msuchard/test_beast issues and pull requests

#33 - Tracer: Doesn't read scientific notation log files

Issue - State: open - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Defect, Tracer, v1.4

#33 - Tracer: Doesn't read scientific notation log files

Issue - State: open - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Defect, Tracer, v1.4

#32 - BEAUti adds a constraint to every taxon sets

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Defect

#32 - BEAUti adds a constraint to every taxon sets

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Defect

#31 - Taxon sets not being properly loaded from templates

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Defect

#31 - Taxon sets not being properly loaded from templates

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Defect

#30 - BEAUti - some prior plots not displayed properly

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Defect

#29 - Bug in AlignmentParser prevents the use of general data types

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Priority-Medium, Type-Defect, Status-WontFix

#29 - Bug in AlignmentParser prevents the use of general data types

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Priority-Medium, Type-Defect, Status-WontFix

#28 - Prior table not updates when tree prior is changed in BEAUti

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Defect

#28 - Prior table not updates when tree prior is changed in BEAUti

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Defect

#27 - exception in tracer (development source)

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Defect

#27 - exception in tracer (development source)

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Defect

#26 - offset seems to be ignored for exponentialPriors

Issue - State: closed - Opened by msuchard over 9 years ago - 2 comments
Labels: Status-Fixed, Priority-Medium, Type-Defect

#26 - offset seems to be ignored for exponentialPriors

Issue - State: closed - Opened by msuchard over 9 years ago - 2 comments
Labels: Status-Fixed, Priority-Medium, Type-Defect

#25 - BEAST ignores the offset value in an exponential prior

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Priority-Medium, Type-Defect, Status-Invalid

#25 - BEAST ignores the offset value in an exponential prior

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Priority-Medium, Type-Defect, Status-Invalid

#24 - BEAUti ignores the offset value given for gamma priors

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Defect

#24 - BEAUti ignores the offset value given for gamma priors

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Defect

#23 - TMRCA constraint fails with a taxa set which is a union of other sets

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Defect

#23 - TMRCA constraint fails with a taxa set which is a union of other sets

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Defect

#22 - Taxa set table is sorted alphabetically but monophyly choices are not

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Defect

#22 - Taxa set table is sorted alphabetically but monophyly choices are not

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Defect

#21 - Error checking for compatible monophyly in BEAUti

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Defect

#21 - Error checking for compatible monophyly in BEAUti

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Defect

#20 - Error reporting when parsing XML

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Enhancement

#20 - Error reporting when parsing XML

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Enhancement

#19 - Setting lognormal priors in real-space

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Enhancement, BEAST, 1.5

#19 - Setting lognormal priors in real-space

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Enhancement, BEAST, 1.5

#18 - Tracer hangs on large trace files

Issue - State: closed - Opened by msuchard over 9 years ago - 3 comments
Labels: Priority-Medium, Type-Defect, Status-Invalid

#18 - Tracer hangs on large trace files

Issue - State: closed - Opened by msuchard over 9 years ago - 3 comments
Labels: Priority-Medium, Type-Defect, Status-Invalid

#17 - BSP options don't disappear when a different tree prior is selected in BEAUti

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Defect

#17 - BSP options don't disappear when a different tree prior is selected in BEAUti

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Defect

#16 - Forwards/Backwards date selection becoming corrupted in BEAUti

Issue - State: open - Opened by msuchard over 9 years ago - 2 comments
Labels: Status-Fixed, Priority-Medium, Type-Defect

#16 - Forwards/Backwards date selection becoming corrupted in BEAUti

Issue - State: open - Opened by msuchard over 9 years ago - 2 comments
Labels: Status-Fixed, Priority-Medium, Type-Defect

#15 - getDemographic method in PiecewiseLinearPopulation was returning the wrong value

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Defect, Component-Logic

#14 - Null-Pointer Exception when a Newick tree doesn't finish with a ';' (semicolon)

Issue - State: closed - Opened by msuchard over 9 years ago - 2 comments
Labels: Status-Fixed, Priority-Medium, Type-Enhancement

#14 - Null-Pointer Exception when a Newick tree doesn't finish with a ';' (semicolon)

Issue - State: closed - Opened by msuchard over 9 years ago - 2 comments
Labels: Status-Fixed, Priority-Medium, Type-Enhancement

#13 - BEAUTi provides no simple way to run an analysis without data

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Enhancement

#12 - BEAUTi does not generate a valid starting tree when hard bounds on some nodes are specified in the prior

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Type-Defect, Priority-High

#11 - x86 platform giving RESTORE failure error with some files

Issue - State: closed - Opened by msuchard over 9 years ago - 4 comments
Labels: Type-Defect, Priority-Low, Status-WontFix

#10 - The exponential prior code sends mean rather than rate to ExponentialDistribution constructor!

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Priority-Critical, Status-Fixed, Type-Defect

#9 - Need to exclude src/org/virion/jam/maconly directory from build under Linux

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Defect

#8 - LogCombiner incorrectly assumes taxon order is the same when combining tree files

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Type-Defect, Priority-High

#7 - ESS and ACT code not shared between Tracer and LogAnalyzer

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Priority-Medium, Type-Other

#6 - Can't set group count for skyline plot in BEAUti

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Priority-Critical, Status-Fixed, Type-Defect

#5 - Guess dates bug in BEAUti 1.4

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Status-Fixed, Type-Defect, Priority-Low

#4 - Feature request: Exponential Bayesian Skyline

Issue - State: open - Opened by msuchard over 9 years ago
Labels: Priority-Medium, Type-Enhancement, Status-Accepted

#3 - Null pointer registering datatypes

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Priority-Critical, Status-Fixed, Type-Defect

#2 - Fix all compiler warning messages

Issue - State: closed - Opened by msuchard over 9 years ago - 3 comments
Labels: Type-Task, Status-Fixed, Priority-Medium, Maintainability

#1 - Source repository is messed up with java files in the bin directory

Issue - State: closed - Opened by msuchard over 9 years ago - 1 comment
Labels: Type-Task, Priority-Critical, Status-Fixed

GitHub / msuchard/test_beast issues and pull requests