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https://github.com/dereneaton/ipyrad
22 May 2024, 15:02:59 UTC
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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
d49f8e8 deren 29 November 2015, 23:36:13 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 29 November 2015, 23:36:13 UTC
c362f33 deren 29 November 2015, 23:35:23 UTC docs update 29 November 2015, 23:35:23 UTC
a663a30 deren 29 November 2015, 21:12:07 UTC docs edits 29 November 2015, 21:12:07 UTC
90015ce deren 29 November 2015, 21:09:11 UTC docs edits 29 November 2015, 21:09:11 UTC
57ec9db deren 29 November 2015, 19:33:08 UTC docs edits 29 November 2015, 19:33:08 UTC
877b357 deren 29 November 2015, 19:29:12 UTC docs edits 29 November 2015, 19:29:12 UTC
8f66cd0 deren 29 November 2015, 19:05:33 UTC docs edits 29 November 2015, 19:05:33 UTC
7afaec9 deren 29 November 2015, 18:31:47 UTC docs testing 29 November 2015, 18:31:47 UTC
941b64e deren 29 November 2015, 18:27:38 UTC docs testing 29 November 2015, 18:27:38 UTC
765a990 deren 29 November 2015, 06:00:30 UTC trying to fix rtd error with gnureadline 29 November 2015, 06:00:30 UTC
8f0f6d6 deren 29 November 2015, 05:19:25 UTC trying to fix rtd error with gnureadline 29 November 2015, 05:19:25 UTC
f99fe5c deren 29 November 2015, 04:37:06 UTC trying to fix rtd error with gnureadline 29 November 2015, 04:37:06 UTC
1717c6c deren 29 November 2015, 04:30:40 UTC trying to fix rtd error with gnureadline 29 November 2015, 04:30:40 UTC
5891da6 deren 29 November 2015, 04:21:31 UTC trying to fix rtd error with gnureadline 29 November 2015, 04:21:31 UTC
0f18e58 deren 29 November 2015, 03:55:56 UTC trying to fix rtd error with gnureadline 29 November 2015, 03:55:56 UTC
9328650 deren 29 November 2015, 03:00:28 UTC docs editing. New TOC arrangement 29 November 2015, 03:00:28 UTC
fabef2b Deren Eaton 29 November 2015, 02:29:41 UTC Merge pull request #20 from gitter-badger/gitter-badge Add a Gitter chat badge to README.rst 29 November 2015, 02:29:41 UTC
2da9f76 deren 29 November 2015, 02:25:05 UTC merge pairs working. Ipyparallel engines start in try statements to wait for Engines to start. A lot more testing of Exception handling. 29 November 2015, 02:25:05 UTC
0318c54 The Gitter Badger 28 November 2015, 21:20:48 UTC Add Gitter badge 28 November 2015, 21:20:48 UTC
2a5921a deren 26 November 2015, 20:56:46 UTC logging message for CLI 26 November 2015, 20:56:46 UTC
19301d5 deren 26 November 2015, 19:16:40 UTC working step2 filtering w/ paired data and error logging. 26 November 2015, 19:16:40 UTC
4f87c7d deren 26 November 2015, 18:07:51 UTC remove failed sidebranch plan files from trying to launch ipcluster at init again. 26 November 2015, 18:07:51 UTC
5e0337f deren 26 November 2015, 18:06:49 UTC parallel fix to avoid launching duplicate clusters. Logging working for engines. Module __loglevel__ used for hacking. Rawedit pair filtering working. 26 November 2015, 18:06:49 UTC
3e5ef6e deren 24 November 2015, 00:27:01 UTC notebook for testing merge options 24 November 2015, 00:27:01 UTC
93228b9 deren 24 November 2015, 00:26:13 UTC Merge remote-tracking branch 'origin/master' into mergepairs Conflicts: tests/data1_results.csv tests/test_rad.ipynb 24 November 2015, 00:26:13 UTC
3b6ee06 deren 24 November 2015, 00:21:07 UTC starting mergepairs, and some edits to run ipp on consens 24 November 2015, 00:21:07 UTC
49779fd deren 23 November 2015, 21:20:52 UTC added Assembly files @property attribute to see all files in Samples. 23 November 2015, 21:20:52 UTC
8b00afb isaacovercast 23 November 2015, 02:19:06 UTC Fixed another <<<<HEAD i forgot to delete in assembly.py 23 November 2015, 02:19:06 UTC
a2c8ab3 isaacovercast 23 November 2015, 02:13:52 UTC FIxed a merge messup 23 November 2015, 02:13:52 UTC
eebabdc isaacovercast 23 November 2015, 02:10:44 UTC Fixed merge conflicts, nothing serious Merge branch 'master' of https://github.com/dereneaton/ipyrad into refseq Conflicts: ipyrad/__main__.py ipyrad/core/assembly.py setup.py 23 November 2015, 02:10:44 UTC
db0cb76 isaacovercast 23 November 2015, 02:00:42 UTC Fixed all reference sequence mapping routines to use the new .fq files from sample.files.edits. 23 November 2015, 02:00:42 UTC
9080afb deren 23 November 2015, 01:42:03 UTC prettier printing CLI help message 23 November 2015, 01:42:03 UTC
4327714 deren 23 November 2015, 01:38:58 UTC CLI now prints --help if no args are passed 23 November 2015, 01:38:58 UTC
b8951ba deren 23 November 2015, 01:25:32 UTC Merge branch 'CLI' CLI functional with --version, --help, -n, -p, -s, and parsing params file to an Assembly object. 23 November 2015, 01:25:32 UTC
522f09d deren 23 November 2015, 01:24:56 UTC CLI working to parse params file. Need to decide upon params ordering still. 23 November 2015, 01:24:56 UTC
33e03d2 deren 23 November 2015, 01:24:23 UTC function to write default params file for CLI 23 November 2015, 01:24:23 UTC
30cf462 iovercast 23 November 2015, 01:16:37 UTC Rawedit wasn't properly splicing the tmp files back together, i added a out.write("\n") on line 245. It fixes the problem, but not sure if this is the optimal solution. 23 November 2015, 01:16:37 UTC
b0bd1c2 deren 22 November 2015, 21:46:07 UTC added more requirements to setup.py that seemed necessary to run the CLI 22 November 2015, 21:46:07 UTC
294f350 isaacovercast 22 November 2015, 19:40:13 UTC Fixed call to assemble.stamp to handle api change to _stamp 22 November 2015, 19:40:13 UTC
074f535 isaacovercast 22 November 2015, 19:12:02 UTC Merged conflicts in assembly.py, nothing serious Merge branch 'master' of https://github.com/dereneaton/ipyrad into refseq Conflicts: ipyrad/__main__.py ipyrad/core/assembly.py 22 November 2015, 19:12:02 UTC
5e95445 isaacovercast 22 November 2015, 18:58:23 UTC A beginning framework for getting aligned mapped reads. 22 November 2015, 18:58:23 UTC
947b757 deren 22 November 2015, 18:03:11 UTC removed test file 22 November 2015, 18:03:11 UTC
4a9a68a deren 22 November 2015, 18:01:56 UTC Merge branch 'allfastqs' fastq tuples for R1 and R2 reads are retained through step2. 22 November 2015, 18:01:56 UTC
2dc122a deren 22 November 2015, 17:59:38 UTC edits is now a tuple with (R1, R2) fastq files. Improvements to linked_fastqs() 22 November 2015, 17:59:38 UTC
2ba3258 isaacovercast 22 November 2015, 03:29:38 UTC Added paramsinfo for assembly_method and reference_sequence 22 November 2015, 03:29:38 UTC
08d34da isaacovercast 22 November 2015, 02:01:28 UTC Moved assembly_method into the assembly paramsdict. Updated all parts of the code that test for assembly method to use this param rather than testing for existence of the reference sequence. 22 November 2015, 02:01:28 UTC
d1df671 deren 22 November 2015, 00:39:13 UTC launch parallel clients on Assembly.__init__. Step2 changed to fastq input 22 November 2015, 00:39:13 UTC
54bbc8d isaacovercast 21 November 2015, 03:58:54 UTC Fixed assembly.stats so it only writes out columns that are not all NaN 21 November 2015, 03:58:54 UTC
4923bbe isaacovercast 21 November 2015, 03:55:24 UTC Added unmapped_reads to sample.files. Also fixed mapreads() and cleanup() in cluster_within so the reads map properly, and so the sample.stats get updated right. NB: ipyparallel clients get stuff passed in by value, so if you want to update sample member variables for example you have to do it OUTSIDE ipyparallel. This hosed me today.... 21 November 2015, 03:55:24 UTC
fae3c12 iovercast 21 November 2015, 03:44:41 UTC added a smidge of code to assemble.stats to dropna(axis=1, how='all') to drop all columns (axis=1) where all results are NaN 21 November 2015, 03:44:41 UTC
449793a isaacovercast 21 November 2015, 00:31:54 UTC Updated mapreads to use the new *_refmapping directory for dumping sam and bam files to, as well as cleaning up the file names, tracking the mapped reads bam file for downstream, and _trying_ to grap stats for mapped and unmapped reads from flagstat, but it's not working yet. 21 November 2015, 00:31:54 UTC
148d63a isaacovercast 21 November 2015, 00:30:52 UTC Added files.mapped_reads and stats for mapped and unmapped reads for the sample class 21 November 2015, 00:30:52 UTC
271d36b isaacovercast 20 November 2015, 22:21:43 UTC Fixed couple small bugs, assert assembly_method didn't like the call to list(), and setting default dir for reference_sequence wasn't working in my current idea reference sequence is a full path to a .fq.gz file, there's an argument to be made that this should be a directory esp if people want to map to references dl'd by chromosome, rather than the full sequence. This is maybe a v2 feature. 20 November 2015, 22:21:43 UTC
567fe7a isaacovercast 20 November 2015, 20:18:28 UTC Merge conflicts in ipynotebooks are annoying. Merge branch 'refseq' of https://github.com/dereneaton/ipyrad into refseq Conflicts: tests/test_refseq.ipynb 20 November 2015, 20:18:28 UTC
94448d0 isaacovercast 20 November 2015, 20:14:11 UTC minor changes 20 November 2015, 20:14:11 UTC
9da5e9c isaacovercast 20 November 2015, 20:02:05 UTC Fixed a merge conflict in __main__ 20 November 2015, 20:02:05 UTC
e35f17a isaacovercast 20 November 2015, 20:00:19 UTC Merge remote-tracking branch 'origin/master' into refseq 20 November 2015, 20:00:19 UTC
239233a deren 18 November 2015, 19:47:35 UTC adding some comments in cell blocks w/ code formatting ideas 18 November 2015, 19:47:35 UTC
1e28b98 deren 18 November 2015, 19:46:55 UTC run set_params() for args that set dir/ paths during _init_ so that these paths are set even if the user is using the default location. 18 November 2015, 19:46:55 UTC
2770d8c deren 18 November 2015, 17:41:23 UTC testing with vsearch 1.9.2 18 November 2015, 17:41:23 UTC
6794f8a deren 18 November 2015, 02:04:14 UTC ipyparallel now called in ipyrad/__init__.py with ipcontroller function to modifiy controller types. 18 November 2015, 02:04:14 UTC
258947b deren 18 November 2015, 02:02:36 UTC update test_rad tutorial 18 November 2015, 02:02:36 UTC
38402d6 deren 17 November 2015, 15:04:42 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad merging small edits with Isaac's commits 17 November 2015, 15:04:42 UTC
6ab24c7 deren 17 November 2015, 15:04:32 UTC small code cleanup w/ assert message 17 November 2015, 15:04:32 UTC
266957f deren 17 November 2015, 15:03:53 UTC warning message if ipcluster was not started 17 November 2015, 15:03:53 UTC
ce7022b deren 17 November 2015, 15:02:53 UTC docs edits 17 November 2015, 15:02:53 UTC
294d150 isaacovercast 17 November 2015, 03:45:06 UTC mapreads() was writing out fastq, so i had to hack it to write out fasta so the rest of step3 would work. It works now! unmapped reads finish derep, sort, cluster and muscle align. 17 November 2015, 03:45:06 UTC
55b09b2 isaacovercast 16 November 2015, 21:26:04 UTC First successful integration of reference sequence mapping. It worked out of the box, fucking somehow, god only knows. There was one stupid type-o in the initial commit which took me a lifetime to track down, but it works now, writes out unmapped fasta and sorted mapped bams. 16 November 2015, 21:26:04 UTC
a7e81cc iovercast 15 November 2015, 23:27:22 UTC oops added samtools license 15 November 2015, 23:27:22 UTC
acca7c1 iovercast 15 November 2015, 23:26:30 UTC Added samtools binaries. 15 November 2015, 23:26:30 UTC
58736ea Isaac 15 November 2015, 21:19:10 UTC Replaced zcat with gunzip -c for portability. See the tix here for more info: https://github.com/dereneaton/ipyrad/issues/8 15 November 2015, 21:19:10 UTC
21cc519 iovercast 15 November 2015, 16:14:28 UTC In step3 I changed call from link_edits() to link_fastas(), since link_edits didn't exist and link_fastas seemed to do what we want. 15 November 2015, 16:14:28 UTC
085aa04 iovercast 15 November 2015, 16:10:27 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 15 November 2015, 16:10:27 UTC
68ef3c1 Isaac 15 November 2015, 01:09:36 UTC The initial broad brush strokes for reference mapping. Doesn't yet handle the mapped reads, and still needs some cleanup before unmapped reads drop back into the pipeline cleanly. On the up side it the code shouldn't interfere so long as you DON'T attempt to define a reference sequence (it's all guarded by conditional blocks). 15 November 2015, 01:09:36 UTC
e87aac0 Isaac 14 November 2015, 21:26:19 UTC Update assembly with some reference sequence stuff, test for index. 14 November 2015, 21:26:19 UTC
759daa9 deren 13 November 2015, 23:58:35 UTC docs edits 13 November 2015, 23:58:35 UTC
eb49f81 deren 13 November 2015, 23:43:04 UTC testing docs links 13 November 2015, 23:43:04 UTC
b92ad3e deren 13 November 2015, 23:31:46 UTC docs updates 13 November 2015, 23:31:46 UTC
0548616 iovercast 10 November 2015, 04:48:21 UTC fixed a bad path to vsearch binary. I think we should simplify the binary path names in bin to 'vsearch', 'muscle', etc..., then when we include new binaries in the distro we only need to copy them to the ipyrad/bin directory with these names rather than tweeking a bunch of fully qualified names inside python file paths. 10 November 2015, 04:48:21 UTC
9d40031 iovercast 10 November 2015, 04:44:50 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 10 November 2015, 04:44:50 UTC
2911e78 iovercast 10 November 2015, 03:22:08 UTC First draft of refseq ipynb, this is more like an experimental sandbox, so don't think it'll work at this point. 10 November 2015, 03:22:08 UTC
93e3c01 iovercast 10 November 2015, 03:12:39 UTC Adding code to test for reference sequence indexing, and if not exist then to build the index. 10 November 2015, 03:12:39 UTC
f188865 iovercast 09 November 2015, 22:12:04 UTC Merge remote-tracking branch 'origin/master' into refseq Conflicts: setup.py 09 November 2015, 22:12:04 UTC
f96b878 Isaac 09 November 2015, 20:13:40 UTC Fixed conda build script. Conda package builds clean, but doesn't install yet. Added code on setup.py to incude everything in the ./bin directory during the install. 09 November 2015, 20:13:40 UTC
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