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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
80182fe deren 28 November 2016, 08:12:20 UTC "Updating ipyrad/__init__.py to version - 0.5.8 28 November 2016, 08:12:20 UTC
d998c39 deren 28 November 2016, 08:11:49 UTC improved progress bar 28 November 2016, 08:11:49 UTC
15f04dc deren 28 November 2016, 07:20:53 UTC merge fix 28 November 2016, 07:20:53 UTC
127c429 deren 28 November 2016, 07:19:19 UTC notebook testing geno build 28 November 2016, 07:19:19 UTC
13fdf6d deren 28 November 2016, 07:19:01 UTC Fix to memory handling on vcf build, can now handle thousands of taxa. Also, now saves filepaths to json and API object. 28 November 2016, 07:19:01 UTC
ffddbb6 deren 28 November 2016, 07:17:57 UTC progres on dstats package 28 November 2016, 07:17:57 UTC
b25c37f Isaac 26 November 2016, 22:59:01 UTC More progress on manuscript horserace. Analysis is done, now mostly working on gathering results. 26 November 2016, 22:59:01 UTC
d5aa749 isaacovercast 26 November 2016, 22:27:11 UTC "Updating ipyrad/__init__.py to version - 0.5.7 26 November 2016, 22:27:11 UTC
d4dafd7 isaacovercast 26 November 2016, 22:26:58 UTC Fix error handing during writing of vcf file. 26 November 2016, 22:26:58 UTC
30f9bcc deren 23 November 2016, 23:28:52 UTC "Updating ipyrad/__init__.py to version - 0.5.6 23 November 2016, 23:28:52 UTC
8bdd218 deren 23 November 2016, 23:26:52 UTC "Updating ipyrad/__init__.py to version - 0.5.6 23 November 2016, 23:26:52 UTC
2a38476 deren 23 November 2016, 23:25:09 UTC "Updating ipyrad/__init__.py to version - 0.5.6 23 November 2016, 23:25:09 UTC
ac3555f deren 23 November 2016, 23:23:15 UTC "Updating ipyrad/__init__.py to version - 0.5.6 23 November 2016, 23:23:15 UTC
58c5746 deren 23 November 2016, 23:19:14 UTC "Updating ipyrad/__init__.py to version - 0.5.6 23 November 2016, 23:19:14 UTC
1f6222f deren 23 November 2016, 23:16:20 UTC notebook testing 23 November 2016, 23:16:20 UTC
0c3d646 deren 23 November 2016, 23:14:27 UTC purge after each step to avoid memory spillover/buildup 23 November 2016, 23:14:27 UTC
545f621 deren 23 November 2016, 23:13:49 UTC better handling of memory limits in vcf build. Now producing geno output files. Better error reporting when building output files 23 November 2016, 23:13:49 UTC
8511315 deren 23 November 2016, 23:12:53 UTC added a global dict to util 23 November 2016, 23:12:53 UTC
9bfbdab deren 23 November 2016, 23:12:36 UTC new smaller limit of chunk sizes in h5 to avoid memory limits 23 November 2016, 23:12:36 UTC
8f444b6 deren 23 November 2016, 23:11:28 UTC analysis docs update 23 November 2016, 23:11:28 UTC
ad5a656 isaacovercast 21 November 2016, 21:21:31 UTC Document weird non-writable home directory on cluster issues. 21 November 2016, 21:21:31 UTC
787692f deren 21 November 2016, 19:31:16 UTC docs update for filtering differences 21 November 2016, 19:31:16 UTC
5ee57ff deren 21 November 2016, 19:15:05 UTC merge fix 21 November 2016, 19:15:05 UTC
df8a807 deren 21 November 2016, 19:10:56 UTC tetrad notebook edits 21 November 2016, 19:10:56 UTC
17ecabe deren 21 November 2016, 19:10:44 UTC dstat calc script editing 21 November 2016, 19:10:44 UTC
91c7f65 iovercast 18 November 2016, 19:17:00 UTC Added code to copy barcodes during assembly merge. Barcodes are needed for all PE samples in step 2. 18 November 2016, 19:17:00 UTC
2659090 isaacovercast 17 November 2016, 21:12:33 UTC "Updating ipyrad/__init__.py to version - 0.5.5 17 November 2016, 21:12:33 UTC
b6b4ae9 isaacovercast 17 November 2016, 20:33:03 UTC Better handling for PE with loci that have some merged and some unmerged reads. 17 November 2016, 20:33:03 UTC
aa4b8ba isaacovercast 17 November 2016, 20:27:16 UTC Allow other output formats to try to build if vcf fails. 17 November 2016, 20:27:16 UTC
e2ae882 isaacovercast 17 November 2016, 19:38:07 UTC Fixed bug that was forcing creation of the vcf even if it wasn't requested. 17 November 2016, 19:38:07 UTC
63ec592 isaacovercast 17 November 2016, 00:40:43 UTC "Updating ipyrad/__init__.py to version - 0.5.4 17 November 2016, 00:40:43 UTC
9e7d9ec isaacovercast 17 November 2016, 00:40:30 UTC More improved handling for low/no depth samples. 17 November 2016, 00:40:30 UTC
7b1cf01 isaacovercast 17 November 2016, 00:23:09 UTC Better handling for cleanup of samples with very few reads. 17 November 2016, 00:23:09 UTC
25ff3b8 isaacovercast 16 November 2016, 01:58:44 UTC "Updating ipyrad/__init__.py to version - 0.5.3 16 November 2016, 01:58:44 UTC
fa603e5 isaacovercast 16 November 2016, 01:58:26 UTC Catch sample names that don't match barcode names when importing demux'd pair data. 16 November 2016, 01:58:26 UTC
e84d29e isaacovercast 16 November 2016, 01:57:02 UTC Serious errors now print to ipyrad_log.txt by default. 16 November 2016, 01:57:02 UTC
9c292a8 isaacovercast 15 November 2016, 18:55:31 UTC "Updating ipyrad/__init__.py to version - 0.5.2 15 November 2016, 18:55:31 UTC
edc857c isaacovercast 15 November 2016, 18:55:14 UTC Handle sample cleanup if the sample has no hidepth clusters. 15 November 2016, 18:55:14 UTC
111f9cf isaacovercast 15 November 2016, 18:23:10 UTC Fix for declone_3rad on merged reads. 15 November 2016, 18:23:10 UTC
68bd8be isaacovercast 12 November 2016, 18:26:25 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 12 November 2016, 18:26:25 UTC
f4a2d38 isaacovercast 12 November 2016, 18:26:22 UTC Better support for 3rad lining presorted fastqs. 12 November 2016, 18:26:22 UTC
95ab585 dereneaton 11 November 2016, 14:14:07 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 11 November 2016, 14:14:07 UTC
c4402f1 dereneaton 11 November 2016, 14:13:58 UTC bucky cookbook updated 11 November 2016, 14:13:58 UTC
a26e47d deren 11 November 2016, 14:01:24 UTC docs update 11 November 2016, 14:01:24 UTC
61433dc deren 10 November 2016, 22:59:14 UTC docs update 10 November 2016, 22:59:14 UTC
2db706b deren 10 November 2016, 22:56:10 UTC dstat updates 10 November 2016, 22:56:10 UTC
fa732c7 deren 10 November 2016, 18:33:06 UTC docs update 10 November 2016, 18:33:06 UTC
9f2a505 deren 09 November 2016, 00:46:03 UTC docs update 09 November 2016, 00:46:03 UTC
10dc737 deren 09 November 2016, 00:35:50 UTC docs update 09 November 2016, 00:35:50 UTC
b63e11e deren 09 November 2016, 00:23:24 UTC docs update 09 November 2016, 00:23:24 UTC
287d346 deren 09 November 2016, 00:00:52 UTC docs update 09 November 2016, 00:00:52 UTC
4356ac0 deren 08 November 2016, 23:36:42 UTC docs updates 08 November 2016, 23:36:42 UTC
00c3720 deren 08 November 2016, 23:30:38 UTC docs update 08 November 2016, 23:30:38 UTC
746f3ee deren 08 November 2016, 23:13:49 UTC bucky cookbook uploaded 08 November 2016, 23:13:49 UTC
e4d2556 deren 08 November 2016, 19:48:17 UTC "Updating ipyrad/__init__.py to version - 0.5.1 08 November 2016, 19:48:17 UTC
57efc33 deren 08 November 2016, 19:10:31 UTC docs update 08 November 2016, 19:10:31 UTC
7af9b15 deren 08 November 2016, 18:53:11 UTC docs update 08 November 2016, 18:53:11 UTC
f6c4f94 deren 08 November 2016, 18:50:14 UTC docs update 08 November 2016, 18:50:14 UTC
a2e5a6e deren 08 November 2016, 18:34:30 UTC cosmetic changes 08 November 2016, 18:34:30 UTC
2b14798 deren 08 November 2016, 18:34:16 UTC cosmetic changes 08 November 2016, 18:34:16 UTC
b44eed9 deren 08 November 2016, 18:32:48 UTC updating docs 08 November 2016, 18:32:48 UTC
c5b0c09 deren 08 November 2016, 18:25:02 UTC updating docs 08 November 2016, 18:25:02 UTC
ade3fc7 deren 08 November 2016, 18:23:10 UTC updating docs 08 November 2016, 18:23:10 UTC
b019e53 deren 08 November 2016, 18:20:53 UTC updating docs 08 November 2016, 18:20:53 UTC
84ba37a deren 08 November 2016, 18:18:30 UTC updating docs 08 November 2016, 18:18:30 UTC
ed06ce1 deren 08 November 2016, 18:09:48 UTC updating docs 08 November 2016, 18:09:48 UTC
259c761 deren 08 November 2016, 18:02:13 UTC updating docs 08 November 2016, 18:02:13 UTC
5b8975f deren 08 November 2016, 17:57:35 UTC updating docs 08 November 2016, 17:57:35 UTC
4901c72 deren 08 November 2016, 17:45:34 UTC updating docs 08 November 2016, 17:45:34 UTC
111476e deren 08 November 2016, 01:25:09 UTC added some tetrad docs 08 November 2016, 01:25:09 UTC
b66a8cf deren 08 November 2016, 01:21:35 UTC make tetrad work through API 08 November 2016, 01:21:35 UTC
7f34e87 deren 08 November 2016, 01:21:12 UTC added tetrad notebook 08 November 2016, 01:21:12 UTC
309427a isaacovercast 06 November 2016, 23:54:25 UTC "Updating ipyrad/__init__.py to version - 0.5.0 06 November 2016, 23:54:25 UTC
052db13 isaacovercast 06 November 2016, 23:53:58 UTC Swap out smalt for bwa inside refmapping. Also removes reindexing of reference sequence on -f in step 3. 06 November 2016, 23:53:58 UTC
f150604 deren 06 November 2016, 21:06:37 UTC . 06 November 2016, 21:06:37 UTC
d0a2552 deren 06 November 2016, 20:59:39 UTC "Updating ipyrad/__init__.py to version - 0.4.9 06 November 2016, 20:59:39 UTC
c509a83 deren 06 November 2016, 20:59:23 UTC fix for array error that was hitting in Ed's data, related to 2X count for merged reads. This is now removed. 06 November 2016, 20:59:23 UTC
093c8af deren 06 November 2016, 18:54:34 UTC bug fix for 4/4 entries in vcf when -N at variable site. 06 November 2016, 18:54:34 UTC
958fb0d deren 06 November 2016, 18:38:29 UTC prettier printing of stats file 06 November 2016, 18:38:29 UTC
eef3420 deren 05 November 2016, 21:31:32 UTC "Updating ipyrad/__init__.py to version - 0.4.9 05 November 2016, 21:31:32 UTC
edd49c8 deren 05 November 2016, 21:25:42 UTC hotfix for large array size bug introduced in last update 05 November 2016, 21:25:42 UTC
ab85da8 isaacovercast 05 November 2016, 17:00:10 UTC "Updating ipyrad/__init__.py to version - 0.4.8 05 November 2016, 17:00:10 UTC
7957906 deren 05 November 2016, 16:00:35 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 05 November 2016, 16:00:35 UTC
28b777c deren 05 November 2016, 16:00:30 UTC fix for geno output 05 November 2016, 16:00:30 UTC
e1a1631 deren 05 November 2016, 16:00:09 UTC bug fix to measure array dims from mindepth settings, uses statistical for s4, and majrule for s5 05 November 2016, 16:00:09 UTC
bfa7f0b isaacovercast 04 November 2016, 19:50:39 UTC adding mac bwa binary 04 November 2016, 19:50:39 UTC
269d572 iovercast 04 November 2016, 19:33:34 UTC Adding bwa binary for linux. 04 November 2016, 19:33:34 UTC
7b02ba8 deren 04 November 2016, 19:09:41 UTC improved N removal from edges of paired reads with variable lengths 04 November 2016, 19:09:41 UTC
d26be03 deren 03 November 2016, 22:40:53 UTC new parsing of output formats, and fewer defaults 03 November 2016, 22:40:53 UTC
8b457b5 deren 03 November 2016, 22:40:08 UTC only snps in the vcf is new default. Added pair support but still need to decide on spacer default. New cleaner output-formats stored as a tuple 03 November 2016, 22:40:08 UTC
973c17b deren 03 November 2016, 19:37:00 UTC small fix for better error catching 03 November 2016, 19:37:00 UTC
2016f2a deren 03 November 2016, 19:36:34 UTC new hidepth_min attr to save the mindepth setting at the time when it is used 03 November 2016, 19:36:34 UTC
a61fe6c deren 03 November 2016, 19:35:38 UTC mindepth settings are now checked separately from other parameters before 'run' to see if they are incompatible. Avoids race between the two being compared individually in set-params. 03 November 2016, 19:35:38 UTC
ea4606a deren 03 November 2016, 19:34:07 UTC new functions in steps 3-5 to accomodate changes to mindepth settings so that clusters-hidepth can be dynamically recalculated 03 November 2016, 19:34:07 UTC
9873aca deren 03 November 2016, 00:30:06 UTC fix to tunnel doc 03 November 2016, 00:30:06 UTC
7303939 deren 02 November 2016, 23:20:10 UTC "Updating ipyrad/__init__.py to version - 0.4.7 02 November 2016, 23:20:10 UTC
37c3c5a deren 02 November 2016, 23:20:00 UTC hotfix for step5 sample save bug. pushed to soon 02 November 2016, 23:20:00 UTC
2f1aec8 deren 02 November 2016, 23:06:35 UTC "Updating ipyrad/__init__.py to version - 0.4.7 02 November 2016, 23:06:35 UTC
ceab488 deren 02 November 2016, 23:05:56 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 02 November 2016, 23:05:56 UTC
096a474 deren 02 November 2016, 23:05:48 UTC make compatible with changes to s6 02 November 2016, 23:05:48 UTC
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