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https://github.com/kussell-lab/ReferenceAlignmentGenerator
18 February 2022, 11:37:47 UTC
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RevisionAuthorDateMessageCommit Date
49bf399 Asher Preska Steinberg07 February 2022, 16:12:20 UTCCommit for ReduceCoreGenome07 February 2022, 16:12:20 UTC
86759f7 Asher Preska Steinberg07 February 2022, 16:10:21 UTCCommit for ReduceCoreGenome07 February 2022, 16:10:21 UTC
ada21ba Asher Preska Steinberg29 October 2021, 14:16:15 UTCREADME update29 October 2021, 14:16:15 UTC
e03b82e Asher Preska Steinberg16 September 2021, 15:51:53 UTCtest commit16 September 2021, 15:51:53 UTC
de01041 Asher Preska Steinberg16 September 2021, 15:33:24 UTCUpdated README.md16 September 2021, 15:33:24 UTC
129fbdc Asher Preska Steinberg24 June 2021, 13:48:07 UTCUpdates to README.md and commits for hinfluenzae example24 June 2021, 13:48:07 UTC
f59a2af Asher Preska Steinberg23 June 2021, 19:59:02 UTCUpdates to README.md; deletion of hpc_submissions folder23 June 2021, 19:59:02 UTC
165c191 Asher Preska Steinberg23 June 2021, 19:42:27 UTCUpdates to README.md for publication; Example with H. influenzae23 June 2021, 19:42:27 UTC
ca9768e Asher Preska Steinberg23 June 2021, 18:41:55 UTCmaking RefAligner CLI23 June 2021, 18:41:55 UTC
6ae7ae6 Asher Preska Steinberg23 June 2021, 17:21:56 UTCmaking RefAligner CLI23 June 2021, 17:21:56 UTC
6a9e043 Asher Preska Steinberg22 June 2021, 22:37:17 UTCcleaning up currentbio branch22 June 2021, 22:37:17 UTC
1d15a9c Asher Preska Steinberg22 June 2021, 22:35:59 UTCcleaning up currentbio branch22 June 2021, 22:35:59 UTC
b8e7b84 Asher Preska Steinberg22 June 2021, 22:18:33 UTCcleaning up currentbio branch22 June 2021, 22:18:33 UTC
d13ad48 Asher Preska Steinberg22 June 2021, 22:18:15 UTCcleaning up currentbio branch22 June 2021, 22:18:15 UTC
32054fe Asher Preska Steinberg22 June 2021, 22:13:01 UTCcleaning up currentbio branch22 June 2021, 22:13:01 UTC
82c69f3 Asher Preska Steinberg22 June 2021, 20:38:49 UTCupdated readme for currentbio branch22 June 2021, 20:38:49 UTC
57a651f Asher Preska Steinberg22 June 2021, 20:33:23 UTCSecond test commit for currentbio branch22 June 2021, 20:33:23 UTC
61fb958 Asher Preska Steinberg22 June 2021, 20:30:51 UTCtest commit for currentbio branch ...22 June 2021, 20:30:51 UTC
58a33d0 Asher Preska Steinberg22 June 2021, 20:29:58 UTCtest commit for currentbio branch ...22 June 2021, 20:29:58 UTC
b282478 Asher Preska Steinberg22 June 2021, 19:23:58 UTCAPS202 submission script commits22 June 2021, 19:23:58 UTC
2188ea9 Asher Preska Steinberg19 May 2021, 00:42:31 UTCAPS180 submission scripts; APS183-190 submission scripts, APS192-202 submission scripts; ReduceCoreGenome commit19 May 2021, 00:42:31 UTC
03cc5d7 Asher Preska Steinberg30 March 2021, 14:39:30 UTCAPS180 commit for GeneBins code; Additional commits for APS169, and slurm submission scripts for APS170, APS171, and APS17330 March 2021, 14:39:30 UTC
d92b48f Asher Preska Steinberg10 March 2021, 15:15:52 UTCAPS168-169 commits; commit of FilterGaps to filter gapped alignments; commit of updated version of SplitGenome to split into core and flexible genomes after gap filtering; submission scripts10 March 2021, 15:15:52 UTC
bb3aaa9 Asher Preska Steinberg05 March 2021, 20:14:12 UTCAPS168 commits; commit of FilterGaps to filter gapped alignments05 March 2021, 20:14:12 UTC
30aeef1 Asher Preska Steinberg24 February 2021, 15:33:56 UTCAPS168 further cleanup; incorporation of appropriate go packages from both PangenomeAlignmentGenerator and go-misc24 February 2021, 15:33:56 UTC
4a618e4 Asher Preska Steinberg24 February 2021, 15:22:57 UTCAPS168 cleanup24 February 2021, 15:22:57 UTC
9b66eec Asher Preska Steinberg01 December 2020, 16:25:47 UTCAPS156 fetchnmap_v2 readme file01 December 2020, 16:25:47 UTC
00c7ccb Asher Preska Steinberg28 November 2020, 17:12:15 UTCAPS156 fetchnmap; mapncleantars for unpacking tarballs and mapping them28 November 2020, 17:12:15 UTC
06a5764 Asher Preska Steinberg28 November 2020, 16:39:45 UTCAPS156 fetchnmap gnu parallel speedup28 November 2020, 16:39:45 UTC
3fdad27 Asher Preska Steinberg27 November 2020, 18:48:37 UTCAPS156 fetchnmap package edits; "mapnclean" deploy to HPC27 November 2020, 18:48:37 UTC
85657d4 Asher Preska Steinberg26 November 2020, 18:47:28 UTCAPS156 fetchnmap package v1 with tarball compression for downloads26 November 2020, 18:47:28 UTC
f676bf7 Asher Preska Steinberg25 November 2020, 21:22:35 UTCAPS156 fetchnmap package fix for running multiple parallel jobs25 November 2020, 21:22:35 UTC
484d9e2 Asher Preska Steinberg25 November 2020, 16:04:00 UTCAPS156 fetchnmap package fix to setuptools to include non-python files in package install25 November 2020, 16:04:00 UTC
1eec005 Asher Preska Steinberg25 November 2020, 15:03:34 UTCAPS156 potential speedup for fetchnmap package25 November 2020, 15:03:34 UTC
0a68df1 Asher Preska Steinberg24 November 2020, 21:33:59 UTCAPS156 edit to fetchnmap package24 November 2020, 21:33:59 UTC
bbf675e Asher Preska Steinberg24 November 2020, 18:49:33 UTCAPS156 initial commit for fetchnmap package24 November 2020, 18:49:33 UTC
a739c19 Asher Preska Steinberg20 October 2020, 16:58:24 UTCTrying a speed up for FetchSRA_APS2.py; also updates for ReferenceAlignmentGenerateENA20 October 2020, 16:58:24 UTC
e127e8d Asher Preska Steinberg29 September 2020, 21:35:45 UTCAPS138 updated ReferenceAlignmentGenerateENA29 September 2020, 21:35:45 UTC
1544fa1 Asher Preska Steinberg14 September 2020, 16:39:18 UTCref alignments from ENA using ftp client14 September 2020, 16:39:18 UTC
35bc3d2 Asher Preska Steinberg14 September 2020, 14:35:05 UTCcorrection of small error in FetchENA.py14 September 2020, 14:35:05 UTC
78b462c Asher Preska Steinberg14 September 2020, 14:30:42 UTCupdate to FetchENA; looks for existing files and utilizes NYU HPC dtn14 September 2020, 14:30:42 UTC
9c3bf33 Asher Preska Steinberg12 September 2020, 23:21:30 UTCAlignments for sra files from ENA12 September 2020, 23:21:30 UTC
666ee87 Asher Preska Steinberg29 July 2020, 18:34:10 UTCno progress bar29 July 2020, 18:34:10 UTC
34ef078 Asher Preska Steinberg29 July 2020, 13:17:19 UTCcue when done with Gene Alignment29 July 2020, 13:17:19 UTC
a3a2e78 Asher Preska Steinberg28 July 2020, 17:46:02 UTCattempt to write to moving back to scratch28 July 2020, 17:46:02 UTC
5beb969 Asher Preska Steinberg28 July 2020, 14:30:58 UTCattempt to write to beegfs28 July 2020, 14:30:58 UTC
e66d967 Asher Preska Steinberg28 July 2020, 13:54:53 UTCattempt to write to beegfs28 July 2020, 13:54:53 UTC
5454eb3 Asher Preska Steinberg28 July 2020, 13:54:17 UTCattempt to write to beegfs28 July 2020, 13:54:17 UTC
86aba8c Asher Preska Steinberg28 July 2020, 12:56:31 UTCusing new version of sra toolkit28 July 2020, 12:56:31 UTC
2e77737 Asher Preska Steinberg27 July 2020, 22:15:05 UTCnew path for sra files27 July 2020, 22:15:05 UTC
7353d89 Asher Preska Steinberg27 July 2020, 22:05:04 UTCnew path for sra files27 July 2020, 22:05:04 UTC
c55c46c Asher Preska Steinberg27 July 2020, 21:39:07 UTCUpdates for new versions of sra tools27 July 2020, 21:39:07 UTC
ce4cb2e Mingzhi Lin29 January 2018, 17:49:32 UTCUpdate ReferenceAlignmentGenerate29 January 2018, 17:49:32 UTC
fe3ca00 Mingzhi Lin29 January 2018, 17:46:50 UTCadd more documentation29 January 2018, 17:46:50 UTC
404404e Mingzhi Lin28 January 2018, 22:20:21 UTCUpdate README.md28 January 2018, 22:20:21 UTC
ba35c9d Mingzhi Lin28 January 2018, 22:19:38 UTCUpdate README.md28 January 2018, 22:19:38 UTC
4a64e91 Mingzhi Lin26 January 2018, 21:56:21 UTCUpdate README.md26 January 2018, 21:56:21 UTC
e51013d Mingzhi Lin26 January 2018, 21:42:48 UTCAdd Dockerfile26 January 2018, 21:42:48 UTC
00b5f99 Mingzhi Lin26 January 2018, 21:32:40 UTCfix bug26 January 2018, 21:32:40 UTC
7f01bea Mingzhi Lin26 January 2018, 21:29:36 UTCv0.126 January 2018, 21:29:36 UTC
0511df4 Mingzhi Lin26 January 2018, 20:56:34 UTCadd README.md26 January 2018, 20:56:34 UTC
18f09cb Mingzhi Lin26 January 2018, 20:52:14 UTCfirst commit26 January 2018, 20:52:14 UTC
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