jul2023)
Correction:
- In the situation with a locus that has one or more identicals, where
the representative locus is excluded while an identical locus is
included, combined with having the locus or one of its identicals
in a fixed order, then the map calculations will lead to a runtime
error (Access violation at ...). This is fixed.
=== 7 October 2022 ===
Maintenance release of JoinMap 5
(Build: 7oct2022.12jan2022)
Correction:
- In some instances a change of the Windows Theme and/or the use of
the lock screen could corrupt the navigation tree. One of the
symptoms was that many nodes are shown as marked (red). Subsequent
use of the navigation tree (i.e. change of the selected node)
resulted in runtime errors (Access violation at ...). This is fixed.
=== 21 March 2022 ===
Maintenance release of JoinMap 5
(Build: 21mar2022.12jan2022)
Corrections:
- With the preceding release the SQLite library was updated as well.
However, this update introduced a very subtle change in the
behaviour of SQLite regarding the automatic ROWID variable in
subqueries. This caused the inability of JoinMap to show the tables
of several tabsheets, with error messages like 'Failed to prepare
statement for query: ...'. This is fixed.
- ML maps of CP type populations did not show the plausible positions
of P1, only those of P2. This is fixed.
=== 14 March 2022 ===
Maintenance release of JoinMap 5
(Build: 14mar2022.12jan2022)
Correction:
- Calculating the linkages of data of CP type populations could result
in an incorrect error message 'error in determine_phasecomb()', if
dominant observations (h-, k-) are present. This bug was introduced
in the maintenance release of 30 March 2021. It is now fixed.
=== 22 July 2021 ===
Maintenance release of JoinMap 5
(Build: 22jul2021.22jul2021)
Correction:
- With very large datasets (over 50,000 loci), the function 'Create
Groups Using the Groupings Tree' would sometimes not finish. This
is fixed.
- The determination of the strongest cross links did not show its
progress. This is fixed.
Minor enhancement:
- Similar to the progress of some database actions being shown with
sequences of '>' symbols on the progress bar, this is now also shown
in the Windows task bar element of the program with sequences of dot
characters.
=== 30 March 2021 ===
Maintenance release of JoinMap 5
(Build: 30mar2021.26mrt2021)
Correction:
- The ML mapping algorithm applied to population type RIx with dense
regions on the map could result in tiny negative estimates of
recombination frequencies and map distances, to be seen in the
Session Log as -0.000. An attempt to invert the resulting map order
would result in the error message:
'ReadLoci_SQLite() map position of locus X before that of Y'.
This problem is solved.
Enhancements:
- The chart title, axis titles and map chart title are enhanced to
accept unicode.
- Various minor user interface elements are improved.
=== 1 October 2019 ===
Maintenance release of JoinMap 5
(Build: 1oct2019.19aug2019)
Enhancements:
- The software is enhanced to accept unicode characters in file and
directory names instead of just the limited set of ASCII characters.
This means e.g. that if you have an MS-Windows user name consisting
of non-ASCII characters, JoinMap will now be able to access your
MS-Windows personal folder 'Documents' (which is accessed internally
as 'C:\Users\<username>\Documents'). As a result, JoinMap can now
access its program settings in the 'Documents\JoinMap5' subdirectory
and can also place projects there. Another advantage is that JoinMap
can load data into a project from files with names consisting of
non-ASCII characters; note, however, that the data in these files
must still be in ASCII.
However, it is not clear if this works correctly for languages with
right-to-left directionality.
The remarks on pages 4 and 17 of the User Manual about ASCII
characters can now be ignored.
- The various notes tabsheets are also enhanced to accept unicode.
Although it is not perfect, it works fine under most practical
circumstances for languages with left-to-right directionality, e.g.
typing, copying, pasting, exporting and printing. Only under extreme
conditions the odd character can become corrupted, e.g. an extended
character at the end of a very long line (lines are limited in
length to 1024 basic [BMP] characters, while extended [non-BMP]
characters take up the space of two characters and thus reduce the
maximum line length). Another aspect is that notes tabsheets are
based on fixed width fonts and despite of this many non-ASCII
characters are wider than ASCII characters, which all occupy the
same width. Due to this, the notes tabsheets may not look very
elegant.
When notes tabsheets are exported to file, the file format will be
'UTF-8-BOM', which preserves all unicode characters. This format is
recognized properly by most MS-Windows software, e.g. by the text
editors Notepad++ and MS-Windows Notepad.
[BMP: Unicode characters are grouped into so-called planes, one of
which is the Basic Multilingual Plane. This plane contains the
characters for nearly all modern languages and many symbols.]
- The file with release notes can be viewed using a new option of the
Help menu.
=== 22 March 2019 ===
Maintenance release of JoinMap 5
(Build: 22mar2019.21dec2018)
Corrections:
- Computing the linkages of groups of DH and HAP population types
resulted in 'Access violation' errors. This is corrected.
- Computing the Genotype Probabilities of map nodes of population type
CP would change the genotype data: the genotypes in linkage phases
other than {00} would become their genetic equivalents in linkage
phases {00}. These changed data would be visible on the data
tabsheets. Also, any further computation (Genotype Probabilities,
Plausible Positions, Locus Genot. Freq.) would be based on the
modified data. The change would not be permanent, i.e. re-selecting
the map node, would reload the correct genotype data.
This is corrected.
- The print preview and print of colorized data tabsheets of DH, HAP
and CP population types did not take the linkage phases into
account. Now they do.
=== 5 January 2019 ===
Final edition of JoinMap 5
(Build: 5jan2019.21dec2018)
This version is the final release of version 5.
The User Manual is completely rewritten so that it will present all
essential information regarding version 5.
Enhancements:
- The function 'Exclude Marked Loci in Group Node' will now also check
the Exclude checkboxes of the loci that are identical.
- The marking of nodes in the navigation tree and the groupings tree
is improved and made more consistent. Pressing the F8 and the space
key will mark a node, while the Esc key will clear all marks.
- The effect of using of the keys PageUp, PageDown, Home and End,
possibly in combination with holding a Shift or Ctrl key, is made
more consistent.
- A Print Setup button was added to the tool bar.
Various minor errors and glitches were corrected.
=== 8 October 2018 ===
Update and maintenance release of JoinMap 5
(Build: 8oct2018.30apr2018)
This release is the last before the final release. The only planned
addition for the final release is the new User Manual, which will be a
full revision for this version number 5.
Enhancement:
- What was achieved previously for all other population types, is now
also accomplished for population type CP: the time consuming Gibbs
sampling method (a Monte Carlo EM algorithm) for the multipoint
recombination frequency estimation in the ML mapping procedure is
replaced by a much faster deterministic EM algorithm. The estimates
are obtained not only faster but also with greater accuracy.
Adjustments:
- The labels on the buttons of the three options dialogs (environment,
calculation and map chart options) were changed so that their
meaning is more intuitive.
Correction:
- When computing the linkages of a group of population type CP, the
linkage phase determination may be unsuccessful. In this case, the
groups between which the linkage phases could not be determined,
were printed as a single list of loci without indicating the groups.
The indicator 'group' is now printed as intended.
=== 21 August 2018 ===
Update and maintenance release of JoinMap 5
(Build: 21aug2018.30apr2018)
Added functionality:
- The Find tool is enabled for all tables and plain text windows. The
tool is available from the Edit menu and with the usual key
combination Ctrl+F. Searching can be done case sensitive or case
insensitive. Pressing the F3 key will search again for a text
entered previously in the Find tool.
Corrections:
- Computing the groupings and the linkages for population type CP,
where the data contain dominant h- or k- genotypes for <hkxhk> type
markers, could result in the error 'error in determine_phasecomb()'.
This bug is repaired.
- The Population menu function 'Exclude Similar Loci' always excluded
the second locus in a pair with a similarity above or equal to the
given value, regardless whether or not the first locus was excluded
previously due to similarity with another locus. This could result
e.g. in excluding locus C if locus B is similar to locus A, and
locus C to B but not to A. The function works now as intended.
=== 12 June 2018 ===
Update and maintenance release of JoinMap 5
(Build: 12jun2018.30apr2018)
Added functionality:
- Printing is enabled for most tables and plain text windows.
In order to print something, first the to be printed range must
be marked in the regular way (key combination Ctrl+A will mark the
entire content). Next, pressing key combination Ctrl+P will open the
Print Preview window, from which the result can be judged prior to
printing.
The Preview window's toolbar contains buttons for zooming in or
out, for fitting page, width or height, and for opening the dialogs
for the page setup, the print setup and the printing.
Moving through the preview page(s) can be done by dragging the
mouse pointer and with the usual keys and key combinations. In
addition, the numeric keypad plus and minus keys as well as left and
right double-clicking with the mouse all act on the zoom state.
Rolling the mouse wheel will scroll the current page, rolling
combined with pressing the Ctrl key will zoom the page, while
rolling combined with the Shift key will move through the pages.
Clicking the Print button or using key combination Ctrl+P (from
the Preview window) will open the print dialog.
Pressing key combination Shift+Ctrl+P from the main program window
will open the print dialog directly without showing the Print
Preview window. The File menu contains the page setup, print setup,
the print preview and the print functions.
Whenever the required width of a print is wider than is available
on one page, then the remaining parts will automatically be printed
on a next page or even next pages. In this case for tables, the
first column is always repeated on such pages to facilitate an easy
alignment.
If the number of pages you are starting to print is larger than
100, then a warning will be issued and you are prompted whether to
continue or cancel the printing. Also, during the actual printing
(i.e. sending the data to the MS-Windows print spooler), the print
job may be cancelled by pressing the Esc or Break key (similar to
cancelling computations).
The Data tabsheet's print will not show the 'frozen' top row(s),
because their contents are usually not very legible anyway (they do
not fit inside a column).
It is not possible to print the dataset node's Dataset tabsheet,
because this is considered not very useful. If you do wish to obtain
a print of a Dataset tabsheet, then you can copy the content, paste
it into MS-Excel and print it from there.
=== 2 May 2018 ===
Update and maintenance release of JoinMap 5
(Build: 2may2018.30apr2018)
Added functionality:
- Charts can be created for the data in the tabsheets, for which it
can be considered useful (i.e. Individual Genot. Freq., Locus Genot.
Freq., Mean Chisquare Contribs., Genot. Probs.: Indiv. Means, Genot.
Probs.: Locus Means, Expected Rec. Count, Fit & Stress).
If the relevant tabsheet is selected, then click on the 'Create
Chart' button on the tool bar or use the 'Create Chart' function of
the Calculate menu. This will result in a chart node being created
in the navigation tree. The corresponding Chart Control tabsheet has
many (self explaining) options to set the chart to your preference.
The available chart types are: bar, stacked bar, stacked area and XY
chart. Identical loci, if present, will not be shown in the charts.
Charts can be copied to the clipboard for pasting with other
software and they can be exported to file in the enhanced metafile
format (emf).
Correction:
- Combining maps from several nodes could result in a runtime error
and also mess up the marking of nodes in the navigation tree. This
is corrected.
=== 21 February 2018 ===
Update and maintenance release of JoinMap 5
(Build: 21feb2018.11oct2017)
Added functionality:
- Map nodes resulting directly from mapping contain various tabsheets
with diagnostics about the loci, such as the N.N. Fit and Stress. In
these tabsheets, rows can be marked and subsequently the Map menu
function 'Exclude Marked Loci in Group Node' can be applied. In the
map node's grandparental group node this will check the Exclude
checkboxes of the loci that correspond to the marked rows.
- Marked regions in the Dataset tabsheet and in editable plain text
tabsheets (e.g. Notes) can be deleted with key combination Ctrl+Del
and with an option of the Edit menu.
- A new menu function 'Flip Marked Genotypes' was added for the
dataset node. Sometimes genotypes may have been coded erroneously,
e.g. the A was used instead of the B and vice versa; this may result
in recombination frequency estimates larger than 0.5, showing up in
a group node's Suspect Linkages tabsheet. This 'Flip' function will
allow easy correction of such genotype data in the dataset node.
The function will replace genotype codes in the marked region in
their opposite codes. The type of replacement depends on the
population type.
In a BC1, the A's will be replaced by H's and v.v. if there are
A's in the marked range, while if there are B's in the marked range
then B's will be replaced by H's and v.v..
For population types DH, HAP, HAP1, DH1 and DH2 the A's will be
replaced by B's and v.v..
For population types BCpxFy, RIx, IMxFy and F2 the same happens,
and in addition C's will be replaced by D's and v.v..
For population type CP the following genotype mutual replacements
take place: ad <=> bc, ef <=> eg, ll <=> nn, lm <=> np,
while in addition the segregation types <lmxll> and <nnxnp> will be
replaced by each other as well as their corresponding phase and
classification types.
In all cases the replacement is case-insensitive and also the
genotype code must be a correct one, incorrect codes are left
unchanged. Therefore, it is advised to apply (and pass succesfully)
the 'Check for Coding Errors' function in advance to the flip.
- Another function was added to the Dataset menu: 'Create Dataset from
Data Tabsheet'. This function creates a new dataset node and fills
it with the genotype data of a marked population, group or map node
that has a Data tabsheet with genotype data. The data of loci and
individuals that are checked as excluded on the Loci and Individuals
tabsheets, if present, will not be transfered to the new dataset
node.
Adjusted:
- The color of marked regions in the tables is changed to red. (Marked
regions in plain text remains the MS-Windows default, usually blue.)
- The system of marking nodes in the navigation panel is improved.
=== 8 January 2018 ===
Update and maintenance release of JoinMap 5
(Build: 8jan2018.11oct2017)
Corrections in the ML mapping algorithm:
- The expected recombination counts, the map distances and possibly
the map order were estimated erroneously for population type BCbxFy.
- The N.N. Stress was computed erroneously for a few population types:
BC1 (only if coded with H's and B's), BCbxFy, DH and HAP.
These errors were present since the first pre-release.
=== 20 December 2017 ===
Update and maintenance release of JoinMap 5
(Build: 20dec2017.11oct2017)
Adjusted functionality:
- The map building approach of the ML mapping algorithm was adjusted
to become more reliable for high density maps. Spatial sampling is
still being used for gradually building the map. After the sampling
threshold becomes 0, then now the building proceeds with adding
batches of loci instead of adding all remaining loci in one go.
The loci in each batch are selected at random. The batches are of a
fixed size, which can be adjusted in the Calculation Options. Three
of the map optimization (simulated annealing) parameters are now
specific to each spatial sampling level (now called S1 to S5) and to
the building with batches after the sampling threshold of 0 is
reached (called T0). This is meant to be able to speed up the first
map building levels. The three parameters are: (1) the number of
optimization rounds per sample, (2) the chain length with constant
acceptance probability and (3) the stop criterion (stop after #
chains without improvement).
- The history of the status bar is increased to 50 messages.
- Two parameters used in the true EM approach with the multipoint
recombination frequency estimation are adjustable in the Calculation
Options: the maximum number of iterations and the recombination
frequency tolerance. These parameters determine when the EM
iterations should stop.
Correction:
- When applying the 'Invert Map' function of a map node, the Plausible
Positions tabsheet did invert the map, but failed to show the
position counts at their inverted positions and a recalculation
would be required. This is now working as expected.
=== 6 November 2017 ===
Update and maintenance release of JoinMap 5
(Build: 6nov2017.11oct2017)
Added functionality:
- The 'Colorize' function for graphical genotypes takes the linkage
phases (if available) into account for population types CP, DH and
HAP.
The following adjustment was made:
- The new (more efficient) locus replacement strategy in the map order
optimization method (i.e. simulated annealing) turned out to work
not very well if the number of loci that is added after the last
spatial sampling threshold is large. For the time being the strategy
is returned to that of JoinMap v4.1.
Remark: This does not apply to population type CP. Here the new
strategy is not yet applied.
=== 27 October 2017 ===
Update and maintenance release of JoinMap 5
(Build: 27oct2017.11oct2017)
Added functionality:
- Export Map tabsheets from multiple marked map nodes as one joint
map-file (e.g. for use with MapQTL).
- Export Data tabsheets from multiple marked nodes (population, group
or map nodes) as one joint loc-file (e.g. for use with MapQTL).
The following corrections were made:
- Individual Genot. Freq. tabsheet would compute all frequencies to
be 0 for certain individuals if some loci were excluded.
- Assigning ungrouped loci to their SCL-groups at a grouping node
could lead to an 'access violation' error if a threshold value other
than the default is used.
- In extreme situations the multipoint recombination frequecy
estimation procedure could result in a floating point error
(division by zero).
- Using the 'Move Marked Loci' of grouping nodes did not adjust the
corresponding group nodes correctly.
=== 7 October 2017 ===
Update and maintenance release of JoinMap 5
(Build: 7oct2017.2jun2017)
Added functionality:
- Export Map tabsheets as map-files.
The following corrections were made:
- Selecting another node after a map node was selected could lead to
an 'access violation' error causing the program to stop working.
- Repeatedly doing computations that are done in parallel, like
calculating groupings, could make the program appear to freeze.
=== 25 September 2017 ===
Update and maintenance release of JoinMap 5
(Build: 25sep2017.2jun2017)
Added functionality:
- Map charts.
- Copying marked regions in the Further Information window.
The following corrections were made:
- In the computations of pairwise data, numerical problems could lead
to tiny negative LOD values instead of exactly 0.
- The new, true EM algorithm for multipoint recombination frequency
estimation could result in some runtime errors ('root not
bracketed ...', 'division by zero', 'rec.freq. larger than 0.5'),
preventing the computation of the map or the plausible positions.
NB:
Because some parameter settings had to be changed, the first time
the new release is run JoinMap will show two error messages about
reading the program and page setup; these can be ignored.
=== 11 August 2017 ===
Update and maintenance release of JoinMap 5
(Build: 11aug2017.2jun2017)
Added functionality:
- Copying and cutting marked regions in plain text tabsheets
(previously the entire text was taken).
The following corrections were made:
- Due to repeated rounding errors, the interpolation to compute the
integrated map with population type CP could result in map positions
of <lmxll> and <nnxnp> markers just outside their interval (less
than 1e-14 cM). This would result in the next type of error message
when trying to view the Data tabsheet of or do computations with a
map node:
'ReadLoci_SQLite() map position of locus X before that of Y'.
This is now prevented.
- Fixed and Start order tabsheets were made tolerant for the type of
newline characters (CR, LF, CR+LF, LF+CR) used with pasted orders.
Previously this could lead to unrecognized locus names.
- Pasting into plain text tabsheets was made tolerant for the type of
newline character and for lines longer than the maximum of 1024
characters. This applies to the Notes, Start and Fixed order
tabsheets.
- The Dataset node function 'Check for Coding Errors' did not accept
correct phase type codes for segregation type <nnxnp>; repaired.
=== 14 July 2017 ===
Update and maintenance release of JoinMap 5
(Build: 14jul2017.2jun2017)
Added functionality:
- 'Move Marked Loci' menu function for grouping nodes.
The following corrections were made:
- The Individual Genotypes Frequencies were determined without taking
the exclusion of loci into account. Now they are.
- In fields of floating point parameters (e.g. in the Calculation
Options) the decimal point could not be entered. Now it is possible.
- The reporting about any incompleteness in linkage phase
determination in the population node computations of groupings was
poor. Now identicals are not reported anymore and the status whether
loci are excluded is given.
The Help menu document with the new features of v5 is updated.
=== 3 June 2017 ===
Update and maintenance release of JoinMap 5
(Build: 3jun2017.26apr2017)
Added functionality:
- marking regions in tables for functions on the marked loci or
individuals;
- 'Exclude Marked Items' menu function for Individual Genot. Freq. and
Locus Genot. Freq. tabsheets of population nodes;
- 'Set X2-Test Classification for Marked Loci' menu function for Locus
Genot. Freq. tabsheet of population and map nodes;
- checking or un-checking a range of checkboxes in marked rows;
- copying and exporting marked rows of tables;
- toggling a checkbox with the Enter key.
The Help menu document with the new features of v5 is updated.
Some bugs were removed, one of which is the 'Invalid floating point
operation' obtained when computing a maximum likelihood map for
population type CP.
=== 16 May 2017 ===
Maintenance release of JoinMap 5
(Build: 16may2017.26apr2017)
The computations of locus pairs did not deal correctly with
situations, where a locus has all observations missing. This
would lead to the error message
'Par_Task_Interface->Status not completed'.
This is corrected.
=== 26 April 2017 ===
Early release of JoinMap 5
(Build: 26apr2017.26apr2017)
= First public release. The final edition of JoinMap v5 is
several months in the future. Because of the demand, a
first stable early edition is released. Following this
first release, subsequent updates with the remaining to be
added functions will be released in the coming months.
JoinMap 4 & 4.1 Release notes
=============================
=== 31 July 2013 ===
Maintenance releases of JoinMap 4 and 4.1
(Build: 31jul13.4feb11)
= A function is added to the Grouping node menu:
'Assign Identical Loci to Their Groups'. The procedure to
create a grouping node (see 6 and 19 March 2013) assigns
sets of identical loci to group number 0, with the
exception of one representing locus for each set. The new
function will assign the identicals with group number 0 to
the groups of their representing loci.
=== 19 March 2013 ===
Maintenance release of JoinMap 4
(Build: 19mar13.4feb11)
= The same changes are applied to JoinMap 4 as in the recent
maintenance release of JoinMap 4.1 of 6 March 2013.
See below.
=== 6 March 2013 ===
Maintenance release of JoinMap 4.1
(Build: 6mar13.4feb11)
= The grouping procedure of sets of loci into linkage
groups used to be limited to sets of roughly 4000 loci due
to available RAM memory. As the program is 32-bit it is
limited by the maximum addressable amount of RAM. A new
algorithm is implemented that is designed to store
intermediate results on hard disk rather than in RAM. The
program can now accommodate sets of up to ~50,000 loci,
while keeping computation time within acceptable limits.
On a typical present-day PC, the grouping procedure of
50,000 loci takes about one hour. The speed of the hard
disk is an important limiting factor. As the computations
scale quadratically with the number of loci, groupings of
smaller sets are still quite fast: 10,000 loci in about
three minutes, 5000 loci in just about twenty seconds and
1000 loci in a second.
Beware that such oversized datasets require extreme file
sizes: the 50,000 loci require a file of ~30 GB for the
pairwise data. When creating the grouping node and group
nodes, this file with pairwise data will be duplicated.
Thus, ensure that the hard disk in use has sufficient free
space when dealing with such datasets.
In large datasets there will often be some redundancy (in
fact, in most cases there should be). As an new feature
the grouping procedure determines which loci are
identical. Being identical is based on the entire set of
genotype observations of all included (not excluded)
individuals, including the missing observations. Sets of
identical loci will be represented by one of them (the
first not excluded locus). Identical loci will be
specified at the bottom part of the 'Groupings (text)'
tabsheet, while a numerical summary is given with the blue
'Further information' tool bar button. One advantage is
that the pairwise data will only be calculated for the
loci that represent their identicals, thus reducing the
computations.
When determining a grouping node and group nodes, only the
representing loci of sets of identical loci will be
grouped, while in the grouping node tabsheet the identical
loci will automatically obtain group number 0 (i.e. will
not be part of a group), with 'identical' as Node name.
The determination of the SCL-Values takes the identicals
into account and will list 'identical' as SCL-Value to
link them to their representing locus. The
representing loci will obtain a regular SCL-Value.
The procedure 'Assign Ungrouped Loci to SCL-Groups' will
leave the identicals assigned to group 0.
The procedure for determining a grouping based on a map or
another grouping node will take the identicals into
account and assign them to group 0.
The grouping procedure may also be done based on the
recombination frequency or the linkage LOD. For
population types CP, DH and HAP, this means that the
linkage phases must be determined to obtain these values.
In the original procedure the pairs were sorted to their
independence LOD value prior to the linkage phase
determination. To be able to deal with very large datasets
this sorting is not done anymore. The independence LOD
threshold for pairs subject to phase determination, which
used to be internally set at a LOD value 1.0, is now a
Calculation Options parameter at the Population tabsheet:
'Determine linkage phases ...'. When in doubt about the
linkage phase determination you can increase this
parameter value.
= The navigation panel could disappear after resizing it to
the smallest size (by dragging the splitter between the
navigation and the contents-and-results panel).
Disappearing is now prevented.
=== 11 June 2012 ===
Maintenance release of JoinMap 4
(Build: 11jun12.4feb11)
= In text tabsheets, like the 'Map (text)' tabsheet,
sometimes a non-printable character got inserted at a
random position (visible as a square character). It
prevented copying the area around it. It is corrected.
=== 14 March 2012 ===
Maintenance releases of JoinMap 4 and 4.1
(Build: 14mar12.4feb11)
= For population types DH, HAP and CP, the Linkage LODs for
the Groupings (text and tree) tabsheet as well as the
corresponding SCL-values of derived Grouping nodes were
calculated erroneously. This is corrected.
= The calculation option 'Determine linkage phases (CP, DH,
HAP) with a LOD larger than' was reset to the value 1.0
each time the groupings of a population node were
(re)calculated. This is corrected.
=== 4 August 2011 ===
Maintenance release of JoinMap 4.1
(Build: 4aug11.4feb11)
= The Population menu functions 'Exclude Identicals' and
'Exclude Similar Loci' could lead to runtime errors with
larger datasets. The functions have been recoded and are
now also much faster.
= Renaming the project file without renaming the project
directory would lead to a rewritten, empty project file.
This is corrected.
=== 3 August 2011 ===
Maintenance release of JoinMap 4
(Build: 3aug11.4feb11)
= The Population menu functions 'Exclude Identicals' and
'Exclude Similar Loci' could lead to runtime errors with
larger datasets. The functions have been recoded and are
now also much faster.
= The following minor errors were corrected:
The heading in the Genotype Probabilities tabsheet had
'R.Genotype' instead of 'Genotype' for the central
genotype.
Long group and map node names were made shorter than the
allowed 20 characters when closing the project.
Map charts would inexplicably draw some 'homologs' lines
between loci that did not have identical names.
The simulated annealing sometimes appeared to continue
too long.
For map nodes the 'Info on Tabsheet Contents' button and
function in the File menu should be active for several
tabsheets while they were not.
Any fixed order used in the determination of plausible
orders was not reported in the
'Info on Tabsheet Contents'.
The name of the HTTP Host of the proxy settings in the
environment options was not saved.
Sometimes the decimal separator (the point) was reset to
the preference in the MS-Windows Regional Options. This
would lead to error messages like
'0.000 is not a valid floating point value'.
Renaming the project file without renaming the project
directory would lead to a rewritten, empty project file.
=== 20 July 2011 ===
Final version of JoinMap 4.1
(Build: 20jul11.4feb11)
= The only, but very important, enhancement of version 4.1
of JoinMap is the ability to use the multipoint maximum
likelihood mapping algorithm on populations of type CP,
i.e. the outbreeding species full-sib family. The new
method is described in a paper that was accepted for
publication:
Van Ooijen, J.W. (2011). Multipoint maximum likelihood
mapping in a full-sib family of an outbreeding species.
Genetics Research, accepted June 2011.
=== 7 February 2011 ===
Maintenance release of JoinMap 4
(Build: 7feb11.4feb11)
= The Colorize function to show graphical genotypes now
takes the linkage phases into account for DH and HAP
population types. For instance, genotype a of a marker
with phase {1} is shown in the same color as genotype b
of a marker with phase {0}.
= A function was added to work on the Similarity of Loci
tabsheet: Population menu > Exclude Similar Loci.
It works like the Exclude Identicals function, but instead
of using a similarity value of 1.0 this function prompts
for a similarity value to use. If two loci have a
similarity above the given value, the second locus will be
excluded on the Loci tabsheet, unless the first locus is
already excluded (to prevent excluding locus C if locus B
is similar to locus A, and locus C to B but not to A).
This function allows spatial sampling of the loci.
= The grouping process was given a somewhat higher speed.
=== 6 October 2010 ===
Maintenance release of JoinMap 4
(Build: 6oct10.9feb10)
= In recent maintenance releases JoinMap was set to use
Windows Desktop Themes. Several users experienced runtime
errors due to this. The use of themes by JoinMap is
stopped.
= Clicking on the 'no data' header of an empty Data tabsheet
resulted in an 'OLE error' message. This is repaired.
=== 20 April 2010 ===
Maintenance release of JoinMap 4
(Build: 20apr10.9feb10)
= When creating maternal and paternal population nodes of a
CP type dataset node, now loci with a <hkxhk> segregation
type are also exported, unless the classification type is
(hh,k-) or (h-,kk). The genotypes hk, h- and k- are all
exported as unknowns --; genotypes hh and kk are exported
as ll and lm, respectively, for the first (=maternal)
parent, and as nn and np, respectively, for the second
(=paternal) parent.
=== 19 Februay 2010 ===
Maintenance release of JoinMap 4
(Build: 19feb10.9feb10)
= Creating a population node of a CP type dataset node
resulted in an error. A similar bug resulted with the
exporting as loc-file from Data tabsheets in minor
errors in the loc-file. The bugs were repaired.
=== 16 Februay 2010 ===
Maintenance release of JoinMap 4
(Build: 16feb10.9feb10)
= To make working with large marker datasets of a population
a bit faster, new options are introduced:
-A checkbox option on the tool bar controls whether or not
the various Data tabsheets are loaded; it can also be set
in the Options menu.
-Large datasets create huge tables of pairwise linkages
and if they are not going to be inspected things are
faster if the tables are left out altogether. Therefore,
in the Group tabsheet of the calculation options two new
checkboxes control whether or not weak and strong linkages
tables are created when the linkages are calculated.
= The Colorize function to show graphical genotypes now
takes the linkage phases into account (if available) for
all segregation types except <hkxhk>. For instance,
genotype lm of a marker with phase {1-} is shown in the
same color as genotype ll of a marker with phase {0-}. The
default colors are modified for a better correspondence
between the segregation types.
= An option is added that controls whether the current
selection or the entire tabsheet contents must be printed,
copied, or exported; it is a check box on the tool bar and
is also available in the Options menu.
= The Highlight Errors function now also allows
classification types (a,h) and (h,b) for population types
BCpxFy. And when the y-generation is zero (i.e. it is a
normal BC1), only genotypes a and h (BCAxFy), or h and b
(BCBxFy) are allowed.
= With an added option in the Help menu you can now check
via the internet whether a newer release is available.
If your internet connection requires the use of a proxy,
you can supply the proxy name and port in the environment
options.
= Several internal actions that may take a while now change
the cursor temporarily into the hourglass cursor.
= Map-files or pwd-files in which the comma is used as
decimal separator (instead of the point) will be loaded
correctly.
= Maps with multiple linkage groups are now inverted
group by group with the Invert Map function of the
Map menu.
= The time stamp now also shows the seconds.
=== 11 August 2008 ===
Maintenance release of JoinMap 4
(Build: 11aug08.7apr08)
= In the ML mapping algorithm the fixed order was not always
maintained; this is corrected.
= The tabsheet with the Locus Means of the Genotype
Probabilities is sorted on the map position of the loci.
This will result in a proper chart when plotted against
the map position.
= The tabsheet with the Individual Means of the Genotype
Probabilities is given in the original order of the
individuals.
=== 23 July 2008 ===
Maintenance release of JoinMap 4
(Build: 23jul08.7apr08)
= If the grouping cannot be calculated for a population
type CP, better information will now be shown.
= The situation with three (or more) loci at the same map
position could lead to a floating point error in the ML
map calculations. This is corrected.
= The cooling control parameter of the ML Mapping algorithm
had a lower limit of 0.001 which is now reduced to
0.00001; the upper limit is now set to 1.0.
= The tabsheet with the Locus Means of the Genotype
Probabilities now also shows the map position of the loci.
= When no project is open, pressing the OK button on the
Environment and the Calculation Options dialogs will save
the options as default options that will apply to all
future projects (similar to the 'Save as default' button).
= The About box was renewed.
=== 8 April 2008 ===
Maintenance release of JoinMap 4
(Build: 8apr08.7apr08)
= For a BCpxFy the genotype probabilities given the map
given two heterozygous or dominant flanking markers were
not completely right. This is corrected.
= The map chart options dialog can be opened when no map
chart is visible; changing the options will have the same
effect as 'Save as Default Map Chart Options'. Any future
map chart will be drawn according to these options.
= Also, when no map chart is visible the 'Reset to Preset
Map Chart Options' can be activated, which will affect
all future map charts.
= The loading of MAPMAKER raw data is slightly improved.
= Various minor (internal) improvements were made.
=== 4 May 2007 ===
Maintenance release of JoinMap 4
(Build: 4may07.4oct06)
Changes:
= JoinMap 4 was enabled to run under Windows Vista.
For installation of the user license under Windows Vista,
please see the 'Installation ReadMe' file on the CDROM or
in the program directory after running the program
installation 'setup.exe'
(typically: 'C:\Program Files\JoinMap4').
=== 18 April 2007 ===
Maintenance release of JoinMap 4
(Build: 18apr07.4oct06)
Changes:
= When exporting the Data tabsheet of a Map node of a CP
type population as a loc-file, the map position of
markers was given at the wrong place in the file.
This is corrected.
= The exporting of a Dataset tabsheet of a Dataset node as
a loc-file did not function properly. This is corrected.
=== 5 March 2007 ===
Maintenance release of JoinMap 4
(Build: 5mar07.4oct06)
Changes:
= When calculating the linkages for groups of population
type CP, it is possible that the linkage phases cannot
be determined and thus also no recombination frequencies
can be calculated. In such instances the program could
generate an unclear runtime error message: 'unknown error
in sclastype()'.
This problem is corrected and the information given in
the 'Info on Tabsheet Contents' has become more complete
about the linkage phases determination status.
=== 4 October 2006 ===
Maintenance release of JoinMap 4
(Build: 2oct06.4oct06)
Changes:
= For extremely large values of the chisquare distribution
the P-value in the Grouping tabsheet could not be
calculated and resulted in the freezing of the program.
The P-value is calculated irrespective of the Grouping
parameter chosen.
A new algorithm to calculate the P-value is now used.
= For very large linkage groups the computations of the
linkages may appear to take extremely long. Actually,
it is not the computations that take a long time but
the loading of the resulting data into the Linkages
tabsheets. For such large linkage groups there may
be very, very many pairs to display on the Weak and
Strong linkages tabsheets, depending on the chosen
corresponding thresholds.
To allow for more precision here, the recombination
frequency thresholds on the Group tabsheet of the
Calculation Options now have up to four decimals.
Unfortunately the loading of the data into the
tabsheets cannot be shown on the progress bar, but the
progress of the program is now shown with some simple
comments on the status bar:
'loading table "Weak Linkages"'
'loading table "Strong Linkages"'
'loading table "Suspect Linkages"'
together with the numbers of rows that must be loaded,
allowing the user to see and estimate the progress.
These comments are usually only visible with very large
groups.
=== 25 July 2006 ===
Final edition of JoinMap 4
(Build: 25jul06.16jun06)
