Blossoc - 1.0.7 =============== - 0000087: [Feature Request] Highlighting of significance should depend on scoring function (mailund) - 0000112: [Feature Request] Highlighting regions and loci (mailund) - 0000130: [Feature Request] Importing highlight annotations (mailund) - 0000134: [Feature Request] Drag'n'drop of annotations (mailund) - 0000139: [Feature Request] Export annotations (mailund) - 0000132: [Feature Request] automatically add .blossoc suffix to file names (mailund)
Blossoc - 1.0.6 =============== - 0000093: [Documentation] Add a few test-examples in the distribution (mailund) - 0000121: [Feature Request] accept blossoc files through drag-n-drop (mailund) - 0000125: [Feature Request] remember which plots are open (mailund) - 0000124: [Feature Request] Add QTL SMA (mailund) - 0000123: [Feature Request] add SMA code to the cmd-line version (mailund)
Blossoc - 1.0.5 =============== - 0000122: [Bug] zoom in and out cursors not working... (mailund)
Blossoc - 1.0.4 =============== - 0000108: [Feature Request] MIME type for blossoc? (mailund) - 0000098: [Feature Request] Store full path to positions file and haplotypes file (mailund) - 0000103: [Bug] online help is missing for permutation test (mailund) - 0000097: [Feature Request] Add button for toggling visibility of SMA plot (mailund) - 0000092: [Feature Request] Warning when running prob. score on large datasets... (mailund) - 0000110: [Bug] perm. score not shown when opening (mailund) - 0000109: [Bug] permutation test p-values are not exported (mailund) - 0000106: [Feature Request] Customizable installation path... (GUI) (mailund) - 0000088: [Feature Request] Navigation of graph without wheel... (besen) - 0000105: [Feature Request] Accept project file on the command line for the GUI (mailund) - 0000090: [Bug] Margin around plots (besen) - 0000078: [Bug] setting default scoring function is not handled correctly in the cmdline interface (besen) - 0000060: [Feature Request] Provide QTL support (besen)
Blossoc - 1.0.3 =============== - 0000083: [Feature Request] Permutation test in GUI (mailund) - 0000101: [Feature Request] Add an 'Apply' button to the parameters dialogue (mailund) - 0000100: [Bug] SMA should *only* be invalidated when data changes, not when mapping parameters change (mailund) - 0000099: [Bug] Running/Suspended label in progress dialog... (mailund) - 0000094: [Feature Request] Export SMA (mailund) - 0000095: [Bug] Hide old SMA plot (mailund) - 0000091: [Feature Request] Pressing Enter in the text entries for positions and haplotypes files should load the files (mailund)
Blossoc - 1.0.2 =============== - 0000085: [Feature Request] SMA in GUI (mailund) - 0000089: [Bug] warning when opening a file into a modified window (mailund)
Blossoc - 1.0.1 =============== - 0000081: [Bug] crashing when double-clicking an empty graph (mailund) - 0000073: [Bug] Mirroring when zooming in GUI (mailund) - 0000080: [Feature Request] More appropriate choice of ticks in the graph widget (mailund) - 0000077: [Bug] Crash when running CF with Prob. score and minSNPs=9 (mailund) - 0000063: [Feature Request] Loaded/not-loaded status for positions and haplotypes files (mailund) - 0000079: [Feature Request] Store window geometry settings (mailund) - 0000076: [Bug] Re-map if min SNPs changes (mailund) - 0000019: [Documentation] Write a "Getting Started" manual (mailund) - 0000072: [Feature Request] Warning when closing unsaved (mailund) - 0000071: [Feature Request] Warning when overwriting a file (mailund) - 0000067: [Bug] Crash when positions and haplotypes are not consistent. (mailund) - 0000070: [Feature Request] Recent file (mailund) - 0000069: [Feature Request] Add current file name to title (mailund)
Blossoc - 1.0 ============= - 0000007: [Feature Request] Unit tests of all modules - 0000016: [Feature Request] unit test of 'score' (besen) - 0000062: [Feature Request] Fix GUI for distributions and installation scripts (mailund) - 0000065: [Feature Request] Mapping parameters should be saved in the binary format (mailund) - 0000064: [Bug] Stop mapping if there is an input error! (mailund) - 0000066: [Feature Request] Add online help to the mapping progress dialogue. (mailund) - 0000059: [Feature Request] GUI (mailund)
Blossoc - 0.4 ============= - 0000055: [Bug] maxlen option default is assuming that positions are in the unit interval (besen) - 0000058: [Feature Request] Clean up progress bar code (mailund) - 0000057: [Feature Request] Terminate permutation test without loosing values so far...
Blossoc - 0.2 ============= - 0000012: [Feature Request] unit test of 'incompatibility' (mailund) - 0000013: [Feature Request] unit test of 'io' (mailund) - 0000014: [Feature Request] unit test of 'matrix' (mailund) - 0000017: [Feature Request] unit test of 'tree builder' (mailund) - 0000018: [Feature Request] unit test of 'tree' (mailund)
CoaSim - 4.1.0 ============== - 0000127: [Documentation] code snippet from guile-manual-4.2.pdf causes error (mailund) - 0000032: [Feature Request] ...also callbacks for the other populations and epochs events... (mailund) - 0000037: [Bug] incorrect epoch nesting... (mailund) - 0000034: [Bug] Entering epochs is broken -- the start time is *wrong* (mailund) - 0000031: [Feature Request] Callback for migration events (mailund)
CoaSim - 4.0.5 ============== - 0000029: [Feature Request] Phased genotype support does not cover multiple markers (mailund) - 0000026: [Documentation] Samples in populations (mailund)
CoaSim - 4.0.4 ============== - 0000028: [Bug] implicit end times for epochs does not work (mailund)
CoaSim - 4.0.3 ============== - 0000001: [Feature Request] Step-wise mutation model in a module (mailund) - 0000004: [Documentation] Documentation of disease models modules. (mailund) - 0000024: [Feature Request] The genotype module should work with both phased and unphased genotypes (mailund) - 0000005: [Documentation] Figures for population structure documentation (mailund)
GeneRecon - Change Log
GeneRecon - 1.2.1 ================= - 0000056: [Bug] The tree prior caching is disabled (mailund)
GeneRecon - 1.1 =============== - 0000022: [Feature Request] Finer control over MCMC-changes (mailund) - 0000052: [Feature Request] sample of likelihood for "all" positions (mailund) - 0000053: [Feature Request] temperature... (mailund) - 0000008: [Feature Request] Markov-chain model of background-regions. (mailund) - 0000023: [Feature Request] Monitoring acceptance/rejections of changes (mailund)
GeneRecon - 1.0 =============== - 0000047: [Bug] GeneRecon accepts non-positive initial population sizes (mailund) - 0000020: [Bug] Placement of initial disease locus (mailund) - 0000011: [Documentation] User Manual (mailund) - 0000027: [Documentation] Better R code snippets in the Getting Started document (mailund)
HapCluster++ - 1.3.1 ==================== - 0000196: [Feature Request] Output average ancestral sequenc (mailund) - 0000194: [Feature Request] Output summary of cluster membership (mailund) - 0000195: [Bug] If -w is not set, the tool now crashes if we output cluster samples (mailund) - 0000190: [Feature Request] Output Bayes factor for association after a run (mailund)
HapCluster++ - 1.3.0 ==================== - 0000193: [Documentation] Update examples on homepage to reflect integer positions (mailund) - 0000175: [Feature Request] change position type (mailund) - 0000189: [Feature Request] Add option for outputting the cluster (mailund)
HapCluster++ - 1.2.0 ==================== - 0000148: [Feature Request] interactions between two unliked genes... (mailund)
HapCluster++ - 1.1.3 ==================== - 0000128: [Feature Request] optimize score computation (mailund) - 0000118: [Bug] crash if the 0-allele count for a column is zero (mailund)
SNPFile - 1.0 ============= - 0000169: [Documentation] Update documentation for snp_file_convert (now text2snpfile) (mailund) - 0000165: [Feature Request] Output to haploview (mailund) - 0000164: [Feature Request] Conversion to and from fastPHASE (mailund) - 0000173: [Feature Request] Add program for extracting phenotypes, positions and marker names (mailund) - 0000160: [Bug] snpfile_convert should be able to add markerNames metadata to files. (mailund) - 0000176: [Feature Request] provide marker names and positions to fastPHASE2snpfile in the same format as snpfile_markers (mailund) - 0000162: [Feature Request] Better integration with read-only files (jn) - 0000170: [Bug] Opening non-existing file gives weird error (jn) - 0000163: [Feature Request] Maybe filename in SNPFile constructor should be a std::string (jn) - 0000174: [Feature Request] Add a reverse to text2snpfile (mailund) - 0000166: [Feature Request] Python bindings (mailund) - 0000167: [Feature Request] change snp_file to snpfile (jn) - 0000183: [Feature Request] Move Blossoc specific matrix functionality to Blossoc (jn) - 0000172: [Bug] Import programs should clean up upon errors. (jn) - 0000159: [] snpfile_convert does not conform to new format for status vectors (jn) - 0000158: [] snpfile_convert and permissions on newly created files (jn) - 0000161: [] Better messages in exceptions (jn)
