| 5c9ec6b | Robert Vickerstaff | 19 January 2018, 14:40:21 UTC | fixed link to QTL pipelines | 19 January 2018, 14:40:21 UTC |
| b928b4e | Robert Vickerstaff | 19 January 2018, 14:39:40 UTC | added link to QTL pipelines | 19 January 2018, 14:39:40 UTC |
| 830477b | Robert Vickerstaff | 19 January 2018, 11:21:49 UTC | minor changes | 19 January 2018, 11:21:49 UTC |
| e304a15 | Robert Vickerstaff | 05 April 2017, 13:18:05 UTC | created master pipeline script to facilitate replication of the test runs on simulated data | 05 April 2017, 13:18:05 UTC |
| de1ae21 | Robert Vickerstaff | 05 April 2017, 11:39:52 UTC | added explanation of bug fix to README | 05 April 2017, 11:39:52 UTC |
| c8b5d6f | Robert Vickerstaff | 05 April 2017, 11:25:50 UTC | made further changes to correctly implement the marker type correction bug fix, now tested as well on rgxha | 05 April 2017, 11:25:50 UTC |
| 5989029 | Robert Vickerstaff | 04 April 2017, 16:43:17 UTC | now marker type correct switch lm,ll to nn,np and vice versa as intended. compiles but not yet tested | 04 April 2017, 16:43:17 UTC |
| 5188240 | Robert Vickerstaff | 04 April 2017, 15:20:38 UTC | updating the match Bioinf manuscript testing runs | 04 April 2017, 15:20:38 UTC |
| bda0fd5 | Robert Vickerstaff | 30 March 2017, 10:20:15 UTC | catching up with changes | 30 March 2017, 10:20:15 UTC |
| 450f6c0 | Robert Vickerstaff | 28 July 2016, 11:57:31 UTC | minor changes plus multiway map comparison plotter under development | 28 July 2016, 11:57:31 UTC |
| b6f0d5d | Robert Vickerstaff | 08 June 2016, 16:19:43 UTC | updated manual | 08 June 2016, 16:19:43 UTC |
| 35d5282 | Robert Vickerstaff | 08 June 2016, 16:17:16 UTC | minor changes to docker files | 08 June 2016, 16:17:16 UTC |
| 161b4ac | Robert Vickerstaff | 08 June 2016, 15:57:52 UTC | minor changes to docker files | 08 June 2016, 15:57:52 UTC |
| 1474dbe | Robert Vickerstaff | 08 June 2016, 11:33:21 UTC | now the simplified rgxha build script also can output a map in csv format for use with compare_maps.py | 08 June 2016, 11:33:21 UTC |
| 97fb2bf | Robert Vickerstaff | 08 June 2016, 10:43:41 UTC | added more progress indication to simplified rgxha map script | 08 June 2016, 10:43:41 UTC |
| ef07892 | Robert Vickerstaff | 08 June 2016, 10:02:09 UTC | minor change to rgxha full build script | 08 June 2016, 10:02:09 UTC |
| 8b431a0 | Robert Vickerstaff | 07 June 2016, 13:51:57 UTC | minor changes | 07 June 2016, 13:51:57 UTC |
| 6bd6f99 | Robert Vickerstaff | 03 June 2016, 17:48:22 UTC | updated fig_data to correct map version, added comparison to vesca | 03 June 2016, 17:48:22 UTC |
| 43e0a17 | Robert Vickerstaff | 02 June 2016, 11:19:25 UTC | now included the correct version of the full rgxha pipeline | 02 June 2016, 11:19:25 UTC |
| 209d13b | Robert Vickerstaff | 02 June 2016, 09:18:29 UTC | removed temporary exit statement | 02 June 2016, 09:18:29 UTC |
| b285f66 | Robert Vickerstaff | 01 June 2016, 15:10:19 UTC | added docker info to README | 01 June 2016, 15:10:19 UTC |
| b627e25 | Robert Vickerstaff | 01 June 2016, 14:56:05 UTC | fixed docker image version number in manual | 01 June 2016, 14:56:05 UTC |
| 1b16844 | Robert Vickerstaff | 01 June 2016, 13:16:58 UTC | updated manual pdf | 01 June 2016, 13:16:58 UTC |
| 3318d7c | Robert Vickerstaff | 01 June 2016, 12:57:13 UTC | now comparing to Emily x Fenella map | 01 June 2016, 12:57:13 UTC |
| 3976a7b | Robert Vickerstaff | 27 May 2016, 10:24:20 UTC | modified INSTALL | 27 May 2016, 10:24:20 UTC |
| 79a0066 | Robert Vickerstaff | 27 May 2016, 10:20:27 UTC | mentioned inprep publication | 27 May 2016, 10:20:27 UTC |
| 78d808a | Robert Vickerstaff | 26 May 2016, 19:51:54 UTC | line wrapping again | 26 May 2016, 19:51:54 UTC |
| cd63c7e | Robert Vickerstaff | 26 May 2016, 19:49:14 UTC | line wrapping | 26 May 2016, 19:49:14 UTC |
| 5938ce7 | Robert Vickerstaff | 26 May 2016, 19:47:01 UTC | added INSTALL file, and fig_data directory | 26 May 2016, 19:47:01 UTC |
| 7351c64 | Robert Vickerstaff | 26 May 2016, 15:43:14 UTC | raw figure data added | 26 May 2016, 15:43:14 UTC |
| d4960c1 | Robert Vickerstaff | 26 May 2016, 11:33:21 UTC | added copyright notices to test_src | 26 May 2016, 11:33:21 UTC |
| 552fd39 | Robert Vickerstaff | 26 May 2016, 11:31:30 UTC | added copyright notices to test_script dir, excluded old,tmp,bin dirs | 26 May 2016, 11:31:30 UTC |
| 1d87715 | Robert Vickerstaff | 26 May 2016, 11:16:35 UTC | adding more copyright notices | 26 May 2016, 11:16:35 UTC |
| cd9f2af | Robert Vickerstaff | 26 May 2016, 11:02:44 UTC | adding copyright notices ready for first release | 26 May 2016, 11:02:44 UTC |
| dec5199 | Robert Vickerstaff | 17 May 2016, 10:10:20 UTC | changed name of manual back to crosslink_manual.pdf | 17 May 2016, 10:10:20 UTC |
| 60df12c | Robert Vickerstaff | 16 May 2016, 15:52:46 UTC | modified some figure scripts | 16 May 2016, 15:52:46 UTC |
| 75b846a | Robert Vickerstaff | 10 May 2016, 15:54:19 UTC | catching up with changes: now making multiplot figures, testing crosslink against other programs | 10 May 2016, 15:54:19 UTC |
| 3f0755c | Robert Vickerstaff | 30 April 2016, 21:11:32 UTC | crosslink_viewer now explicitly frees resources before exiting | 30 April 2016, 21:11:32 UTC |
| 2de3dcd | Robert Vickerstaff | 30 April 2016, 19:34:08 UTC | tidying up crosslink_viewer, also made new example script build_one_group | 30 April 2016, 19:34:08 UTC |
| 82824b3 | Robert Vickerstaff | 29 April 2016, 16:38:59 UTC | modified example pipelines slightly, now assuming CROSSLINK_PATH variable is set, to allow access to sample data from the example scripts without having to edit them first | 29 April 2016, 16:38:59 UTC |
| c167a08 | Robert Vickerstaff | 29 April 2016, 14:07:31 UTC | modified readme again | 29 April 2016, 14:07:31 UTC |
| a4d13f0 | Robert Vickerstaff | 29 April 2016, 13:53:43 UTC | modified readme | 29 April 2016, 13:53:43 UTC |
| 090b971 | Robert Vickerstaff | 29 April 2016, 13:34:57 UTC | build_rgxha script outputs progress messages | 29 April 2016, 13:34:57 UTC |
| 1995422 | Robert Vickerstaff | 29 April 2016, 13:26:50 UTC | added draft of the manual to docs folder | 29 April 2016, 13:26:50 UTC |
| e7a9b07 | Robert Vickerstaff | 28 April 2016, 16:19:46 UTC | making sure tag is registered | 28 April 2016, 16:19:46 UTC |
| 9b90462 | Robert Vickerstaff | 28 April 2016, 15:02:29 UTC | graphical should show filename(s) in title bar | 28 April 2016, 15:02:29 UTC |
| 886056e | Robert Vickerstaff | 28 April 2016, 14:56:51 UTC | a few changes to graphical and viewer colour schemes | 28 April 2016, 14:56:51 UTC |
| 65ebaff | Robert Vickerstaff | 27 April 2016, 18:07:07 UTC | more work on documentation | 27 April 2016, 18:07:07 UTC |
| 94b1cfe | Robert Vickerstaff | 26 April 2016, 17:19:11 UTC | create example crosslink_viewer plot image, minor changes to crosslink_viewer and Dockerfile | 26 April 2016, 17:19:11 UTC |
| 050d86d | Robert Vickerstaff | 26 April 2016, 08:39:01 UTC | bug fix dockerfile | 26 April 2016, 08:39:01 UTC |
| 4ebea6e | Robert Vickerstaff | 26 April 2016, 08:37:03 UTC | changed docker username to crosslink_user | 26 April 2016, 08:37:03 UTC |
| 601aa90 | Robert Vickerstaff | 25 April 2016, 17:34:46 UTC | added an icon | 25 April 2016, 17:34:46 UTC |
| 0c40949 | Robert Vickerstaff | 25 April 2016, 16:09:12 UTC | trying to fix the dbus error message which appears in docker container when running graphical programs | 25 April 2016, 16:09:12 UTC |
| 08f5930 | Robert Vickerstaff | 25 April 2016, 15:44:04 UTC | make.sh now makes bin directory if required | 25 April 2016, 15:44:04 UTC |
| fd97847 | Robert Vickerstaff | 25 April 2016, 15:21:20 UTC | reorganised directories, created cl_detect_crosslg.sh | 25 April 2016, 15:21:20 UTC |
| 1979082 | Robert Vickerstaff | 22 April 2016, 17:08:51 UTC | reorganised into different subdirectories for src doc bin etc | 22 April 2016, 17:08:51 UTC |
| e677c88 | Robert Vickerstaff | 19 April 2016, 15:04:56 UTC | working on simulated data pipeline, now all features are quantified to a single value from 0 to 1 to allow automated parameter optimisation | 19 April 2016, 15:04:56 UTC |
| f174105 | Robert Vickerstaff | 15 April 2016, 16:51:50 UTC | now able to automatically flag crosslinkage group markers, also can simulate then. written methods to quantify accuracy of all parts of the pipeline except for the final Pearson correlation of map position accuracy | 15 April 2016, 16:51:50 UTC |
| 28670f1 | Robert Vickerstaff | 13 April 2016, 17:23:09 UTC | creating new example pipeline for simulated data | 13 April 2016, 17:23:09 UTC |
| da793e7 | Robert Vickerstaff | 13 April 2016, 13:43:16 UTC | minor changes to command line options, during refactoring of flxch map to use helper scripts | 13 April 2016, 13:43:16 UTC |
| 138df3d | Robert Vickerstaff | 08 April 2016, 18:01:26 UTC | cleaned up the global optimisation method so that it only builds a new elist once per ga cycle not every iteration, also combined the the ga_optimise options into one, will need to update all affected pipelines and helper scripts | 08 April 2016, 18:01:26 UTC |
| ada4790 | Robert Vickerstaff | 08 April 2016, 16:27:41 UTC | changed name of tmpdir created by helper scripts | 08 April 2016, 16:27:41 UTC |
| 8ef7980 | Robert Vickerstaff | 06 April 2016, 16:54:25 UTC | moved rgxha map build script to axiom_strawberry repo | 06 April 2016, 16:54:25 UTC |
| 1250156 | Robert Vickerstaff | 17 March 2016, 18:38:09 UTC | order refinement wrapper script cl_refine_order tries multiple orders and keeps the best one, also wrote a new global order evaluation function to try to get out of locally optimal but globally suboptimal orderings | 17 March 2016, 18:38:09 UTC |
| 852721c | Robert Vickerstaff | 15 March 2016, 12:10:01 UTC | modified cl_*.sh wrapper scripts to use header-less loc files, still needs testing | 15 March 2016, 12:10:01 UTC |
| 9742a94 | Robert Vickerstaff | 15 March 2016, 11:46:27 UTC | crosslink now loading/saving loc files without any header, also rjvparser string options now can contain spaces, added support for multiple file loading to crosslink_viewer and crosslink_graphical, graphical now shows lg boundaries, but still lacking support for clicking on markers to get information | 15 March 2016, 11:46:27 UTC |
| 3bbe591 | Robert Vickerstaff | 14 March 2016, 16:10:23 UTC | completed refactor of the cl_*.sh scripts pipeline to remove the redundant ${FNAME} prefixes | 14 March 2016, 16:10:23 UTC |
| 30c16c3 | Robert Vickerstaff | 11 March 2016, 18:34:55 UTC | halway through removing unnecessary ${FNAME} prefixes from the main build pipeline, reworking the cl_split operation | 11 March 2016, 18:34:55 UTC |
| 9e3fcff | Robert Vickerstaff | 10 March 2016, 23:29:28 UTC | now using separate bash scripts for each step in the map building pipelines, hopefully more reusable than before | 10 March 2016, 23:29:28 UTC |
| 81729d0 | Robert Vickerstaff | 08 March 2016, 18:37:42 UTC | crosslink_viewer now shows rf/lod info in one triangle and distance information in the other making misorderings much easier to spot | 08 March 2016, 18:37:42 UTC |
| 576c26c | Robert Vickerstaff | 08 March 2016, 10:41:54 UTC | wrote simulated data tests for grouping, type error correction and phasing | 08 March 2016, 10:41:54 UTC |
| ebedb0d | Robert Vickerstaff | 03 March 2016, 18:32:46 UTC | fixed bug in rjvparser, started testing grouping accuracy versus marker density and error/missing rate on simulated data | 03 March 2016, 18:32:46 UTC |
| 96733e2 | Robert Vickerstaff | 01 March 2016, 15:58:53 UTC | docker graphical output via X11 mount now working | 01 March 2016, 15:58:53 UTC |
| e2f2f48 | Robert Vickerstaff | 01 March 2016, 13:52:06 UTC | trying out ssh -X for graphical access | 01 March 2016, 13:52:06 UTC |
| a22fafe | Robert Vickerstaff | 01 March 2016, 13:39:13 UTC | try out x11vnc for gui access | 01 March 2016, 13:39:13 UTC |
| 94d6004 | Robert Vickerstaff | 01 March 2016, 13:28:37 UTC | minor changes | 01 March 2016, 13:28:37 UTC |
| 286ebf6 | Robert Vickerstaff | 01 March 2016, 13:22:57 UTC | forgot the orig file | 01 March 2016, 13:22:57 UTC |
| c2a9341 | Robert Vickerstaff | 01 March 2016, 13:21:25 UTC | adding sample data files to repo | 01 March 2016, 13:21:25 UTC |
| 36476b3 | Robert Vickerstaff | 01 March 2016, 11:59:58 UTC | now generating useful command line help messages from all crosslink binaries | 01 March 2016, 11:59:58 UTC |
| 685e50b | Robert Vickerstaff | 29 February 2016, 23:13:04 UTC | improving command line argument parsing and automatic usage message generation | 29 February 2016, 23:13:04 UTC |
| 79ce89e | Robert Vickerstaff | 29 February 2016, 15:19:46 UTC | debugging docker build script | 29 February 2016, 15:19:46 UTC |
| adc086b | Robert Vickerstaff | 29 February 2016, 15:06:23 UTC | added a dockerfile to build a docker image, also a script to generate a sample data set | 29 February 2016, 15:06:23 UTC |
| f4a6d43 | Robert Vickerstaff | 19 February 2016, 17:20:32 UTC | now separating the matching process, first match lgs to the reference map (followed by optional manual edit) then rename and reorient | 19 February 2016, 17:20:32 UTC |
| b059262 | Robert Vickerstaff | 18 February 2016, 17:51:59 UTC | added a util to reinsert redundant markers into a map, also converted existing utils to compare two maps and rename and reorient lgs with respect to an existing map | 18 February 2016, 17:51:59 UTC |
| aaa4116 | Robert Vickerstaff | 18 February 2016, 12:24:37 UTC | added script to reinsert redundant markers back into ordered map | 18 February 2016, 12:24:37 UTC |
| 9d27955 | Robert Vickerstaff | 17 February 2016, 17:34:04 UTC | renamed test_rgxha_redundancy.sh to build_rgxha_map.sh, may move this into the octoploid_mapping directory to be with the other map building scripts | 17 February 2016, 17:34:04 UTC |
| 9b402bc | Robert Vickerstaff | 16 February 2016, 12:30:01 UTC | added steps to filter out bad markers by marker id and to reemptively switch marker types for those markers which have been found to be miscorrected during the automated type correction step, now able to get 28 LGs for Redgauntlet x Hapil using only lod 6 and 9 | 16 February 2016, 12:30:01 UTC |
| 5ef1ffc | Robert Vickerstaff | 12 February 2016, 17:58:34 UTC | implemented removal of redundant markers | 12 February 2016, 17:58:34 UTC |
| d05c2a6 | Robert Vickerstaff | 11 February 2016, 10:40:54 UTC | renamed files starting with gg_ to crosslink_ | 11 February 2016, 10:40:54 UTC |
| 1ebb1cb | Robert Vickerstaff | 10 February 2016, 18:07:57 UTC | now with option to use cxr linkage during phasing to allow completion of hk markers phasing which would otherwise need to be split into two lgs, then merged manually before hk imputation | 10 February 2016, 18:07:57 UTC |
| b767009 | Robert Vickerstaff | 10 February 2016, 14:34:03 UTC | added a graphical viewer to view genotype calls in map order, phased or unphased representation. rflod viewer is now also capable of full 2D panning | 10 February 2016, 14:34:03 UTC |
| cb515d8 | Robert Vickerstaff | 09 February 2016, 17:34:50 UTC | now scripts/test_rgxha2.sh with interactive option to try reordering the map | 09 February 2016, 17:34:50 UTC |
| 5e7d317 | Robert Vickerstaff | 08 February 2016, 17:57:41 UTC | scripted splitting lgs at higher lod where neccessary based on user input from rflod viewer | 08 February 2016, 17:57:41 UTC |
| 364458e | Robert Vickerstaff | 05 February 2016, 18:48:46 UTC | made a few improvements to crosslink_group, now trying it out on rgxha | 05 February 2016, 18:48:46 UTC |
| dc18580 | Robert Vickerstaff | 04 February 2016, 17:51:38 UTC | testing refactored crosslink_group on simulated data | 04 February 2016, 17:51:38 UTC |
| 810558a | Robert Vickerstaff | 04 February 2016, 12:22:21 UTC | refactored crosslink_group | 04 February 2016, 12:22:21 UTC |
| a15aae1 | Robert Vickerstaff | 04 February 2016, 09:48:22 UTC | part way through refactoring crosslink_group to remove data from the conf structure to help make functions reuseable | 04 February 2016, 09:48:22 UTC |
| bce0b9c | Robert Vickerstaff | 03 February 2016, 16:57:14 UTC | wrote generic load functions, crosslink_viewer now handles imputed/phased/unphased data better | 03 February 2016, 16:57:14 UTC |
| 39e7558 | Robert Vickerstaff | 02 February 2016, 17:39:28 UTC | refactoring crosslink_viewer pan and zoom to allow easier determination of which marker was clicked on | 02 February 2016, 17:39:28 UTC |
| 19799d5 | Robert Vickerstaff | 01 February 2016, 17:01:47 UTC | crosslink_sorter now able to sort lg fragments to move linked frags next to each other | 01 February 2016, 17:01:47 UTC |
