| 7e57e58 | Jamie K. Teer | 27 April 2020, 14:42:41 UTC | -Documentation updates to point to github. | 27 April 2020, 14:42:41 UTC |
| b2c3f1b | Jamie K. Teer | 31 July 2018, 20:47:27 UTC | - Version 1.9 - adjusted duplicate INFO description handling code | 31 July 2018, 20:47:27 UTC |
| c457a88 | Jamie K. Teer | 15 September 2016, 18:06:11 UTC | - Fixed issue related to GQ and DP FORMAT fields being converted to Type=String when Number!=1 | 15 September 2016, 18:06:11 UTC |
| b94de1c | Jamie K. Teer | 24 November 2015, 14:45:14 UTC | Version 1.8 - no changes; increment version for release | 24 November 2015, 14:45:14 UTC |
| 65fe1ed | Jamie K. Teer | 24 April 2015, 21:51:25 UTC | - Fixed several bugs related to displaying all sample fields - Now loads an empty file (if nothing specified) - Now correctly loads a new window using "View Varients for Selected Gene" | 24 April 2015, 21:51:25 UTC |
| c08a9fb | Jamie K. Teer | 27 March 2015, 19:38:15 UTC | Version 1.8BETA - Now can display any value observed in the sample fields - VS files: still requires genotype, score, coverage to be first, in that order, but further fields can be added (a column for a new field must exists for every sample.) - VCF files: Uses FORMAT fields in header to define which fields to display. Still displays genotype, score, depth in that order. | 27 March 2015, 19:38:15 UTC |
| 3cd338b | Jamie K. Teer | 26 January 2015, 18:19:39 UTC | - Doc updates, wiki folder creation (for bitbucket "read-only" wiki workaround) | 26 January 2015, 18:19:39 UTC |
| 962bce5 | Jamie K. Teer | 26 January 2015, 14:42:02 UTC | -Added overview text | 26 January 2015, 14:42:02 UTC |
| f5d61a4 | Jamie K. Teer | 09 June 2014, 14:18:26 UTC | Version 1.7 -added JSON file for Ensembl Variant Effect Predictor output | 09 June 2014, 14:18:26 UTC |
| 6f6309a | Jamie K. Teer | 11 April 2014, 11:57:43 UTC | Version 1.7BETA1 -Now allows sample format fields to be shorter than the FORMAT descriptor (if empty). Assumes fields present match position in FORMAT descriptor. | 11 April 2014, 11:57:43 UTC |
| 39ab9e5 | Jamie K. Teer | 28 March 2014, 17:40:23 UTC | ## Version 1.7_BETA -multiallelic gene name and type now properly handled in VCF files with Custom Annotations -INFO tags with Number=A now have "Multiallelic" selected by default, which should make it easier to use VCF files. | 28 March 2014, 17:40:23 UTC |
| c50537d | Jamie K. Teer | 29 March 2013, 12:28:58 UTC | ## Version 1.6 - Allowing a "Gene delimeter" (by default, ";") in order to allow a Gene Filter file to be used correctly (exact match) against each gene in a list of multiple genes - Added a JSON file for SnpEff version 3: handles the format change which resulted in the wrong column being used for Gene Name. | 29 March 2013, 12:28:58 UTC |
| 3114e13 | Jamie K. Teer | 28 November 2012, 14:31:35 UTC | -1.6_BETA2 - Added JSON file for custom ANNOVAR annotations - Allow Tags with Type=A to be selected as "Multiallelic" - Fixed a bug in Sample Export (wrong columns were being output.) | 28 November 2012, 14:31:35 UTC |
| 72d0395 | teerj | 24 July 2012, 20:20:51 UTC | - added ability to export annotations in the "Sample Export" window - added Hemizygous Reference and Hemizygous Variant filters in the custom query window | 24 July 2012, 20:20:51 UTC |
| 01f149f | teerj | 10 May 2012, 17:39:16 UTC | -added ability to sort sample names in the custom query window (Thanks to Timothy Gall) -documentation additions | 10 May 2012, 17:39:16 UTC |
| 1df549c | teerj | 16 April 2012, 20:13:49 UTC | Version 1.5 - Improved speed and memory usage when saving large files - Improved speed when using custom queries (maybe memory as well) Accomplished the above two items by ignoring encapsulation. It seems better in this case to avoid copying the massive amounts of data. - Configuration file added: VarSifter.config This file allows setting of options, including IGV interation options as well as filtering options. - New feature: IGV interaction! If IGV is opened, VarSifter can communicate with it. Courtesy of Timothy Gall A. Double-clicking a line in the top annotation window will navigate to that position (be sure to use the same genome versions!) B. Double-clicking a line in the bottom sample window will attempt to open that sample's bam file. File locations are defined in the VarSifter.config file. - Changed the float regex to accept scientific notation (which Java seems to generate when coverting floats to String, on occasion.) - Fixed CustomQuery bug (saving a query did not previously include the array of BitSets used to store results of string matches, which resulted in an ArrayIndexOutOfBoundsException. Solved by inlucding that in the serialized object, but this does not fix old saved objects with string queries.) - Fixed a very minor memory leak having to do with the Sample table header. | 16 April 2012, 20:13:49 UTC |
| 2f5dc6a | teerj | 12 April 2012, 18:07:20 UTC | - Improved speed and memory usage when saving large files - Improved speed when using custom queries (maybe memory as well) Accomplished the above two items by ignoring encapsulation. It seems better in this case to avoid copying the massive amounts of data. - Fixed CustomQuery bug (saving a query did not previously include the array of BitSets used to store results of string matches, which resulted in an ArrayIndexOutOfBoundsException. Solved by inlucding that in the serialized object, but this does not fix old saved objects with string queries.) - Changed the float regex to accept scientific notation (which Java seems to generate when coverting floats to String, on occasion.) | 12 April 2012, 18:07:20 UTC |
| 5550ef2 | teerj | 13 March 2012, 19:22:02 UTC | - !!! Initial commit of this feature - it is working, but needs refinement !!! - Added ability to parse complex single-column annotations (generally, gene model annotations) using a JSON config file - In this version, CustomAnnotation object looks specifically for Gene name and variant type fields. This could be made more general in the future (to be able to split single columns.) - Modified README, other accessory files to include new external lib. | 13 March 2012, 19:22:02 UTC |
| eb32b9d | teerj | 08 March 2012, 17:47:04 UTC | - Added ability to designate a column for Gene_name and for type. type uses MULTISTRING (based on the sub-delimiter character entered), and is also multiallelic, splitting on "," | 08 March 2012, 17:47:04 UTC |
| 83bfb88 | teerj | 23 February 2012, 14:57:24 UTC | - fixed bug introduced in r5587 - deselecting any fields for viewing in a VCF file would result in a crash (due to fixed fields being removed from field hash.) | 23 February 2012, 14:57:24 UTC |
| d24815a | teerj | 23 February 2012, 14:12:43 UTC | -changed "NAN" regex for floats to also match "NA" -Now, attempt to append a unique suffix "_[a-z]" to VS column header if it is same as an earlier header. (Try to fix before dying.) -Check for VCF INFO Descriptions that are the same as other VCF INFO Descriptions, or are the same as VarSifter reserved headers. Try to append "_[a-z]" to make it unique. (Try to fix before dying.) | 23 February 2012, 14:12:43 UTC |
| ce2bec7 | teerj | 06 January 2012, 16:35:19 UTC | -added documentation for Sample Export function | 06 January 2012, 16:35:19 UTC |
| 6db817e | teerj | 06 January 2012, 16:20:57 UTC | Version 1.4 -fixed a bug where using score filtering on floating point scores did not work properly. -Sample Export function now can use score and score/cov as a filter. Also allows selection of information to output. | 06 January 2012, 16:20:57 UTC |
| 2dc7563 | teerj | 21 December 2011, 20:47:20 UTC | -1.4BETA - intermediate commit before larger changes -Added a Sample Export function. This prints location, ref and var alleles, muttype, and then sample information if the sample variant matches the types specified by the user. !!! Although there are options for score and score/coverage thresholds, these don't work yet !!! -Made selections in sample table visible. ##OLD -VERSION 1.3 -Added Documentation and Troubleshooting to "Help" menu. (These are included in the .jar as static html files, and are loaded by Java) -When no file specified on the commandline, now opens with a dummy blank file, and a helpful, non-snarky mesaage. -"Apply" and "Clear All" buttons have been moved to the bottom right of the screen. They will no longer be hidden in a scrolling window when window size is decreased. This has the added benefit of making the genotype window fill all available space on the bottom. -Clicking "Finalize Query" button in the Custom Query window now automatically checks the "Custom Query" checkbox, and shift focus back to the main window. Additionally, the "Custom Query" checkbox has been moved to the main window. (This now requires two clicks instead of four to run a custom query.) -More visual cues when building a custom query: -Whole sections highlighted / greyed out when appropriate. -Message box in lower right now hints at what to do. -Bugfix: Remove all listeners when opening a new file. This fixes a bug where users would be presented with multiple file loading windows when trying to load a bedfile/gene file. -Allowing "Case/Control" filter without "Control" samples. -Fix - grey out Case/Control filter labels when filter is not available -Fix - previously was preventing first 8 columns from being selectable to not load. Of course, as any annotation column order is selectable, first 8 might not be the required ones. Now, specifically mask the required ones (as one shouldn't be able to NOT load them, only to see an error.) -Makefile changed to create a parent version directory within the zip file. -Code cleanup - moved bulky messages out of VarSifter.java, and into VSMessages.java -Other code cleanup | 21 December 2011, 20:47:20 UTC |
| 65e9a20 | teerj | 29 November 2011, 20:11:34 UTC | -Updated README.txt to reflect changes in opening behavior. | 29 November 2011, 20:11:34 UTC |
| 4b91913 | teerj | 29 November 2011, 19:52:14 UTC | -VERSION 1.3 -Added Documentation and Troubleshooting to "Help" menu. (These are included in the .jar as static html files, and are loaded by Java) -When no file specified on the commandline, now opens with a dummy blank file, and a helpful, non-snarky mesaage. -"Apply" and "Clear All" buttons have been moved to the bottom right of the screen. They will no longer be hidden in a scrolling window when window size is decreased. This has the added benefit of making the genotype window fill all available space on the bottom. -Clicking "Finalize Query" button in the Custom Query window now automatically checks the "Custom Query" checkbox, and shift focus back to the main window. Additionally, the "Custom Query" checkbox has been moved to the main window. (This now requires two clicks instead of four to run a custom query.) -More visual cues when building a custom query: -Whole sections highlighted / greyed out when appropriate. -Message box in lower right now hints at what to do. -Bugfix: Remove all listeners when opening a new file. This fixes a bug where users would be presented with multiple file loading windows when trying to load a bedfile/gene file. -Allowing "Case/Control" filter without "Control" samples. -Fix - grey out Case/Control filter labels when filter is not available -Fix - previously was preventing first 8 columns from being selectable to not load. Of course, as any annotation column order is selectable, first 8 might not be the required ones. Now, specifically mask the required ones (as one shouldn't be able to NOT load them, only to see an error.) -Makefile changed to create a parent version directory within the zip file. -Code cleanup - moved bulky messages out of VarSifter.java, and into VSMessages.java -Other code cleanup | 29 November 2011, 19:52:14 UTC |
| 23973cc | teerj | 15 November 2011, 20:42:23 UTC | - fixed an issue where Java doesn't recognize "not-a-number" designations in 1000 genomes files. ("-nan" used, when Java only recognized "NaN") - fixed a bug where VarSifter files did not accept floating point genotype scores (a problem when a vcf with float scores is saved as VS, reloaded.) | 15 November 2011, 20:42:23 UTC |
| b193efe | teerj | 19 October 2011, 13:39:52 UTC | - new Version - 1.2 - Added dialog to select annotation columns to load/display when loading a file. - Corrected use of List.toArray. | 19 October 2011, 13:39:52 UTC |
| d9d2185 | teerj | 02 September 2011, 12:53:01 UTC | - new Version - 1.1 - New Feature - can change sample settings (aff/norm, case/control) on the fly by clicking File->Sample Settings. Check the appropriate boxes. Saving the file will save the new settings. - Added ToolTips to give users more info - Renamed some Custom Query buttons to improve clarity - Code Cleanup | 02 September 2011, 12:53:01 UTC |
| 6337a7f | teerj | 19 August 2011, 19:40:18 UTC | - fixed "bug" in VCF handling. Apparently, the rest of the world missed the memo (from the VCF standards committee) that '.' is a legal floating point value. This "value" is now converted to "NaN" to indicate the metric is missing. - performance improvements as suggested by findbugs. (Probably no noticable effect) - fixed Makefile bug (had previously renamed .sh to .command, and not updated makefile)) | 19 August 2011, 19:40:18 UTC |
| b369793 | teerj | 27 July 2011, 19:36:27 UTC | - Version bump to 1.0 -changed Makefile to allow creation of a complete .zip file - containing everything needed to run VarSifter, including JUNG files, collections-generic, and wrapper scripts -added more error checking - correct number of Tab-delimited columns for VCF files - louder squawking if there's a file problem - more useful "check" behavior for developer -Now correctly reads floating point genotype qualities from 'GQ' FORMAT field of VCF. (Also highlights correctly.) -plainer language in custom query boxes ("equals" instead of "==") -small correction in VarData.java- now closing a filehandle when reading a bedfile #OLD 0.12e -changed samples regex - more specific for \.NA(\.\w+)? | 27 July 2011, 19:36:27 UTC |
| 1ce3d18 | teerj | 21 June 2011, 11:17:59 UTC | 0.12e -changed samples regex - more specific for \.NA(\.\w+)? | 21 June 2011, 11:17:59 UTC |
| b8fb69c | teerj | 17 May 2011, 19:48:46 UTC | 0.12d -can now save and load queries. Saved query object remembers the name of the data file used to generate the query, and checks that the current data file has the same name upon query loading. -can now use <enter> to start filtering when gene regex field has focus | 17 May 2011, 19:48:46 UTC |
| 5b87c61 | teerj | 05 May 2011, 19:27:10 UTC | -12d_BETA -added functionality to save (and reload) the extra information needed to parse VCF files. This should make loading these files much less painful. | 05 May 2011, 19:27:10 UTC |
| 7db4d0a | teerj | 28 April 2011, 13:08:32 UTC | -version bump to 0.12c -added a check for required columns; should prevent a number of odd bugs when expected column isn't present. -comment lines (start with '#') now ignored (really stored, re-written, but ignored for data reading purposes.) -"dbID" column no longer required - dbID checkbox disabled if absent -delete temporary VSQueryModule.class if compile fails. | 28 April 2011, 13:08:32 UTC |
| 9786595 | teerj | 22 March 2011, 20:21:54 UTC | - "RS#" changed to "dbID" to avoid character issues - VarSifter still reads old files, but changes header to "dbID". #OLD -general code cleanup - removing unneeded comments, code, import statements -Defining Collection variables as the interface rather than the implementation, as this is accepted practice. | 22 March 2011, 20:21:54 UTC |
| 232d2e5 | teerj | 16 March 2011, 19:34:28 UTC | -general code cleanup - removing unneeded comments, code, import statements -Defining Collection variables as the interface rather than the implementation, as this is accepted practice. | 16 March 2011, 19:34:28 UTC |
| a81170c | teerj | 10 March 2011, 20:34:06 UTC | -version bump to 0.12 -clarified"Genotypes" in the Custom Query window - "homnonref" now "Homozygous Variant" - Have added "Homozygous" and "Heterozygous" genotypes that test for that state. These filters should not allow single allele DIVs, but requires the alleles are separated by a colon (:). To facilitate this, fixed "Genotypes" can only be chosen last, not first. -The custom query class (VSQueryModule.class) is now written to the user's home directory (defined by the system). This fixes write permission issues (everyone should be able to write to their home). A test has also been added to ensure we are not clobbering some file of the same name. VarSifter still deletes the custom class when it is finished using it. -added a button to the Custom Query Window to allow a user to reset the current query. -added some homemade icons for fun (also helps draw attention to important buttons.) -added XOR button to Custom Query filter. XOR, like AND and OR, works on two tests at a time. However, chaining together doesn't work as expected without fancy handling (eg. true XOR true XOR true results in true, not false as one may want.) So for now, only allow two nodes to be linked with XOR. | 10 March 2011, 20:34:06 UTC |
| 06df52a | teerj | 01 March 2011, 22:51:17 UTC | -version bump to 0.11b -Split multiallelic VCF lines. - To acccomplish this correctly, displays a dialog box for users to check boxes for multiallelic info fields, give sub-delimiters for subfield within a field. - For now, sub-delimiters just let VarSifter know data is string. Later, can be used for splitting those fields. - Several new classes to get a JCheckBox to properly be handled by a table. (Wanted a real JCheckBox that could be disabled, not just a boolean.) -Data typing now assited by above dialog - correct data type determined. | 01 March 2011, 22:51:17 UTC |
| 8453a0b | teerj | 25 February 2011, 19:30:55 UTC | -separate VCF handling to a new VarData subclass -changed access of class variables, methods so above will work | 25 February 2011, 19:30:55 UTC |
| 9ac908f | teerj | 21 February 2011, 20:49:56 UTC | -Can now use regular expressions to filter string type data in custom queries | 21 February 2011, 20:49:56 UTC |
| a3f9ca6 | teerj | 21 February 2011, 14:36:16 UTC | -Prepare to handle regular expressions in CustomQuery of String objects - This will lay groundwork work for possible shift in filtering strategy: Would first run filters against Mapper objects using new method, and return some set (HashSet or BitSet) indicating indices that pass filter. Then, for each line, col, test if index is in set. (Would not work for bedfilters.) -Small improvements to VCF handling (still not splitting multi-allele lines) -Added bounds check to MultiStringMapper | 21 February 2011, 14:36:16 UTC |
| 20f1810 | teerj | 15 February 2011, 19:33:43 UTC | -Compound Het View now respects the most recently applied filters. If only "non-synonymous" is checked (and then "Apply filter" is clicked!), only non-syn positions in compound het with other non-syn positions will be shown. | 15 February 2011, 19:33:43 UTC |
| bf39b94 | teerj | 04 February 2011, 22:22:36 UTC | -version 0.11 -Improved Custom Query view and function -better cleaner display -can now filter on annotation columns based on data type! | 04 February 2011, 22:22:36 UTC |
| 7c2a568 | teerj | 28 January 2011, 21:45:52 UTC | -label correction - dbSNP130->dbSNP refseq->Gene_name (! "refseq" will be converted to "Gene_name"!) -update TableModel.java - new Oracle version which uses a different way to determine which column clicked. Seems to work... | 28 January 2011, 21:45:52 UTC |
| 6c8a026 | teerj | 20 January 2011, 16:09:48 UTC | -version bump to 0.10b - fixed a bug introduced in 0.9b where the custom query no longer returned correct results. This was due to getting an improper index from the "type" field. Now, indels determined ONLY from "muttype" field. | 20 January 2011, 16:09:48 UTC |
| d366109 | teerj | 17 January 2011, 22:26:47 UTC | -version bump to 0.10 -Changed mutation type JCheckBox code - boxes now generated based on the mutation types observed. Filtering is linked to boxes by the same data being sorted the same way to set up the boxes (and the order of the filter mask) and the order the filter mask is read. -Allow for compound het filtering if CD_Pred column missing (really, test for presence of all column headers) -Removing old lines that were commented out due to non-use or improvement -Continued code clean-up -Removed deprecated VarData methods countAffNorm() and isMendFilt() -fixed recently introduced File open bugs (had to reinit Frame, either by calling again, or by calling frameInit() in main class. -fixed memory leak, in which opening a new file didn't really release memory of old file!! Not sure when it was introduced, but it seems to be fixed now. -Some minor label changes ##OLD -0.9b_BETA -can now read in a list of mutation types, in column 'type'. Delimiter String defined in MultiStringMapper constructor. Can appropriately filter mutation types, and save them (although order is altered in save.) -code simplification - moved test for Mapper entry presence to addData(Object) methods - removed multiple instances from VarData -added error message and recognition when jdk not present. -removed Hiding of value '301', which was originally implemented to hide CD_Pred scores that were NA (but which cannot be displayed as NA for the column to stay as int.) CD_Pred 'NA' values will remain as 301, but won't be hidden. -All Strings center aligned, numbers right aligned. -fixed some bugs with Compound Het Filtering - exceptions when trying to filter on variant or gene that is not mendHetRec. Now shows an error dialog instead of throwing an exception. | 17 January 2011, 22:26:47 UTC |
| 35a4359 | teerj | 14 January 2011, 22:42:46 UTC | -0.9b_BETA -can now read in a list of mutation types, in column 'type'. Delimiter String defined in MultiStringMapper constructor. Can appropriately filter mutation types, and save them (although order is altered in save.) -code simplification - moved test for Mapper entry presence to addData(Object) methods - removed multiple instances from VarData -added error message and recognition when jdk not present. -removed Hiding of value '301', which was originally implemented to hide CD_Pred scores that were NA (but which cannot be displayed as NA for the column to stay as int.) CD_Pred 'NA' values will remain as 301, but won't be hidden. -All Strings center aligned, numbers right aligned. -fixed some bugs with Compound Het Filtering - exceptions when trying to filter on variant or gene that is not mendHetRec. Now shows an error dialog instead of throwing an exception. | 14 January 2011, 22:42:46 UTC |
| 787afce | teerj | 17 December 2010, 20:22:41 UTC | -Version bump to 0.9 -can now read files without genotypes (VS and VCF) | 17 December 2010, 20:22:41 UTC |
| 9751178 | teerj | 15 December 2010, 21:55:13 UTC | -Commiting version 0.9BETA before attempting to allow annotations without genotypes -Added Genotype Score threshold (replace final THRESHOLD in VarData), Genotype Score / coverage ratio threshold (allow changing of lowlighting cutoff) -Now handling all preferences in the prefApply action section. Removed separate getMinMPG* methods. - BugFix -Opening a new file now appropriately reinitilizes the Custom Query Window, and applies the query correctly. - Added myself as the author in the docs | 15 December 2010, 21:55:13 UTC |
| a67fe8f | teerj | 13 December 2010, 19:02:12 UTC | -Work on implementing VCF parsing -This seems to work. No specific handling of refseq, type, etc. Need to choose some VCF flags as standards. -Bugfix: aff/normal filter was not properly matching the "NA" genotypes. Shouldn't affect our data, as "NA" genotypes also failed the MPG qual threshold, but could have affected future queries when genotype qual threshold can be changed. -Bugfix: custom queries would fail if DIV type was overwritten. Fixed by requiring muttype field, and looking for 'INDEL' - !!!! Bug detected !!!! -Matching probably not being handled correctly for single allele genotypes! -Also affecting perl script count_case_control_vs.pl! - ?? Bug ?? -Apparently, vcf can have, in comma delimited fields, commas in the values. Grrrrr. - Solved by limiting split, but will format be expandable? | 13 December 2010, 19:02:12 UTC |
| 68da56f | teerj | 19 November 2010, 14:57:31 UTC | moved VS file parsing from constructor to private method in prep for VCF handling | 19 November 2010, 14:57:31 UTC |
| 58d205e | teerj | 18 November 2010, 18:04:54 UTC | Remerging opt_mem branch | 18 November 2010, 18:04:54 UTC |
| 96581d9 | teerj | 22 September 2010, 17:14:19 UTC | Incremental minor change - fixed bug in javadoc | 22 September 2010, 17:14:19 UTC |
| 7442eb7 | teerj | 21 September 2010, 19:34:00 UTC | Version bump to 0.7b - bugfix: compound het views were not working. Now working. Preferences, other spinner data included in filtering. (But spinnerdata included is from last press of "Apply Filter"). Will pass quality filter for initial position; its pairs aren't checked. | 21 September 2010, 19:34:00 UTC |
| f7ad186 | teerj | 20 September 2010, 20:33:56 UTC | Version bump to 0.7a - changed filter mechanism. Now passes a new DataFilter object which contains the filtering information. - allow filtering on MPG score and MPG/cov ratio (in "Preferences") - GUI tidying | 20 September 2010, 20:33:56 UTC |
| d37be9e | teerj | 15 September 2010, 14:38:45 UTC | Intermediate commit... - now allows case insensitice gene list searching - darker background and red text in sample table when MPG/coverage < 0.5 - fixed bug with "No result" searches. (Due to implementing MPG/coverage rendering) - added "Transforming" view for Custom Query view (via JUNG) | 15 September 2010, 14:38:45 UTC |
| 7c73c36 | teerj | 03 September 2010, 15:33:23 UTC | Version bumpt to 0.7 - changed structure of sample table - samples now arranged vertically to allow sorting on sample name, genotype, etc. - Can filter against homozygous reference, "NA" in custom query - Fixed Bedfiltering so the actual start position (left flank + 1, not left flank) is the position considered. May be less accurate for indels... - Fixed custom query comparisons where the indel genotype incorrectly mismatched the homozygous reference due to the lack of a ":" | 03 September 2010, 15:33:23 UTC |
| c22bb91 | teerj | 20 August 2010, 22:05:07 UTC | - More documentation, added doc creation to makefile - Deleted user documentation (now being stored in the saturn wiki) | 20 August 2010, 22:05:07 UTC |
| a932727 | teerj | 05 August 2010, 13:27:05 UTC | -Javadoc comments added -Some error handling for custom queries if not using java 1.6 | 05 August 2010, 13:27:05 UTC |
| eb7caa9 | teerj | 19 July 2010, 14:18:42 UTC | Version bump to 0.6d - now allows custom dynamic filtering. - uses JUNG framework to allow visual query generation - uses run-time compiling and custom class re-loading to achieve this | 19 July 2010, 14:18:42 UTC |
| 8d0e9d3 | teerj | 09 July 2010, 21:56:12 UTC | -Version bump 0.6c -Ability to filter different DIV types -Bugfixes: -fixed a bug where shifting columns (didn't know java did this) would screw up gene view, and compound het views | 09 July 2010, 21:56:12 UTC |
| d9619d4 | teerj | 28 June 2010, 20:18:10 UTC | - CompileCustomQuery working - CustomQuery View has basic functionality, but not good enough - try JGraph | 28 June 2010, 20:18:10 UTC |
| 3c40dad | teerj | 14 June 2010, 21:41:37 UTC | - Version 0.6b - added option to show genotype data to compound het view | 14 June 2010, 21:41:37 UTC |
| c1839b8 | teerj | 14 June 2010, 19:48:47 UTC | -added ability to scroll the filter panel when needed (right side of display) | 14 June 2010, 19:48:47 UTC |
| be205f2 | teerj | 09 June 2010, 20:16:54 UTC | - Version bump to 0.6a - Can now display all compound hets - fixed bug in compound het display - wasn't showing everything | 09 June 2010, 20:16:54 UTC |
| a2e5099 | teerj | 09 June 2010, 15:13:08 UTC | -fixed one more bug related to showing errors in GUI | 09 June 2010, 15:13:08 UTC |
| e156498 | teerj | 09 June 2010, 15:09:47 UTC | - Added method to show errors via GUI - fixed bug where compHetPairViewButton enabled when it shouldn't be - now returns error | 09 June 2010, 15:09:47 UTC |
| 9380b2d | teerj | 09 June 2010, 14:31:33 UTC | -fixed bug (comphet variant view button would get enabled after filter (even if no MenHetRec field) -added a word doc User Guide | 09 June 2010, 14:31:33 UTC |
| 8c90b65 | teerj | 09 June 2010, 12:58:39 UTC | - New Version = 0.6 - fixed bug (clicking gene compound het view on gene with no compound hets no longer throws exception) | 09 June 2010, 12:58:39 UTC |
| 6c7d69f | teerj | 08 June 2010, 22:32:05 UTC | - Allow view of all compound hets in a gene - viewable from variant or gene view. !!! Must deal with errors when a non-compound het gene selected! !!! - Added more info to compound het view - Bugfix - if something was in regex field when any "view" button clicked, the VarData reset was not including it - mapping errors. Fixed. | 08 June 2010, 22:32:05 UTC |
| 98be498 | teerj | 04 June 2010, 18:23:02 UTC | - bugfixes, including problems with case/control filter (homnonref was not being included), error when opening a subgene view before filtering. | 04 June 2010, 18:23:02 UTC |
| 81c7b60 | teerj | 03 June 2010, 22:03:44 UTC | - can now display compound hets in separate windows, but needs polishing | 03 June 2010, 22:03:44 UTC |
| 7d82aeb | teerj | 26 May 2010, 19:16:14 UTC | -Version 0.5c -Added ability to look at thing NOT in a gene file (for gene kill lists) -Added column counter to check for spacing issues (dies is column count diff from header) -GUI tweaks, including moving checkboxes around. | 26 May 2010, 19:16:14 UTC |
| c6a9fb0 | teerj | 21 May 2010, 20:11:59 UTC | -basic compound het filtering (only on presence) | 21 May 2010, 20:11:59 UTC |
| 94730d7 | teerj | 18 May 2010, 19:37:51 UTC | - GUI tweaks | 18 May 2010, 19:37:51 UTC |
| bc4a7ea | teerj | 13 May 2010, 19:53:09 UTC | - Version 0.5 - Added ability to filter on regions in a bed file - Added ability to filter on variants in at least X cases, but not more than Y controls - updated Makefile to use java6 compiler, but still work on java5 | 13 May 2010, 19:53:09 UTC |
| 956d321 | teerj | 11 May 2010, 18:49:26 UTC | - Bed File filtering now works in a much more efficient (memory and time) way, but can still be slow with large VarSifter data files and bed files with many lines. Not sure what else can be easily done. | 11 May 2010, 18:49:26 UTC |
| 2855007 | teerj | 11 May 2010, 13:47:42 UTC | - added ability to filter using a bed file. !!!!! NOTE: !!!!!!! The implementation takes lots of memory, and it quite slow, so I will be attempting a different implementation. !!!!!!!!!!!!!!!!!!!!!! | 11 May 2010, 13:47:42 UTC |
| f382907 | teerj | 06 May 2010, 15:17:21 UTC | - Version 0.4 - Added ability to display variant counts by gene - From the gene view, can select a single gene to display all variants in new window - Added ability to search gene names with a regex - Added ability to save the current filtered set as a file | 06 May 2010, 15:17:21 UTC |
| 9850811 | teerj | 27 April 2010, 20:27:48 UTC | - Added UTR filter - GUI tweaks - Improved filter framework - Fixed bugs in which checked filters would not get any hits, and would then pass everything (Now, nothing is passed, which is the correct behavior). | 27 April 2010, 20:27:48 UTC |
| a8d2e46 | teerj | 23 April 2010, 21:28:54 UTC | -minor GUI tweaks | 23 April 2010, 21:28:54 UTC |
| 61e4556 | teerj | 23 April 2010, 18:19:17 UTC | - Version 0.3a - added a number field under "aff different from normal". to pass, at least this many aff/norm pairs must have different non-NA genotypes with score >=10 - fixed a genefile loading bug (when cancle clicked, old file removed.) | 23 April 2010, 18:19:17 UTC |
| 671fe94 | teerj | 15 April 2010, 22:38:39 UTC | - New Feature: - Opening a new window (recursive) on a subset of VarData (the subset is aware of its parent) - To accomplish above, moved much of GUI initialization out of constuctor into method - ToDo: - parse compound het info, format of which to be determined | 15 April 2010, 22:38:39 UTC |
| 7852f27 | teerj | 14 April 2010, 21:56:13 UTC | - Can now read in a file of Gene names, separated by line, and show only variants in thoses genes. | 14 April 2010, 21:56:13 UTC |
| d53115a | teerj | 14 April 2010, 14:39:22 UTC | - Version 0.3 - Now has filtering for - different genotype in norm v. aff - reads boolean flag columns for different mendelian filters - "Synonymous", "NC" - BugFixes - now clears buttons, disables/enables checkboxes when new file is loaded - Some cleaning - table redrawing following new filter, data, etc, broken out to redrawOutTable(String) - disbaling of unused checkboxes now in redrawOutTable(String); - cleaner constructor | 14 April 2010, 14:39:22 UTC |
| 16f0c79 | teerj | 12 April 2010, 17:43:44 UTC | - version 0.2 - Added file opening. (Including when no file given.) - some cleaning (separating redundant code to new method) | 12 April 2010, 17:43:44 UTC |
| 5d64bc9 | teerj | 07 April 2010, 22:07:12 UTC | - Attempts to improve flexibility, but header types are still hardcoded (ie, "type" is the only header value that will be sorted for Stop,DIV, etc) - Some cleanup | 07 April 2010, 22:07:12 UTC |
| b08ff9e | teerj | 07 April 2010, 17:52:57 UTC | - Editing of columns works correctly (editable columns currently hardcoded) - Edits can be saved to a flat file | 07 April 2010, 17:52:57 UTC |
| a5525e7 | teerj | 06 April 2010, 13:24:51 UTC | -Version 0.1 -Row labels, About added | 06 April 2010, 13:24:51 UTC |
| 68e375b | teerj | 02 April 2010, 20:58:27 UTC | -Cleaning up of GUI -using the TableSorter package correctly -added Makefile | 02 April 2010, 20:58:27 UTC |
| 83cc622 | teerj | 01 April 2010, 20:57:45 UTC | - Filtering works (basic - need to add more) | 01 April 2010, 20:57:45 UTC |
| 06f59c5 | teerj | 31 March 2010, 22:17:31 UTC | -Column width is appropriate | 31 March 2010, 22:17:31 UTC |
| b0bdd07 | teerj | 31 March 2010, 14:44:53 UTC | - Hiding of "empty" values now works with VarScoreRenderer | 31 March 2010, 14:44:53 UTC |
| 2176538 | teerj | 30 March 2010, 22:08:13 UTC | - added TableSorter, VarTableModel, VarScoreRenderer (not really working yet) - Table now does advanced sorting via Sun's TableSorter class, and pulls the correct sample info. | 30 March 2010, 22:08:13 UTC |
| 63c4865 | teerj | 29 March 2010, 22:00:50 UTC | - Added main class, VarSifter. - Displays a table of annotation results, and in a separate table, genotypes of all samples at the highlighted position. | 29 March 2010, 22:00:50 UTC |
| d3061c1 | teerj | 26 March 2010, 22:26:11 UTC | -initial import of VarSifter | 26 March 2010, 22:26:11 UTC |
