| f523075 | isaacovercast | 08 January 2016, 02:18:02 UTC | Fixed tagging in setup.py | 08 January 2016, 02:18:02 UTC |
| e29429b | isaacovercast | 08 January 2016, 02:15:01 UTC | Added code to setup.py to automatically update ipyrad/__init__.py __version__. | 08 January 2016, 02:15:01 UTC |
| f3382e4 | deren | 07 January 2016, 22:22:34 UTC | raise error and return names for bad samples names in _get_samples() | 07 January 2016, 22:22:34 UTC |
| dc1d5bf | deren | 07 January 2016, 21:42:05 UTC | fix to merge conflict | 07 January 2016, 21:42:05 UTC |
| 74bf439 | deren | 07 January 2016, 21:39:36 UTC | improved Error handling. Doc strings for step funcs | 07 January 2016, 21:39:36 UTC |
| 9590478 | deren | 07 January 2016, 21:38:50 UTC | fix to Sample handling and cleanup | 07 January 2016, 21:38:50 UTC |
| 71618e9 | deren | 07 January 2016, 21:38:16 UTC | better optim | 07 January 2016, 21:38:16 UTC |
| f2c382b | deren | 07 January 2016, 21:37:59 UTC | better optim, close open file. | 07 January 2016, 21:37:59 UTC |
| 9731e1f | isaacovercast | 07 January 2016, 21:25:04 UTC | Set consens_se to read from hackersdict["max_fragment_length"] | 07 January 2016, 21:25:04 UTC |
| 27bcf87 | isaacovercast | 07 January 2016, 20:30:50 UTC | updated to 0.1.0 | 07 January 2016, 20:30:50 UTC |
| d005266 | isaacovercast | 07 January 2016, 20:29:30 UTC | Removed some old global variable crust replaced by hackersonly | 07 January 2016, 20:29:30 UTC |
| 3e5b860 | isaacovercast | 07 January 2016, 20:28:34 UTC | Added hackersonly dict to assembly and also added a data._version stamp. Updated refmap, cluster_accross, and loci2SNP to use the new hackersonly params | 07 January 2016, 20:28:34 UTC |
| 8256059 | isaacovercast | 07 January 2016, 17:30:27 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 07 January 2016, 17:30:27 UTC |
| 776811d | isaacovercast | 07 January 2016, 17:30:04 UTC | Implemented 'denovo_only' assembly method. | 07 January 2016, 17:30:04 UTC |
| 1fbd901 | deren | 07 January 2016, 03:34:02 UTC | cleaning up some exception handling code | 07 January 2016, 03:34:02 UTC |
| 32d4119 | deren | 07 January 2016, 03:30:54 UTC | fix to broken rejoining of chunks at cleanup | 07 January 2016, 03:30:54 UTC |
| b2cf7e9 | isaacovercast | 07 January 2016, 03:01:30 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 07 January 2016, 03:01:30 UTC |
| 045369a | isaacovercast | 07 January 2016, 03:01:11 UTC | Fixed output formatting on two more parameters. good idea. | 07 January 2016, 03:01:11 UTC |
| 7bd83d7 | deren | 07 January 2016, 02:52:49 UTC | better exception handling in wrapper | 07 January 2016, 02:52:49 UTC |
| fa66134 | isaacovercast | 07 January 2016, 01:33:50 UTC | Adding a sim_popsfile for testing the population assignments. | 07 January 2016, 01:33:50 UTC |
| c174fd2 | isaacovercast | 07 January 2016, 01:09:27 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 07 January 2016, 01:09:27 UTC |
| b814d2f | isaacovercast | 07 January 2016, 01:08:04 UTC | Fixed preview mode for step3. Fixed a nasty bug with PE where reads that map too far apart were making the refmap process bomb. Fixed a stupid bug in util where i forgot to import sys, so merge was a little broken. | 07 January 2016, 01:08:04 UTC |
| 64d85bc | deren | 07 January 2016, 01:04:44 UTC | Merge branch 'supercat' Conflicts: ipyrad/file_conversion/loci2migrate.py | 07 January 2016, 01:04:44 UTC |
| dfb1278 | deren | 07 January 2016, 01:03:03 UTC | supercatg building, still lacks indels | 07 January 2016, 01:03:03 UTC |
| 299f895 | isaacovercast | 06 January 2016, 22:50:52 UTC | updated version to 0.0.8 | 06 January 2016, 22:50:52 UTC |
| 9b605bd | isaacovercast | 06 January 2016, 22:47:20 UTC | Fixed a bug i'd introduced for R2 for paired reads, when i switched from .gz to .fq i forgot to switch R2 as well, very simple stupid fix. | 06 January 2016, 22:47:20 UTC |
| d366e1a | isaacovercast | 06 January 2016, 21:05:37 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 06 January 2016, 21:05:37 UTC |
| 3c26884 | iovercast | 06 January 2016, 21:05:03 UTC | Bug in sending preview to demultiplex | 06 January 2016, 21:05:03 UTC |
| afde10c | isaacovercast | 06 January 2016, 20:30:43 UTC | Merge branch 'master' into refseq Conflicts: ipyrad/assemble/__init__.py | 06 January 2016, 20:30:43 UTC |
| 8cb7791 | isaacovercast | 06 January 2016, 20:28:45 UTC | Some debug code and dropped gzipping the unmapped reads. | 06 January 2016, 20:28:45 UTC |
| 5493bad | iovercast | 06 January 2016, 20:25:51 UTC | Preview of preview mode for steps 1 and 2. Seems to work okay. | 06 January 2016, 20:25:51 UTC |
| 916c017 | iovercast | 06 January 2016, 19:44:15 UTC | Oops fixed formatting bug | 06 January 2016, 19:44:15 UTC |
| 8b92369 | iovercast | 06 January 2016, 19:21:31 UTC | Initial commit of vcf2loci, it doesn't even pretend to work yet, just fleshing out some ideas. | 06 January 2016, 19:21:31 UTC |
| 3c0fc4e | iovercast | 06 January 2016, 18:16:38 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad Conflicts: ipyrad/assemble/write_outfiles.py | 06 January 2016, 18:16:38 UTC |
| eb8d64a | iovercast | 06 January 2016, 18:14:31 UTC | Finished initial cleanup and migration of all loci2*.make() functions. Still needs testing. | 06 January 2016, 18:14:31 UTC |
| 317541c | deren | 06 January 2016, 16:32:36 UTC | commented out ', r' in path string | 06 January 2016, 16:32:36 UTC |
| ca11bf5 | deren | 06 January 2016, 16:31:13 UTC | fix to key/sample selection | 06 January 2016, 16:31:13 UTC |
| 551cd6f | iovercast | 06 January 2016, 14:28:23 UTC | Added new parameter pop_assign_file, and link_populations() function to populate the assembly.populations dict. Fixes tic #42 | 06 January 2016, 14:28:23 UTC |
| cff841d | iovercast | 05 January 2016, 03:41:06 UTC | Continuing revisions on step7, fixed loci2vcf and loci2phynex. Minor changes to loci2treemix and loci2migrate, still needs more work. Updated write_outfiles to do something "smart" with formatting output files, now you can add a new output format by updated the output_formats variable and creating a file in file_conversion called loci2*whatever.py that defines a make() function that takes assembly and samples list as arguments. | 05 January 2016, 03:41:06 UTC |
| b0bda2d | iovercast | 05 January 2016, 00:37:02 UTC | Step 7 - Added an 'output_files' parameter to assembly. Added the write_outfiles module to do the heavy lifting. Included the list of possible output files as a global at the top of write_outfiles, for convenience. Also imported all the old loci2* file conversion code, though none of it works yet. | 05 January 2016, 00:37:02 UTC |
| 733782e | iovercast | 04 January 2016, 21:55:24 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 04 January 2016, 21:55:24 UTC |
| cf8ccb4 | iovercast | 04 January 2016, 21:54:20 UTC | Added code to run step7(), also added a function to read convert sample names list to list of sample objects so all step*() functions now handle this identically. | 04 January 2016, 21:54:20 UTC |
| 89e239c | deren | 04 January 2016, 20:30:57 UTC | cleanup of test files | 04 January 2016, 20:30:57 UTC |
| 30dccac | deren | 04 January 2016, 20:30:12 UTC | test_rad 1-6 | 04 January 2016, 20:30:12 UTC |
| 22793b5 | deren | 04 January 2016, 20:29:43 UTC | fix for defaults in step5 when step4 is skipped | 04 January 2016, 20:29:43 UTC |
| 848355d | deren | 04 January 2016, 19:02:39 UTC | fixed merge conflicts in cluster_within, consens_se and rawedit | 04 January 2016, 19:02:39 UTC |
| 2f4c4c5 | deren | 04 January 2016, 18:49:01 UTC | new order of params. New set_params. New catching for IPClusterError | 04 January 2016, 18:49:01 UTC |
| af1e53b | isaacovercast | 28 December 2015, 22:14:17 UTC | Merge branch 'master' into refseq | 28 December 2015, 22:14:17 UTC |
| 7296a37 | iovercast | 28 December 2015, 22:10:22 UTC | Fix rawedit to _not_ gzip tmp files, and also not to gzip the edits file Seems to work ok, through step3 | 28 December 2015, 22:10:22 UTC |
| 8b39d1a | isaacovercast | 28 December 2015, 21:04:25 UTC | Fixed a stupid mistake that made PE work but broke SE. Works again | 28 December 2015, 21:04:25 UTC |
| be40668 | isaacovercast | 27 December 2015, 02:48:28 UTC | Fixed all PE merging. Moved reference sequence indexing to refmap.py | 27 December 2015, 02:48:28 UTC |
| 167897f | isaacovercast | 26 December 2015, 23:24:38 UTC | fixed refmap to work with new assembly.bins.* format | 26 December 2015, 23:24:38 UTC |
| dba79c6 | isaacovercast | 26 December 2015, 21:23:57 UTC | Big merge of master into refseq to incorporate refactoring changes Merge branch 'master' of https://github.com/dereneaton/ipyrad into tmpref Conflicts: ipyrad/assemble/__init__.py ipyrad/assemble/cluster_across.py ipyrad/assemble/cluster_within.py ipyrad/assemble/util.py ipyrad/core/assembly.py | 26 December 2015, 21:23:57 UTC |
| 2b61418 | isaacovercast | 26 December 2015, 21:15:27 UTC | wat | 26 December 2015, 21:15:27 UTC |
| 2a43ec7 | iovercast | 26 December 2015, 20:56:41 UTC | Created a new function in util.py called merge_pairs, it takes data, sample, and a tuple of files to merge as args and returns the merged file path, and the number of reads successfully merged. Refactored cluster_within to use the new format. | 26 December 2015, 20:56:41 UTC |
| b27cedb | isaacovercast | 25 December 2015, 20:51:24 UTC | got refmapping working for PE, finalize() still doesn't work. | 25 December 2015, 20:51:24 UTC |
| 21fdd4c | isaacovercast | 25 December 2015, 03:15:08 UTC | Finished mod'ing refmap to handle PE. | 25 December 2015, 03:15:08 UTC |
| 7cc6a3a | iovercast | 25 December 2015, 02:30:16 UTC | Cherry-picked the commit introducing util.py Refactored a bunch of code to move common functions into ipyrad/assemble/util.py Moved functions include ambigcutters() comp() getoptim() getsplits() revcomp() unhetero() uplow() and zcat_make_temps(). Conflicts: ipyrad/assemble/__init__.py ipyrad/assemble/cluster_across.py ipyrad/assemble/cluster_within.py ipyrad/assemble/rawedit.py | 25 December 2015, 02:44:10 UTC |
| 1c8bf13 | iovercast | 25 December 2015, 02:30:16 UTC | Refactored a bunch of code to move common functions into ipyrad/assemble/util.py Moved functions include ambigcutters() comp() getoptim() getsplits() revcomp() unhetero() uplow() and zcat_make_temps(). | 25 December 2015, 02:30:16 UTC |
| 65cde39 | isaacovercast | 24 December 2015, 21:09:19 UTC | Add code to preserve and recover original fastq in the edits directory for both reads in PE. Also removed a block of code that was sorting the unmapped reads, which is not a sensible operation. | 24 December 2015, 21:09:19 UTC |
| d0bba2e | LabUser | 22 December 2015, 04:01:47 UTC | Fixed formatting for GIT_DESCRIBE_TAG | 22 December 2015, 04:01:47 UTC |
| 3e14cdc | isaacovercast | 22 December 2015, 01:43:23 UTC | Completed mapreads() preview mode. Added a function called preview_truncate_fq() that carves off the first 10000 lines of the fq, sets up a dummy tmp fq file and runs the pipeline on the dummy data. | 22 December 2015, 01:43:23 UTC |
| 68b9f7a | deren | 15 December 2015, 22:24:58 UTC | fix to CLI and API launch. Update vsearch linux. rawedit fix for pairgbs. plotting slight mods. new parameter edit_cutsites. | 15 December 2015, 22:24:58 UTC |
| 2ed71bb | deren | 15 December 2015, 01:12:34 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 15 December 2015, 01:12:34 UTC |
| c0dd065 | deren | 15 December 2015, 01:12:28 UTC | clean running CLI, stdout for steps only on CLI | 15 December 2015, 01:12:28 UTC |
| e3a1baa | iovercast | 14 December 2015, 23:17:37 UTC | Added code to create the assembly.files.fastqs directory in the event that link_fastqs() is called. | 14 December 2015, 23:17:37 UTC |
| 715b08d | deren | 14 December 2015, 17:26:27 UTC | load module added. some general code cleanup. | 14 December 2015, 17:26:27 UTC |
| c1f7af5 | deren | 14 December 2015, 17:25:42 UTC | complete overhaul of cluster_across | 14 December 2015, 17:25:42 UTC |
| f8e96c5 | deren | 14 December 2015, 17:25:03 UTC | dstat analysis setup. In progress. | 14 December 2015, 17:25:03 UTC |
| 8201fb3 | deren | 14 December 2015, 17:20:32 UTC | improvement to API structure. Fewer visible methods | 14 December 2015, 17:20:32 UTC |
| 22ca7fe | isaacovercast | 13 December 2015, 23:44:14 UTC | Added -x and -c flag to perform exhaustive search and to apply a clustering threshold. Improved docs. | 13 December 2015, 23:44:14 UTC |
| e1f6221 | isaacovercast | 13 December 2015, 23:18:52 UTC | Bug fix, output for clust.gz format was wonky (i was appending the ints to the end of the names, but muscle_align does that for us). | 13 December 2015, 23:18:52 UTC |
| b66213b | isaacovercast | 13 December 2015, 22:57:08 UTC | Routed around the whole mpileup business. We'll just pull in successfully mapped reads raw from the bam file. Also moved the call to finalize_aligned_reads before the call to muscle align. | 13 December 2015, 22:57:08 UTC |
| caf5d1e | isaacovercast | 13 December 2015, 18:41:12 UTC | Parallelized the get_aligned_clusters method. There is a LOT of overhead here, because it's calling all this external stuff per pileup region. | 13 December 2015, 18:41:12 UTC |
| fd54c29 | isaacovercast | 12 December 2015, 21:18:42 UTC | Finished get_aligned_reads. Pushed mapped reads back into clustS.gz file now. | 12 December 2015, 21:18:42 UTC |
| 1c5b5d5 | isaacovercast | 12 December 2015, 01:05:53 UTC | Added code to do pileup and output fasta of stacks per locus. | 12 December 2015, 01:05:53 UTC |
| f9c5f53 | isaacovercast | 11 December 2015, 20:41:56 UTC | no changes. testing | 11 December 2015, 20:41:56 UTC |
| fb85684 | isaacovercast | 11 December 2015, 20:38:32 UTC | Moved refseq stats from cluster_within to refmap | 11 December 2015, 20:38:32 UTC |
| 6114f97 | isaacovercast | 11 December 2015, 20:00:54 UTC | Moved all refseq mapping code out of cluster_within to refmap. Also, added some logging to cluster_within. | 11 December 2015, 20:00:54 UTC |
| 30a6635 | deren | 11 December 2015, 16:56:50 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad testing merge of master on dstat branch | 11 December 2015, 16:56:50 UTC |
| 1002a42 | deren | 11 December 2015, 16:56:31 UTC | dstat loci parsing | 11 December 2015, 16:56:31 UTC |
| 3b5c4d1 | iovercast | 10 December 2015, 17:58:13 UTC | Fixing ticket #6 (renaming binaries and symlinking to generic names so we dont' have to change the code if we update a binary. | 10 December 2015, 17:58:13 UTC |
| 9891d1f | iovercast | 10 December 2015, 16:42:43 UTC | Added an explicit version to ipython, to fix broken conda build. | 10 December 2015, 16:42:43 UTC |
| dd5d7f4 | iovercast | 10 December 2015, 16:38:17 UTC | Changed a couple print statements to print functions. | 10 December 2015, 16:38:17 UTC |
| d8291be | deren | 09 December 2015, 23:30:22 UTC | dd | 09 December 2015, 23:30:22 UTC |
| 1b703ec | deren | 09 December 2015, 23:23:30 UTC | getting started on dstats | 09 December 2015, 23:23:30 UTC |
| 912bc82 | deren | 08 December 2015, 17:10:40 UTC | CLI is running 1-5 with print messages. Still need to add quiet to messages for the API | 08 December 2015, 17:10:40 UTC |
| 09bac2d | deren | 08 December 2015, 15:33:51 UTC | CLI launches its own ipcluster, API uses whichever is open else reports error (need to improve error message still) | 08 December 2015, 15:33:51 UTC |
| 47865b3 | deren | 08 December 2015, 00:14:31 UTC | Finally found bug in alignment. Pairedgbs is good to go. Muscle is a little faster | 08 December 2015, 00:14:31 UTC |
| 74e0c2f | deren | 07 December 2015, 18:19:05 UTC | clusting working for pairddrad, working on steps 5,6 | 07 December 2015, 18:19:05 UTC |
| b8bc6d5 | deren | 04 December 2015, 19:58:51 UTC | better handling of 'launch'. Lower memory overhead on Assembly.depths. Some beginning edits on cluster_across | 04 December 2015, 19:58:51 UTC |
| 447cce7 | deren | 04 December 2015, 06:22:08 UTC | step5 consens calling working at a basic level on sim data | 04 December 2015, 06:22:08 UTC |
| 164020e | deren | 01 December 2015, 00:13:20 UTC | CLI running steps 1-4 | 01 December 2015, 00:13:20 UTC |
| 60a0a7d | deren | 01 December 2015, 00:12:55 UTC | much better guarded launcher of ipp. Need to test wait/start times | 01 December 2015, 00:12:55 UTC |
| 3ffa09f | deren | 01 December 2015, 00:11:35 UTC | fix for tuple of restriction overhangs | 01 December 2015, 00:11:35 UTC |
| 33e5801 | deren | 01 December 2015, 00:11:01 UTC | code cleanup | 01 December 2015, 00:11:01 UTC |
| 8b96f8b | deren | 01 December 2015, 00:10:25 UTC | cleaner launching in CLI, new args --force and --results | 01 December 2015, 00:10:25 UTC |
| 2f1752d | deren | 01 December 2015, 00:09:30 UTC | code cleanup | 01 December 2015, 00:09:30 UTC |
| 8740c22 | deren | 30 November 2015, 07:17:06 UTC | docs edits | 30 November 2015, 07:17:06 UTC |
| 720e957 | deren | 30 November 2015, 00:51:43 UTC | docs update | 30 November 2015, 00:51:43 UTC |
