-
Notifications
You must be signed in to change notification settings - Fork 4
/
RELEASENOTES.txt
107 lines (94 loc) · 7.47 KB
/
RELEASENOTES.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
LRmix Studio Release Notes
==========================
Version: ${project.version}
Release date: ${buildTimestamp}
------------------------
LRDYN-270: Made location of report template configurable.
Version: 2.1.5-CommunityEdition
Release date: 2018-12-07
------------------------
LRDYN-268: To allow running the application from a read-only folder, the properties file can now also be placed in the ~/.lrmixstudio folder.
LRDYN-269: The file loci.properties - which holds the list of loci presented in the profile editor - can now be located in either the ~/.lrmixstudio folder or the application folder to override the default version.
Version: 2.1.4-CommunityEdition
Release date: 2018-11-16
------------------------
LRDYN-257: Added View menu where the fontsize used for tables can be changed. Also made the parameters panels resizable in the Analysis and Sensitivity Analysis tabs.
LRDYN-259: Fixed a problem where data containing more than 50 loci (e.g. Microhaplotype) would cause undefined behaviour.
LRDYN-260: All LRs calculated in a non contributor test can now be exported to a separate file.
LRDYN-261: The maximum allowed number of unknowns is now configurable through the 'maxUnknowns' setting in the LRmixStudio.properties file. The setting defaults to 4.
LRDYN-262: Empty loci in reference profiles (i.e. loci not containing any alleles) will now be disabled automatically.
LRDYN-263: Fixed behaviour when a logfile is dropped on the Sample Files table.
LRDYN-265: Values entered for dropout and FST are now stored, and used as initial values the next time the software is started.
LRDYN-266: Added a list of disabled loci to the log file and report, explaining the reason why the locus is disabled.
LRDYN-267: Improved handling of ranges in the Sensitivity Analysis tab.
Version: 2.1.3-CommunityEdition
Release date: 2016-07-05
------------------------
LRDYN-253: Added a warning message when the total number of contributors under Hp differs from that under Hd.
LRDYN-256: Changed wording in the report describing rare alleles (i.e. alleles that are not present in the population statistics)
Version: 2.1.2-CommunityEdition
Release date: 2016-07-01
------------------------
LRDYN-249: Fixed a performance issue in the application that caused slow response when enabling or disabling a replicate or sample.
LRDYN-250: In order to reduce the number of combinations for unknown contributors, alleles from the population statistics that are not present in
the samples or profiles are grouped into a single 'other' category that has a combined probability.
LRDYN-251: Sensitivity Analysis and Dropout estimation made more robust.
LRDYN-252: Number of dropout steps has been set to 99 for sensitivity analysis.
Version: 2.1.1-CommunityEdition
Release date: 2016-06-13
------------------------
LRDYN-223: When reading a GeneMapper or LRMix file containing a replicate ID number, this replicate ID
is now incorporated into the sample name.
This fixes a problem in the scenario where replicates are spread over multiple files, in
which case the exported PDF report would only contain the alleles of the last loaded replicate.
LRDYN-224: The application can now be started with a command line argument specifying the name of a logfile
or saved session file from which to restore settings. If loading succeeds, the user is taken
directly to the Analysis tab.
LRDYN-225: Fixed an error message that occurred at the end of an analysis when running on Java 7.
LRDYN-226: Disabling a sample on the summary screen now also disables it on the Sample Files screen.
LRDYN-228: The default number of steps in the sensitivity analysis is set to 10.
LRDYN-230: Fixed a layout problem in the settings box on the Sensitivity Analysis tab.
LRDYN-231: The results of Dropout Estimation (DE) and Sensitivity Analyses (SA) is stored. If Hp or Hd is changed in ways
that do not affect the outcome of DE or SE, the stored DE and SA results are included in the report for analyses run with
the changed hypotheses. This means that a dropout estimation and sensitivity analysis can be performed after which
the dropout values for contributors can be set without having to re-do DE or SA.
LRDYN-232: Reference profile loci with one allele are now treated as homozygote.
LRDYN-233: Fixed the behaviour of the Restart button to properly reset the Analysis tab to accurately reflect the default hypotheses.
LRDYN-234: Fixed scaling issues in the Sensitivity Analysis graph.
LRDYN-235: Changed Y-axis title of sensitivity analysis graph to 'Log 10'.
LRDYN-236: Empty lines in CSV files are now ignored.
LRDYN-237: Added support for the CSV format as used by eDNA. This format uses the following columns:
UD1,UD2,UD3,Panel,Marker,Dye,Allele 1,Height 1,Allele 2 and Height 2
The user defined fields carry the following information:
UD1 contains the Sample Id
UD2 contains the Case Number
UD3 contains the SIN
LRDYN-239: Long sample names are now properly shown in the report.
LRDYN-240: Added a button to show the log of the current analysis.
LRDYN-241: It is now possible to set PrD of selected profiles directly from the Sensitivity Analysis tab.
LRDYN-242: When the Restart button is clicked, the state of the Sensitivity Analysis screen is now properly reset.
LRDYN-243: In the non-contributor tab, profiles that are selected as donor for both Hp and Hd are no longer available as POI for the non-contributor test.
LRDYN-244: If reference profile loci with a single allele are treated as homozygote (see LRDYN-232), this is now reported in the GUI, the log and the report.
LRDYN-245: Fixed the representation of dropout values in the report. E.g. the value 0.07 would sometimes be represented as 0.06999999999999.
LRDYN-246: In the sensitivity analysis the start and end of the graph would seem to be truncated if the number of steps was low and the Log10(LR) at the upper
or lower bound was not representable (e.g. Infinity). For the lower end of the graph, this was fixed by re-calculating the LR at the next-up
value for dropout (i.e. increased by 0.01). For the upper end, the next-down value is used (i.e. reduced by 0.01)
LRDYN-247: If the calculation results in 'Not a Number' (NaN) or Infinity, a dialog is shown with possible causes.
Version: 2.1.0
Release date: 2016-02-18
------------------------
LRDYN-222: Introduced support for a new input file format (called LRM-2 for lack of a better name). Based on the LRmix csv format, with the following changes:
* 'SampleName' in row 0, column 0 changed to 'Sample Name'
* 'AlleleN' in header changed to 'Allele N'
* 'Height N' columns added
Version: 2.0.1
Release date: 2016-01-14
------------------------
LRDYN-220: Replaced approximation of Genotype Probability for Sibling relation if Theta==0 with exact value.
Details:
This version corrects for the relatives formula when questioned profile and profiled relative are
siblings in the configuration ab/ab (following the so-called Buckleton's formulas, see manual for
complete references and more details). It only affects situations where Fst=0.
In 2.0, for siblings, we had, (1+pa+pb+pa*pb)/4, and in this version 2.0.1, we have the
changed formula: (1+pa+pb+2*pa*pb)/4 (note the 2 before the pa*pb)
LRDYN-221: Profile summary is not updated if profiles are enabled or disabled.