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https://github.com/dereneaton/ipyrad
22 May 2024, 15:02:59 UTC
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Revision Author Date Message Commit Date
3e8aca7 deren 18 February 2016, 22:56:37 UTC "Updating ipyrad/__init__.py to version - 0.1.51 18 February 2016, 22:56:37 UTC
8f0fefe deren 18 February 2016, 22:55:56 UTC some docs changes. No more chdir in __main__. Some svd updates 18 February 2016, 22:55:56 UTC
c39ca40 deren 18 February 2016, 02:16:53 UTC "Updating ipyrad/__init__.py to version - 0.1.50 18 February 2016, 02:16:53 UTC
98627eb deren 18 February 2016, 02:16:39 UTC added name parsing to link_fastqs. And some svd updates. 18 February 2016, 02:16:39 UTC
26ba0e2 isaacovercast 17 February 2016, 06:25:13 UTC cosmetic changes 17 February 2016, 06:25:13 UTC
ef5c786 isaacovercast 17 February 2016, 06:13:30 UTC cosmetic changes 17 February 2016, 06:13:30 UTC
60b752d isaacovercast 17 February 2016, 06:08:13 UTC CLI full tutorial V1.0 17 February 2016, 06:08:13 UTC
ac5e2d3 isaacovercast 17 February 2016, 04:31:39 UTC More or step3 17 February 2016, 04:31:39 UTC
dc624d4 isaacovercast 17 February 2016, 04:22:32 UTC More or less finalized step 3 docs for full tutorial 17 February 2016, 04:22:32 UTC
062ab0b isaacovercast 17 February 2016, 03:45:48 UTC Step 3 further docs 17 February 2016, 03:45:48 UTC
10931f4 isaacovercast 17 February 2016, 03:33:19 UTC CLI tutorial through step 3 17 February 2016, 03:33:19 UTC
68db885 isaacovercast 17 February 2016, 03:27:29 UTC More cleanup of full tutorial 17 February 2016, 03:27:29 UTC
8bb2b4f isaacovercast 17 February 2016, 03:19:02 UTC cosmetic changes to tutorial 17 February 2016, 03:19:02 UTC
c2928a1 isaacovercast 17 February 2016, 03:14:19 UTC Fixed bash commands in tutorial 17 February 2016, 03:14:19 UTC
b417273 isaacovercast 17 February 2016, 03:10:36 UTC full tutorial updates 17 February 2016, 03:10:36 UTC
928d0d7 isaacovercast 17 February 2016, 02:58:45 UTC Fixing bash code-blocks 17 February 2016, 02:58:45 UTC
d9a2903 isaacovercast 17 February 2016, 02:52:24 UTC Minor doc updates 17 February 2016, 02:52:24 UTC
bcc84df isaacovercast 17 February 2016, 02:15:14 UTC "Updating ipyrad/__init__.py to version - 0.1.49 17 February 2016, 02:15:14 UTC
ae0123b isaacovercast 17 February 2016, 02:14:33 UTC more CLI tutorial docs 17 February 2016, 02:14:33 UTC
427075c isaacovercast 17 February 2016, 00:31:57 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 17 February 2016, 00:31:57 UTC
34e8290 isaacovercast 17 February 2016, 00:31:14 UTC Initial commit for CLI full tutorial and advanced_CLI 17 February 2016, 00:31:14 UTC
7f45e86 deren 16 February 2016, 23:25:54 UTC "Updating ipyrad/__init__.py to version - 0.1.48 16 February 2016, 23:25:54 UTC
95f5988 deren 16 February 2016, 23:25:36 UTC new svd method framework added. See notebook 16 February 2016, 23:25:36 UTC
4875aed isaacovercast 16 February 2016, 22:56:48 UTC added -i flag to get parameter information at CLI from paramsinfo 16 February 2016, 22:56:48 UTC
8309555 isaacovercast 16 February 2016, 16:46:25 UTC zipped the test data so we can use it for the cli tutorial (users can wget the whole thing) 16 February 2016, 16:46:25 UTC
6521f15 isaacovercast 16 February 2016, 15:44:45 UTC more explicit error handling in the case of no samples in json 16 February 2016, 15:44:45 UTC
b00a1b8 isaacovercast 16 February 2016, 15:38:27 UTC Testing for empty samples in saved .json, if no samples in saved assembly then it raises an ipyradwarningexit. You can get into this situation somewhat easily, and it's better to handle explicitly bcz otherwise you get an index out of bounds error and it's ugly 16 February 2016, 15:38:27 UTC
4e5781a isaacovercast 16 February 2016, 15:26:54 UTC fixed an oops 16 February 2016, 15:26:54 UTC
3c50506 isaacovercast 16 February 2016, 15:11:38 UTC Allow CLI users to start assembly at step2 if they have already demultiplexed fq files. 16 February 2016, 15:11:38 UTC
df881d2 isaacovercast 16 February 2016, 14:57:47 UTC Change error handling in step 7 if output directory already exists, make it easier to see what's happening 16 February 2016, 14:57:47 UTC
0578e21 Isaac 16 February 2016, 14:39:23 UTC Fixed handle all indels for gbs during cluster_within, also handle samples in step 2.5 so they skip straight to muscle aligning 16 February 2016, 14:39:23 UTC
2d21111 Isaac 16 February 2016, 14:29:56 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 16 February 2016, 14:29:56 UTC
651c872 deren 16 February 2016, 05:45:19 UTC "Updating ipyrad/__init__.py to version - 0.1.47 16 February 2016, 05:45:19 UTC
b787587 deren 16 February 2016, 05:44:12 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 16 February 2016, 05:44:12 UTC
fde4960 deren 16 February 2016, 05:44:06 UTC fix to debugger and to launch for api 16 February 2016, 05:44:06 UTC
f542453 isaacovercast 15 February 2016, 23:53:08 UTC Fixed change to ipyrad.bins.* 15 February 2016, 23:53:08 UTC
30d090e deren 13 February 2016, 21:46:59 UTC "Updating ipyrad/__init__.py to version - 0.1.46 13 February 2016, 21:46:59 UTC
6685575 deren 13 February 2016, 21:46:43 UTC hack around __loglevel__ setter for __init__ 13 February 2016, 21:46:43 UTC
3c818d0 deren 13 February 2016, 21:42:41 UTC "Updating ipyrad/__init__.py to version - 0.1.45 13 February 2016, 21:42:41 UTC
388c015 deren 13 February 2016, 21:42:29 UTC fix to 0.1.44 bugs 13 February 2016, 21:42:29 UTC
299face deren 13 February 2016, 21:30:21 UTC "Updating ipyrad/__init__.py to version - 0.1.44 13 February 2016, 21:30:21 UTC
941e946 deren 13 February 2016, 21:30:08 UTC created custom JSON encoder class to conserve tuples and ascii 13 February 2016, 21:30:08 UTC
c9d8bea deren 13 February 2016, 21:29:37 UTC API access 13 February 2016, 21:29:37 UTC
752b603 deren 13 February 2016, 21:29:22 UTC fix to remove error on duplicates, and chunking code 13 February 2016, 21:29:22 UTC
89ae295 deren 13 February 2016, 21:28:55 UTC code cleanup 13 February 2016, 21:28:55 UTC
451ce88 deren 13 February 2016, 20:44:23 UTC fixed debugger for new setup 13 February 2016, 20:44:23 UTC
860d485 deren 13 February 2016, 17:06:04 UTC ensure Objdicts are loaded as Objdicts 13 February 2016, 17:06:04 UTC
df18c45 deren 13 February 2016, 17:05:33 UTC need to ensure names are ascii not unicode for hdf5 attributes. JSON loading pulls in unicode 13 February 2016, 17:05:33 UTC
cd1358f deren 13 February 2016, 03:19:53 UTC "Updating ipyrad/__init__.py to version - 0.1.43 13 February 2016, 03:19:53 UTC
f7af39f deren 13 February 2016, 03:19:22 UTC merge params file naming 13 February 2016, 03:19:22 UTC
79a8c6a deren 13 February 2016, 03:17:51 UTC json saving and loading 13 February 2016, 03:17:51 UTC
9ca92ee deren 13 February 2016, 03:17:23 UTC prettier printing 13 February 2016, 03:17:23 UTC
ccd0f26 deren 13 February 2016, 03:17:05 UTC bins placement 13 February 2016, 03:17:05 UTC
1e155ea deren 13 February 2016, 03:16:37 UTC bins are now ip.bins. not part of assembly 13 February 2016, 03:16:37 UTC
38d3025 deren 13 February 2016, 03:15:58 UTC params-name.txt naming. load from assembly or json 13 February 2016, 03:15:58 UTC
92aa9db deren 13 February 2016, 03:15:01 UTC debug file resets eventually. load_json and save_json added 13 February 2016, 03:15:01 UTC
ef6f75d isaacovercast 13 February 2016, 02:40:34 UTC Fixed new params.txt file creation to reflect the params-watever.txt format. 13 February 2016, 02:40:34 UTC
ccb12a0 isaacovercast 13 February 2016, 02:23:29 UTC Fixed getassembly so it accurately tests for current assemblies before creating a new one. Merge branch 'master' of https://github.com/dereneaton/ipyrad Conflicts: ipyrad/__main__.py 13 February 2016, 02:23:29 UTC
e1f5d24 isaacovercast 13 February 2016, 02:21:26 UTC Fixed CLI so it properly tests for existing assemblies and requests the -f flag if necessary 13 February 2016, 02:21:26 UTC
9d0ab27 Isaac 12 February 2016, 18:51:20 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 12 February 2016, 18:51:20 UTC
2682729 deren 12 February 2016, 01:26:03 UTC "Updating ipyrad/__init__.py to version - 0.1.42 12 February 2016, 01:26:03 UTC
707bf25 deren 12 February 2016, 01:25:53 UTC resolve merge conflict 12 February 2016, 01:25:53 UTC
e77e421 deren 12 February 2016, 01:18:54 UTC doubles count of merged reads 12 February 2016, 01:18:54 UTC
b7b4a9c deren 12 February 2016, 01:18:39 UTC merge pairs parallelized and with suffix 12 February 2016, 01:18:39 UTC
642b151 isaacovercast 12 February 2016, 01:18:05 UTC CLI branching works now 12 February 2016, 01:18:05 UTC
441c743 deren 12 February 2016, 01:18:00 UTC rigorous testing and improvements to clustering of pairgbs 12 February 2016, 01:18:00 UTC
79ca81e deren 12 February 2016, 01:17:27 UTC simple cleanup 12 February 2016, 01:17:27 UTC
ce1db7c deren 12 February 2016, 01:15:50 UTC simplification of logger 12 February 2016, 01:15:50 UTC
b21be9f isaacovercast 12 February 2016, 01:08:13 UTC Refactored preview_truncate_fq so now it actually works for all steps 1,2&3 added a third parameter that defaults to using 10% of the passed in file. Updated demult, rawed, and clust_wi in accordance. Also added try/except around shutil.rmtree calls to protect against the stupid nfs bug i was seeing. 12 February 2016, 01:08:13 UTC
e277fc1 deren 12 February 2016, 00:13:04 UTC need to build tests still, but getting closer.. 12 February 2016, 00:13:04 UTC
be4d379 deren 11 February 2016, 23:09:57 UTC upgrade vsearch. Read merging now parallelized 11 February 2016, 23:09:57 UTC
2563349 isaacovercast 11 February 2016, 22:02:23 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 11 February 2016, 22:02:23 UTC
a6fb904 deren 11 February 2016, 19:06:53 UTC "Updating ipyrad/__init__.py to version - 0.1.41 11 February 2016, 19:06:53 UTC
34d4c5b deren 11 February 2016, 19:06:22 UTC removed old vsearch 11 February 2016, 19:06:22 UTC
8f835dd deren 11 February 2016, 19:04:51 UTC upgrade vsearch to v.1.9.10. 11 February 2016, 19:04:51 UTC
8d23f91 deren 11 February 2016, 18:42:12 UTC some prettier printing for cli and for Errors. Better handling of edit_cutsites tuple 11 February 2016, 18:42:12 UTC
5597606 deren 11 February 2016, 18:41:40 UTC get sample file names for truncate from sample.name not sample.files.fastqs since fastqs are not necessarily in projdir/name_fastqs/ when step1 links_fastqs instead of demultiplexing 11 February 2016, 18:41:40 UTC
2753fb5 deren 11 February 2016, 18:40:29 UTC chdir into proj dir when creating new assembly, but stay in cur dir if just loading and load it from the full path to projdir/name 11 February 2016, 18:40:29 UTC
4a221b2 isaacovercast 11 February 2016, 18:17:50 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 11 February 2016, 18:17:50 UTC
cf75eba isaacovercast 11 February 2016, 18:17:37 UTC Error handling in assembly, and mostly done on -b for CLI 11 February 2016, 18:17:37 UTC
0c2b76f deren 11 February 2016, 17:50:17 UTC "Updating ipyrad/__init__.py to version - 0.1.40 11 February 2016, 17:50:17 UTC
507bca5 deren 11 February 2016, 17:49:58 UTC not in curdir, so don't collapse curdir path. print full path to assembly object 11 February 2016, 17:49:58 UTC
e8ecfe8 deren 11 February 2016, 17:49:31 UTC bug fix for too many open files, was loading multiple ip clients 11 February 2016, 17:49:31 UTC
6b786d0 deren 11 February 2016, 17:49:00 UTC correct orientation for unmerged pairs 11 February 2016, 17:49:00 UTC
5e68f2a deren 11 February 2016, 17:48:41 UTC loads assembly object from project_dir 11 February 2016, 17:48:41 UTC
16091d2 deren 11 February 2016, 17:19:27 UTC step2 does not do link_fastqs, but instead raises warning that step1 should be run 11 February 2016, 17:19:27 UTC
290a917 deren 11 February 2016, 17:19:02 UTC correct orientation of non-merged pairs 11 February 2016, 17:19:02 UTC
ecadfae deren 11 February 2016, 17:18:20 UTC -n flag takes a name argument 11 February 2016, 17:18:20 UTC
1fde58e deren 11 February 2016, 15:52:28 UTC merge fix 11 February 2016, 15:52:28 UTC
cdb1f30 Isaac 11 February 2016, 02:26:30 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 11 February 2016, 02:26:30 UTC
b49a125 isaacovercast 11 February 2016, 02:26:09 UTC oops. bad syntax fixed in cluster_within. 11 February 2016, 02:26:09 UTC
0c2ccb3 Isaac 11 February 2016, 02:24:49 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 11 February 2016, 02:24:49 UTC
6df9bfe isaacovercast 11 February 2016, 02:23:16 UTC Cosmetic merge fixes to documentation/print statements Merge branch 'master' of https://github.com/dereneaton/ipyrad Conflicts: ipyrad/__main__.py ipyrad/core/assembly.py 11 February 2016, 02:23:16 UTC
e372b4e isaacovercast 11 February 2016, 02:17:14 UTC 2/3 done with -b branching for cli 11 February 2016, 02:17:14 UTC
cb8432b isaacovercast 11 February 2016, 02:16:00 UTC Fixed #108 (handle all-indel reverse gbs reads) 11 February 2016, 02:16:00 UTC
9bebc62 deren 11 February 2016, 02:00:13 UTC "Updating ipyrad/__init__.py to version - 0.1.39 11 February 2016, 02:00:13 UTC
943f3a8 deren 11 February 2016, 01:59:39 UTC never need to launch during load. Old idea. 11 February 2016, 01:59:39 UTC
2492d42 deren 11 February 2016, 01:59:11 UTC faster connection to known number of cores. Cleaner interface to data._ipcluster dict. 11 February 2016, 01:59:11 UTC
562878d deren 11 February 2016, 01:58:38 UTC new launch command. Better handling for bad params args. Empty defaults for paths params. 11 February 2016, 01:58:38 UTC
a17e3af deren 11 February 2016, 01:57:53 UTC IPyradWarningExit acts like sys.exit 11 February 2016, 01:57:53 UTC
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