| 1b339f5 | Deren | 25 March 2023, 22:30:28 UTC | new cli subcomand parse | 25 March 2023, 22:30:28 UTC |
| 8bb0a69 | Deren | 25 March 2023, 22:27:55 UTC | pe detection fix | 25 March 2023, 22:27:55 UTC |
| 613c167 | Deren | 25 March 2023, 21:54:47 UTC | new demux sub package, new cli test | 25 March 2023, 21:54:47 UTC |
| 077f77c | Deren | 24 March 2023, 14:15:55 UTC | match bar from right side given maxlen in demux | 24 March 2023, 14:15:55 UTC |
| 03f7f19 | Deren | 23 March 2023, 19:29:38 UTC | maxlen during demux to reduce missing matches | 23 March 2023, 19:29:38 UTC |
| 4435db5 | Deren | 23 March 2023, 15:44:24 UTC | demux chunksize to 1e7 | 23 March 2023, 15:44:24 UTC |
| 5ff0656 | Deren | 23 March 2023, 14:53:16 UTC | cli logger args, demux bytes fix | 23 March 2023, 14:53:16 UTC |
| 360d6c1 | Deren | 23 March 2023, 12:48:50 UTC | demux multi writer | 23 March 2023, 12:48:50 UTC |
| 722d591 | Deren | 22 March 2023, 23:00:08 UTC | demux faster using bytes instead of str | 22 March 2023, 23:00:08 UTC |
| 3c8c3dd | Deren | 22 March 2023, 22:59:15 UTC | demux faster using bytes instead of str | 22 March 2023, 22:59:15 UTC |
| 6bf1011 | Deren | 22 March 2023, 22:54:18 UTC | demux faster using bytes instead of str | 22 March 2023, 22:54:18 UTC |
| 2a87bc4 | Deren | 22 March 2023, 22:10:38 UTC | logger calls removed from demux | 22 March 2023, 22:10:38 UTC |
| 8005692 | Deren | 22 March 2023, 21:35:23 UTC | chunksize increased | 22 March 2023, 21:35:23 UTC |
| 7671040 | Deren | 22 March 2023, 21:20:51 UTC | cosmetic | 22 March 2023, 21:20:51 UTC |
| 3eb9e4c | Deren | 22 March 2023, 21:20:36 UTC | logger during demux | 22 March 2023, 21:20:36 UTC |
| d95c5cf | Deren | 22 March 2023, 21:20:18 UTC | nsites calc in nex output | 22 March 2023, 21:20:18 UTC |
| 2f17dab | Deren | 22 March 2023, 21:20:01 UTC | cores typo | 22 March 2023, 21:20:01 UTC |
| c0d8d43 | Deren | 21 March 2023, 18:35:12 UTC | cosmetic | 21 March 2023, 18:35:12 UTC |
| 5223053 | Deren | 21 March 2023, 18:34:54 UTC | analysis names loading | 21 March 2023, 18:34:54 UTC |
| 923a9cb | Deren | 21 March 2023, 18:34:03 UTC | ncores cli arg | 21 March 2023, 18:34:03 UTC |
| f95d9d8 | Deren | 21 March 2023, 18:33:07 UTC | testing cons refaligned | 21 March 2023, 18:33:07 UTC |
| 8e26ca2 | Deren | 21 March 2023, 18:32:05 UTC | new estimate trim position func | 21 March 2023, 18:32:05 UTC |
| bbeb377 | Deren | 21 March 2023, 18:31:09 UTC | chrom2ints with Path or str fname | 21 March 2023, 18:31:09 UTC |
| a82ad6a | Deren | 21 March 2023, 18:29:47 UTC | misnamed indels filter | 21 March 2023, 18:29:47 UTC |
| c2c9b60 | Deren | 21 March 2023, 18:28:38 UTC | add python 3.11 to cfg | 21 March 2023, 18:28:38 UTC |
| c7c9493 | Deren | 05 March 2023, 16:29:53 UTC | cores arg in cli | 05 March 2023, 16:29:53 UTC |
| c1cb811 | Deren | 05 March 2023, 16:29:07 UTC | iter func for building clusters for better debugging | 05 March 2023, 16:29:07 UTC |
| 7f287ab | Deren | 05 March 2023, 16:28:28 UTC | fix pe joined files suffix is now fastq | 05 March 2023, 16:28:28 UTC |
| 0ef4af4 | Deren | 05 March 2023, 16:27:19 UTC | fix for quiet args in demux | 05 March 2023, 16:27:19 UTC |
| 5544534 | Deren | 05 March 2023, 16:27:04 UTC | fix for quiet args in demux | 05 March 2023, 16:27:04 UTC |
| 9abb325 | Deren | 21 February 2023, 17:11:36 UTC | cosmetic | 21 February 2023, 17:11:36 UTC |
| 406de0b | Deren | 21 February 2023, 17:11:20 UTC | pd df filter indexing cleanup. | 21 February 2023, 17:11:20 UTC |
| 21e1fc0 | Deren | 21 February 2023, 17:10:43 UTC | only set state to 7 for step samples. | 21 February 2023, 17:10:43 UTC |
| 4e059d7 | Deren | 21 February 2023, 17:10:11 UTC | clear old results | 21 February 2023, 17:10:11 UTC |
| 0b32c9e | Deren | 21 February 2023, 17:09:57 UTC | cosmetic | 21 February 2023, 17:09:57 UTC |
| 0c2f8df | Deren | 21 February 2023, 17:09:42 UTC | clear old stats. Drop empty samples and store nans. | 21 February 2023, 17:09:42 UTC |
| da06cf4 | Deren | 21 February 2023, 17:09:14 UTC | cosmetic | 21 February 2023, 17:09:14 UTC |
| 5e8f898 | Deren | 21 February 2023, 17:08:56 UTC | added NoHighDepthClustersError | 21 February 2023, 17:08:56 UTC |
| e14d78f | Deren | 21 February 2023, 17:08:33 UTC | raise and catch error on NoHighDepthClusters. Clear old results. | 21 February 2023, 17:08:33 UTC |
| be73b50 | Deren | 21 February 2023, 17:08:04 UTC | raise and catch error on NoHighDepthClusters | 21 February 2023, 17:08:04 UTC |
| ce86866 | Deren | 21 February 2023, 17:07:33 UTC | clear old results, show only kept samples in stats. | 21 February 2023, 17:07:33 UTC |
| 48aa3b1 | Deren | 21 February 2023, 17:06:44 UTC | cosmetic | 21 February 2023, 17:06:44 UTC |
| e0857b9 | Deren | 21 February 2023, 17:06:09 UTC | clear_old_results func for branching | 21 February 2023, 17:06:09 UTC |
| 061d487 | Deren | 20 February 2023, 14:09:57 UTC | handle empty tmp align files | 20 February 2023, 14:09:57 UTC |
| 8e22e71 | Deren | 20 February 2023, 14:01:07 UTC | cleanup | 20 February 2023, 14:01:07 UTC |
| cc3985b | Deren | 20 February 2023, 14:00:44 UTC | decided on using .seqs.hdf5 not _ separator | 20 February 2023, 14:00:44 UTC |
| 60c2e2f | Deren | 20 February 2023, 13:59:56 UTC | comment debugging | 20 February 2023, 13:59:56 UTC |
| 9ecd666 | Deren | 20 February 2023, 13:59:23 UTC | pathlib updates | 20 February 2023, 13:59:23 UTC |
| 54be11a | Deren | 20 February 2023, 13:58:18 UTC | cosmetic | 20 February 2023, 13:58:18 UTC |
| 36e56b3 | Deren | 20 February 2023, 13:57:49 UTC | cosmetic | 20 February 2023, 13:57:49 UTC |
| 8af8b64 | Deren | 20 February 2023, 13:57:28 UTC | allow for empty alignment tmp files on small samples | 20 February 2023, 13:57:28 UTC |
| a9828b4 | Deren | 28 December 2022, 18:03:00 UTC | cosmetic | 28 December 2022, 18:03:00 UTC |
| 7763104 | Deren | 28 December 2022, 18:01:53 UTC | cosmetic | 28 December 2022, 18:01:53 UTC |
| f00939e | Deren | 28 December 2022, 18:01:35 UTC | trim N from spacer edges in pair data | 28 December 2022, 18:01:35 UTC |
| a490404 | Deren | 28 December 2022, 18:00:46 UTC | comment debug | 28 December 2022, 18:00:46 UTC |
| 9cda467 | Deren | 28 December 2022, 18:00:25 UTC | split batmatcher to other file; better error msg on bad barcodes file. | 28 December 2022, 18:00:25 UTC |
| 2a700e0 | Deren | 28 December 2022, 17:59:12 UTC | cosmetic | 28 December 2022, 17:59:12 UTC |
| 59f1e5f | Deren | 28 December 2022, 17:58:38 UTC | when nnnn separator is variably present, choose most common type | 28 December 2022, 17:58:38 UTC |
| 17a7424 | Deren | 28 December 2022, 17:57:16 UTC | cli exits on finish | 28 December 2022, 17:57:16 UTC |
| c76aa8e | Deren | 28 December 2022, 17:56:29 UTC | logging | 28 December 2022, 17:56:29 UTC |
| fc727a7 | Deren | 28 December 2022, 17:56:04 UTC | write params descriptions | 28 December 2022, 17:56:04 UTC |
| 539c1a4 | Deren | 20 December 2022, 04:35:50 UTC | new fast lowmem vcf writer w/ depths | 20 December 2022, 04:35:50 UTC |
| d2c3b87 | Deren | 15 December 2022, 16:50:19 UTC | shift table comments | 15 December 2022, 16:50:19 UTC |
| 3be4f28 | Deren | 15 December 2022, 16:45:02 UTC | IPyradExit explicitly for clean SystemExit calls | 15 December 2022, 16:45:02 UTC |
| 25b10ee | Deren | 15 December 2022, 16:43:24 UTC | fast denovo vcf build, but not yet w/ depths | 15 December 2022, 16:43:24 UTC |
| ef9bbcc | Deren | 15 December 2022, 16:42:51 UTC | save and load stats and outfiles | 15 December 2022, 16:42:51 UTC |
| 1a95eb7 | Deren | 15 December 2022, 16:42:12 UTC | new shift table method for denovo snp depths | 15 December 2022, 16:42:12 UTC |
| 12fa60a | Deren | 08 December 2022, 23:16:06 UTC | cli update | 08 December 2022, 23:16:06 UTC |
| 85c4b2e | Deren | 08 December 2022, 23:15:12 UTC | step7 rerun cleaning | 08 December 2022, 23:15:12 UTC |
| e14e80f | Deren | 08 December 2022, 23:13:29 UTC | step7 database writing | 08 December 2022, 23:13:29 UTC |
| bc7c392 | Deren | 04 December 2022, 06:49:26 UTC | step7 h5 reformat working | 04 December 2022, 06:49:26 UTC |
| e4572af | Deren | 29 November 2022, 20:25:31 UTC | add comments and remove glob import | 29 November 2022, 20:25:31 UTC |
| c0af027 | Deren | 09 November 2022, 18:02:42 UTC | cosmetic | 09 November 2022, 18:02:42 UTC |
| 982f948 | Deren | 09 November 2022, 18:01:38 UTC | debugging cli parsing | 09 November 2022, 18:01:38 UTC |
| a2600f0 | Deren | 26 October 2022, 16:54:32 UTC | cosmetic | 26 October 2022, 16:54:32 UTC |
| ee89798 | Deren | 01 October 2022, 17:17:35 UTC | reworking to simplify with both class | 01 October 2022, 17:17:35 UTC |
| 4e9b185 | Deren | 01 October 2022, 17:17:05 UTC | moved decloning to both | 01 October 2022, 17:17:05 UTC |
| b364c12 | Deren | 01 October 2022, 17:16:47 UTC | add comments and sample sorting | 01 October 2022, 17:16:47 UTC |
| d3c63a9 | Deren | 01 October 2022, 17:15:59 UTC | declone moved to 'both' | 01 October 2022, 17:15:59 UTC |
| acf8266 | Deren | 12 September 2022, 16:15:53 UTC | path to input from ref method | 12 September 2022, 16:15:53 UTC |
| ce0a292 | Deren | 12 September 2022, 16:15:28 UTC | cosmetic | 12 September 2022, 16:15:28 UTC |
| b63879d | Deren | 12 September 2022, 12:38:38 UTC | reorganized to use Locus object | 12 September 2022, 12:38:38 UTC |
| 951e64c | Deren | 12 September 2022, 12:38:08 UTC | denovo pe insert masking improved | 12 September 2022, 12:38:08 UTC |
| 2ac4e51 | Deren | 12 September 2022, 12:37:19 UTC | import path update | 12 September 2022, 12:37:19 UTC |
| d58017c | Deren | 12 September 2022, 12:37:03 UTC | import path update | 12 September 2022, 12:37:03 UTC |
| db0f2c7 | Deren | 12 September 2022, 12:36:47 UTC | clear stats in step class | 12 September 2022, 12:36:47 UTC |
| 93c9cbf | Deren | 12 September 2022, 12:36:28 UTC | RE is trimmed in step2 by default, suppress w/ negative values | 12 September 2022, 12:36:28 UTC |
| 34cf5f4 | Deren | 12 September 2022, 12:35:58 UTC | split within steps into shared and unique files" | 12 September 2022, 12:35:58 UTC |
| 1796fe5 | Deren | 12 September 2022, 12:35:16 UTC | s6 denovo generator alignments | 12 September 2022, 12:35:16 UTC |
| 8ddc7d6 | Deren | 12 September 2022, 12:34:30 UTC | shift to toml | 12 September 2022, 12:34:30 UTC |
| 4548947 | Deren | 08 September 2022, 19:38:20 UTC | use same mapping minus func, pathfix for checking index exists | 08 September 2022, 19:38:20 UTC |
| 8f0bd0f | Deren | 30 August 2022, 13:57:31 UTC | update bounds on lik optimization | 30 August 2022, 13:57:31 UTC |
| 3e935f9 | Deren | 30 August 2022, 13:49:23 UTC | docstring update | 30 August 2022, 13:49:23 UTC |
| 4ae5169 | Deren | 30 August 2022, 13:44:18 UTC | added comment | 30 August 2022, 13:44:18 UTC |
| 4403550 | Deren | 30 August 2022, 13:43:54 UTC | bugfix, min h5 chunk size | 30 August 2022, 13:43:54 UTC |
| ac22ee9 | Deren | 30 August 2022, 13:43:09 UTC | added debug func for testing | 30 August 2022, 13:43:09 UTC |
| 4d9d5ce | Deren | 29 August 2022, 17:51:54 UTC | added step check if s1 has not been run | 29 August 2022, 17:51:54 UTC |
| 92a8f31 | Deren | 29 August 2022, 17:51:32 UTC | comment out async run | 29 August 2022, 17:51:32 UTC |
| a4c1d98 | Deren | 29 August 2022, 17:51:14 UTC | trim reads arglen=2, store sample filepaths as strs | 29 August 2022, 17:51:14 UTC |
| 7f1cb24 | Deren | 29 August 2022, 17:46:17 UTC | Trim inline barcodes furing demux | 29 August 2022, 17:46:17 UTC |
