Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 07ab21494ad16ff3dd9f9fc04c1da6696fb460b3 https://github.com/galaxyproject/galaxy/commit/07ab21494ad16ff3dd9f9fc04c1da... Author: mtekman <m.tekman@ucl.ac.uk> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py A lib/galaxy/datatypes/test/linkstudies.allegro_fparam A lib/galaxy/datatypes/test/linkstudies.allegro_ihaplo A lib/galaxy/datatypes/test/linkstudies.alohomora_gts A lib/galaxy/datatypes/test/linkstudies.alohomora_maf A lib/galaxy/datatypes/test/linkstudies.alohomora_map A lib/galaxy/datatypes/test/linkstudies.alohomora_ped A lib/galaxy/datatypes/test/linkstudies.linkage_datain A lib/galaxy/datatypes/test/linkstudies.linkage_map A lib/galaxy/datatypes/test/linkstudies.linkage_pedin Log Message: ----------- (squashed) Added common linkage file formats and sniffers Commit: 148b5841ef8d66dab9b67e70a01afe52f35f6599 https://github.com/galaxyproject/galaxy/commit/148b5841ef8d66dab9b67e70a01af... Author: Mehmet Tekman <m.tekman@ucl.ac.uk> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- tokenizer now non-static, eval in doc-test remove Commit: bca3fdec4447663b371309bde70c0f021eef4c5f https://github.com/galaxyproject/galaxy/commit/bca3fdec4447663b371309bde70c0... Author: Mehmet Tekman <m.tekman@ucl.ac.uk> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- whitespace removal Commit: d44f9a0b71951b3375444ede69cede223cf4c419 https://github.com/galaxyproject/galaxy/commit/d44f9a0b71951b3375444ede69ced... Author: Mehmet Tekman <m.tekman@ucl.ac.uk> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- fix to classnames in doc-test Commit: e545ed4848db61b702b261d7602655eadb8aebb9 https://github.com/galaxyproject/galaxy/commit/e545ed4848db61b702b261d760265... Author: Mehmet Tekman <m.tekman@ucl.ac.uk> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py R lib/galaxy/datatypes/test/linkstudies.alohomora_maf R lib/galaxy/datatypes/test/linkstudies.alohomora_map R lib/galaxy/datatypes/test/linkstudies.alohomora_ped Log Message: ----------- retired alohomora pedigree, map, and maf datatypes/sniffers/test files (tabular) Commit: 6115ae8d2dd2be3b41fb7a9dbe86ebd22050505f https://github.com/galaxyproject/galaxy/commit/6115ae8d2dd2be3b41fb7a9dbe86e... Author: Mehmet Tekman <m.tekman@ucl.ac.uk> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- list comparison in header check Commit: 1e28e6231b8c61b6a4b9cd9aff80b4dd535af94b https://github.com/galaxyproject/galaxy/commit/1e28e6231b8c61b6a4b9cd9aff80b... Author: Mehmet Tekman <m.tekman@ucl.ac.uk> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py R lib/galaxy/datatypes/test/linkstudies.linkage_pedin Log Message: ----------- changed PreMakePed to Tabular, and removed sniffer/datatype -> migrated line_op into AllegroHaplo Commit: a5b2929f9e02e96b6fdaa02ebb1a55917d63329e https://github.com/galaxyproject/galaxy/commit/a5b2929f9e02e96b6fdaa02ebb1a5... Author: Mehmet Tekman <m.tekman@ucl.ac.uk> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- removed tokenizer + extra fluff Commit: e6bab259faf5da34cd39eebfb8c44855f3051cf1 https://github.com/galaxyproject/galaxy/commit/e6bab259faf5da34cd39eebfb8c44... Author: Mehmet Tekman <m.tekman@ucl.ac.uk> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/datatypes/test/linkstudies.allegro_fparam R lib/galaxy/datatypes/test/linkstudies.allegro_ihaplo M lib/galaxy/datatypes/test/linkstudies.alohomora_gts M lib/galaxy/datatypes/test/linkstudies.linkage_map Log Message: ----------- smaller test files Commit: 38601e69b1a59ef50c885c153eaa3fb8569fb322 https://github.com/galaxyproject/galaxy/commit/38601e69b1a59ef50c885c153eaa3... Author: Mehmet Tekman <m.tekman@ucl.ac.uk> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py Log Message: ----------- removed AllegroHaplo and AllegroDescent classes (tabular) Commit: 2703b52558236f2faf5401b86cb0a16f90069904 https://github.com/galaxyproject/galaxy/commit/2703b52558236f2faf5401b86cb0a... Author: Mehmet Tekman <m.tekman@ucl.ac.uk> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- removed per-line-op from superclass and into subclasses Commit: c9f44398b1ad48a9510feb2fd361943e96046d3d https://github.com/galaxyproject/galaxy/commit/c9f44398b1ad48a9510feb2fd3619... Author: Mehmet Tekman <m.tekman@ucl.ac.uk> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- reverted back to super in init, line test in header_check Commit: 0ce67da13c311016c80b33d8c36b766895037389 https://github.com/galaxyproject/galaxy/commit/0ce67da13c311016c80b33d8c36b7... Author: Mehmet Tekman <m.tekman@ucl.ac.uk> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- enumerated lines, removed eof_res, header_check Commit: 5c6e4a5c77c07c165918faa2ce635e5b27dd9a77 https://github.com/galaxyproject/galaxy/commit/5c6e4a5c77c07c165918faa2ce635... Author: Eric Rasche <hxr@hx42.org> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py A lib/galaxy/datatypes/test/linkstudies.allegro_fparam A lib/galaxy/datatypes/test/linkstudies.alohomora_gts A lib/galaxy/datatypes/test/linkstudies.linkage_datain A lib/galaxy/datatypes/test/linkstudies.linkage_map Log Message: ----------- Merge pull request #4894 from mtekman/linkage Add Classical linkage and haplotype datatypes Compare: https://github.com/galaxyproject/galaxy/compare/7ee9215c0779...5c6e4a5c77c0