| 162f169 | Luis M. Rodriguez-R | 22 February 2022, 19:51:05 UTC | Release v3.4.1 | 22 February 2022, 19:51:05 UTC |
| 8519231 | Luis M. Rodriguez-R | 22 February 2022, 19:49:40 UTC | Release v4.0.1 | 22 February 2022, 19:49:40 UTC |
| af74492 | Luis M. Rodriguez-R | 22 February 2022, 19:44:46 UTC | Add informative error to empty read sets Close #53 | 22 February 2022, 19:44:46 UTC |
| bdea9fb | Luis M. Rodriguez-R | 11 February 2022, 09:22:55 UTC | Rename binary | 11 February 2022, 09:22:55 UTC |
| 0d43508 | Luis M. Rodriguez-R | 11 February 2022, 09:20:42 UTC | Create nonpareil-3.400-MacOSX-ARM64 | 11 February 2022, 09:20:42 UTC |
| 8b5d95c | Luis M. Rodriguez-R | 28 January 2022, 18:13:10 UTC | Version bump: 3.4.0 | 28 January 2022, 18:13:10 UTC |
| fa25cae | Luis M. Rodriguez-R | 28 January 2022, 17:58:12 UTC | Remove warning on near-saturation Close #47 | 28 January 2022, 17:58:12 UTC |
| d3e2750 | Luis M. Rodriguez-R | 28 January 2022, 17:49:06 UTC | Fix docs | 28 January 2022, 17:49:06 UTC |
| 94101e7 | Luis M. Rodriguez-R | 28 January 2022, 17:43:07 UTC | Reintroduce `-r` - Version bump to 3.4.0 - The `-r` variable is back to the main help message - `-T alignment` consistently implements `-r` - Some code cleanup | 28 January 2022, 17:43:07 UTC |
| 48342ea | Luis M. Rodriguez-R | 28 January 2022, 14:24:32 UTC | Add example with powers of 1000 bp Close #52 | 28 January 2022, 14:24:32 UTC |
| e4e72fe | Luis M. Rodriguez-R | 28 January 2022, 13:57:48 UTC | Minor code style improvements | 28 January 2022, 13:57:48 UTC |
| aba6d34 | Luis M Rodriguez-R | 10 July 2020, 22:22:02 UTC | Update mistaken binary path name | 10 July 2020, 22:22:02 UTC |
| 4ec3895 | Luis M Rodriguez-R | 09 July 2020, 00:18:04 UTC | Release v3.3.4 | 09 July 2020, 00:18:04 UTC |
| c155bd1 | Santosh Gunturu | 08 July 2020, 18:31:05 UTC | limit the number of number of random sequence if too many non ACGT sequences | 08 July 2020, 18:31:05 UTC |
| bf1b3f3 | Luis M Rodriguez-R | 01 February 2019, 19:05:42 UTC | Nonpareil R package -> 3.3.4 Minor check that pre-sorts input .npo files. Documentation overhaul, migrated inlinedocs -> roxygen2. This should have no impact on anything except package building. The inlinedocs package was recently removed from the CRAN repositories, and roxygen documentation is much more stable and widely used. | 01 February 2019, 19:05:42 UTC |
| 180d46b | Luis M Rodriguez-R | 22 October 2018, 17:57:17 UTC | Release v3.3.3 - Remove `@ksize` header from kernel alignment - R code deal with legacy rubbish `@ksize` in kernel alignment - Release v3.3.3 | 22 October 2018, 17:57:17 UTC |
| aa79f07 | Luis M Rodriguez-R | 23 July 2018, 15:24:04 UTC | Nonpareil.legend() now supports single curves CRAN R package 3.3.2 uploaded | 23 July 2018, 15:24:04 UTC |
| 66c03bd | Luis M Rodriguez-R | 26 April 2018, 18:57:02 UTC | Update README.md Added Nonpareil 3 citation | 26 April 2018, 18:57:02 UTC |
| 8daff08 | Luis M Rodriguez-R | 22 March 2018, 22:07:35 UTC | Release v3.3.1 This is the release used in “Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity” | 22 March 2018, 22:07:35 UTC |
| 7cada64 | Luis M Rodriguez-R | 19 January 2018, 20:59:05 UTC | Minor bug fixed A minor bug was preventing external use of `Nonpareil.col`, now solved | 19 January 2018, 20:59:05 UTC |
| deca10b | Luis M Rodriguez-R | 18 December 2017, 21:39:50 UTC | Updated online documentation | 18 December 2017, 21:39:50 UTC |
| 18a2c5d | Luis M Rodriguez-R | 18 December 2017, 21:27:27 UTC | Additional documentation for the R package Related to #27 | 18 December 2017, 21:27:27 UTC |
| 9293ce4 | Santosh Kumar Gunturu | 14 December 2017, 17:53:40 UTC | fixed bug with error correction | 14 December 2017, 17:53:40 UTC |
| f05def4 | Luis M Rodriguez-R | 06 December 2017, 18:47:41 UTC | Package for CRAN distribution | 06 December 2017, 18:47:41 UTC |
| a78998c | Luis M Rodriguez-R | 05 December 2017, 18:14:35 UTC | Example data and additional examples for R code | 05 December 2017, 18:14:35 UTC |
| 2e9a5b5 | Luis M Rodriguez-R | 05 December 2017, 00:09:24 UTC | New skip.model parameter Also, safer estimation of model’s summary when one weight exponent fails | 05 December 2017, 00:09:24 UTC |
| 8cbb903 | Luis M Rodriguez-R | 04 December 2017, 20:57:21 UTC | Obsolete corrections removed | 04 December 2017, 20:57:21 UTC |
| 4b94cdc | Luis M Rodriguez-R | 01 December 2017, 21:00:16 UTC | Maintainer added to R code | 01 December 2017, 21:00:16 UTC |
| c965295 | Luis M Rodriguez-R | 01 December 2017, 20:55:41 UTC | Refactored R code compatible with CRAN R code v3.3 | 01 December 2017, 20:55:41 UTC |
| 3ba869d | Luis M Rodriguez-R | 01 December 2017, 19:38:18 UTC | Updated Nonpareil R package structure | 01 December 2017, 19:38:18 UTC |
| 627f353 | Luis M Rodriguez-R | 01 December 2017, 19:32:07 UTC | Stashed code fixed | 01 December 2017, 19:32:07 UTC |
| 3fb3720 | Luis M Rodriguez-R | 30 November 2017, 23:39:51 UTC | Major refactoring of the R code | 30 November 2017, 23:39:51 UTC |
| bcf2120 | Santosh Kumar Gunturu | 14 November 2017, 18:26:38 UTC | Merge branch 'master' of https://github.com/lmrodriguezr/nonpareil | 14 November 2017, 18:26:38 UTC |
| 40060b4 | Santosh Kumar Gunturu | 14 November 2017, 18:25:47 UTC | kmer size restricted to 1 to 32 | 14 November 2017, 18:25:47 UTC |
| b411bad | Luis M Rodriguez-R | 14 November 2017, 15:26:14 UTC | Updated docs metadata | 14 November 2017, 15:26:14 UTC |
| aea5300 | Luis M Rodriguez-R | 14 November 2017, 15:13:16 UTC | Merge pull request #26 from bebatut/galaxy Add doc about Galaxy installation | 14 November 2017, 15:13:16 UTC |
| 18946ff | Berenice Batut | 14 November 2017, 15:08:47 UTC | Add doc about Galaxy installation | 14 November 2017, 15:08:47 UTC |
| bdc88f9 | Luis M Rodriguez-R | 14 November 2017, 14:58:25 UTC | Merge pull request #25 from bebatut/conda_container Add doc about Conda installation and container usage | 14 November 2017, 14:58:25 UTC |
| 72a0c5f | Berenice Batut | 14 November 2017, 14:38:41 UTC | Add conda and container badges | 14 November 2017, 14:40:27 UTC |
| 2ab34b9 | Berenice Batut | 14 November 2017, 14:38:15 UTC | Add installation info for conda and biocontainer | 14 November 2017, 14:38:15 UTC |
| 78011b5 | Santosh Kumar Gunturu | 13 November 2017, 18:40:42 UTC | Nonpareil Rscript modified for kmer kernel | 13 November 2017, 18:40:42 UTC |
| 602f628 | Luis M Rodriguez-R | 13 November 2017, 16:22:09 UTC | v3.2 | 13 November 2017, 16:22:09 UTC |
| ddf2c03 | Luis M Rodriguez-R | 11 November 2017, 03:13:42 UTC | v3.2rc1 | 11 November 2017, 03:13:42 UTC |
| 29a4cf0 | Luis M Rodriguez-R | 07 November 2017, 20:28:27 UTC | Important bug solved This bug affected the diversity estimates, so this change is a candidate for minor version bump | 07 November 2017, 20:28:27 UTC |
| 177d11b | Luis M Rodriguez-R | 28 September 2017, 18:05:23 UTC | Important change on plotting with -T kmer | 28 September 2017, 18:05:23 UTC |
| 4026445 | Luis M Rodriguez-R | 18 September 2017, 04:23:19 UTC | Warns kmer-fasta | 18 September 2017, 04:23:19 UTC |
| cfaa9e3 | Luis M Rodriguez-R | 18 September 2017, 04:12:26 UTC | v3.1 | 18 September 2017, 04:12:26 UTC |
| 3195e6d | Luis M Rodriguez-R | 18 September 2017, 04:07:44 UTC | Major code cleanup in main() | 18 September 2017, 04:07:44 UTC |
| 2c8428c | Luis M Rodriguez-R | 18 September 2017, 01:52:05 UTC | +docs | 18 September 2017, 01:52:05 UTC |
| 87cb779 | Santosh Kumar Gunturu | 27 June 2017, 15:31:03 UTC | changes to the help printout | 27 June 2017, 15:31:03 UTC |
| b1b9346 | Santosh Kumar G | 27 June 2017, 14:35:44 UTC | removed Repeated buttons | 27 June 2017, 14:35:44 UTC |
| 72ce3c9 | Santosh Kumar Gunturu | 24 May 2017, 14:22:19 UTC | removed test printouts | 24 May 2017, 14:22:19 UTC |
| d3a11fc | Santosh Kumar Gunturu | 24 May 2017, 00:15:43 UTC | fixed a bug with number of query sequences | 24 May 2017, 00:15:43 UTC |
| e567a97 | Luis M Rodriguez-R | 23 May 2017, 14:41:16 UTC | Reduced data.consistency astringency | 23 May 2017, 14:41:16 UTC |
| f0160da | Santosh Kumar Gunturu | 19 May 2017, 23:28:50 UTC | fixed bug sequence reading | 19 May 2017, 23:28:50 UTC |
| 20f9bd0 | Luis M Rodriguez-R | 18 April 2017, 15:29:57 UTC | Compiled utility ignored | 18 April 2017, 15:29:57 UTC |
| 62fb5fb | Santosh Kumar Gunturu | 13 April 2017, 20:09:10 UTC | read wrapped fasta files randomly | 13 April 2017, 20:09:10 UTC |
| 18b36bd | Santosh Kumar Gunturu | 13 April 2017, 20:00:33 UTC | Revert "read wrapped fasta files" This reverts commit caadbef493a157b08623300b313af7e7f3ea4ecb. | 13 April 2017, 20:00:33 UTC |
| caadbef | Santosh Kumar Gunturu | 13 April 2017, 19:55:07 UTC | read wrapped fasta files | 13 April 2017, 19:55:07 UTC |
| 2badbb2 | Luis M Rodriguez-R | 08 February 2017, 17:16:52 UTC | Minor fix to bypass errors in first plot of batch | 08 February 2017, 17:16:52 UTC |
| ace5401 | Luis M Rodriguez-R | 28 November 2016, 23:52:02 UTC | Minor style update | 28 November 2016, 23:52:02 UTC |
| eb6e309 | Luis M Rodriguez-R | 28 November 2016, 23:45:28 UTC | Minor typo fixed | 28 November 2016, 23:45:28 UTC |
| cc8b0a6 | Luis M Rodriguez-R | 28 November 2016, 23:42:04 UTC | Clean compilation in RedHat | 28 November 2016, 23:42:04 UTC |
| d376a4e | Luis M Rodriguez-R | 28 November 2016, 22:35:41 UTC | Clean compilation in OS X | 28 November 2016, 22:35:41 UTC |
| 9a76ece | Santosh Kumar G | 28 November 2016, 22:01:40 UTC | Merge pull request #17 from lmrodriguezr/nonpareil-k Nonpareil k | 28 November 2016, 22:01:39 UTC |
| e3f1f33 | Santosh Kumar Gunturu | 28 November 2016, 20:21:33 UTC | ignore np* files | 28 November 2016, 20:21:33 UTC |
| 0e4ae18 | Santosh Kumar Gunturu | 28 November 2016, 20:20:54 UTC | Merge branch 'master' into nonpareil-k | 28 November 2016, 20:20:54 UTC |
| 8a72fa2 | Santosh Gunturu | 14 November 2016, 16:51:53 UTC | fixed memory leaks | 14 November 2016, 16:51:53 UTC |
| c2ade92 | Santosh Gunturu | 23 September 2016, 15:50:49 UTC | fixed segfault | 23 September 2016, 15:50:49 UTC |
| 772d026 | Santosh Kumar G | 17 August 2016, 20:46:41 UTC | Update redundancy.rst added kmer size option | 17 August 2016, 20:46:41 UTC |
| 3e17855 | Santosh Gunturu | 05 August 2016, 19:16:55 UTC | removed kmer size for alignment mode | 05 August 2016, 19:16:55 UTC |
| 0117143 | Luis M Rodriguez-R | 05 August 2016, 18:51:55 UTC | Nonpareil.R now uses all weights.exp values | 05 August 2016, 18:51:57 UTC |
| 26f7846 | Santosh Kumar G | 29 July 2016, 17:40:02 UTC | changed CLI documentation | 29 July 2016, 17:40:02 UTC |
| d1e265c | Santosh Gunturu | 28 July 2016, 21:05:24 UTC | removed Nonpareil1 exploration file | 28 July 2016, 21:05:24 UTC |
| 031bd00 | Santosh Gunturu | 28 July 2016, 21:02:05 UTC | add minimum read length for KmerCounter | 28 July 2016, 21:02:05 UTC |
| 23a69ae | Santosh Gunturu | 28 July 2016, 20:44:05 UTC | Merge branch 'nonpareil-k' of https://github.com/lmrodriguezr/nonpareil into nonpareil-k | 28 July 2016, 20:44:05 UTC |
| cb35bfd | Santosh Gunturu | 28 July 2016, 20:41:48 UTC | required minimum read length of ksize | 28 July 2016, 20:41:48 UTC |
| d978968 | Luis M Rodriguez-R | 27 July 2016, 22:00:09 UTC | v3.0 | 27 July 2016, 22:00:09 UTC |
| 00c9f9a | Luis M Rodriguez-R | 27 July 2016, 21:55:42 UTC | major version bump | 27 July 2016, 21:55:42 UTC |
| 882ade6 | Luis M Rodriguez-R | 27 July 2016, 18:42:44 UTC | R code adapted for k-mer +Code cleanup | 27 July 2016, 18:42:44 UTC |
| 6a6696c | Santosh Gunturu | 22 July 2016, 22:39:58 UTC | fixed problem with unusal filenaming in linux | 22 July 2016, 22:39:58 UTC |
| 92e9a25 | Santosh Gunturu | 22 July 2016, 22:35:59 UTC | fixed occasional filenaming problem with linux sys | 22 July 2016, 22:35:59 UTC |
| c29bccb | Santosh Gunturu | 20 July 2016, 23:50:58 UTC | intial nonpareil kmer | 20 July 2016, 23:50:58 UTC |
| 19e4630 | Luis M Rodriguez-R | 19 May 2015, 17:55:56 UTC | Old binaries removed | 19 May 2015, 17:55:56 UTC |
| 97c09a5 | Luis M Rodriguez-R | 19 May 2015, 17:53:19 UTC | Unnecessarily large test files removed | 19 May 2015, 17:53:19 UTC |
| 1b6f6ed | Luis M Rodriguez-R | 26 February 2015, 01:20:56 UTC | Update citation and online querying link | 26 February 2015, 01:20:56 UTC |
| 45d7dd8 | Luis M Rodriguez-R | 15 January 2015, 19:56:12 UTC | v2.4 docs | 15 January 2015, 19:56:12 UTC |
| 109c015 | Luis M Rodriguez-R | 15 January 2015, 18:44:51 UTC | v2.400 | 15 January 2015, 18:44:51 UTC |
| ec599e8 | Luis M Rodriguez-R | 13 January 2015, 22:05:08 UTC | Pre-release of v2.4 | 13 January 2015, 22:05:08 UTC |
| 8a097b0 | Luis M Rodriguez-R | 13 August 2014, 21:14:09 UTC | Additional weights.exp for Nonpareil.curve() Only with nonpareil -d option. | 13 August 2014, 21:14:09 UTC |
| 42919a3 | Luis M Rodriguez-R | 13 August 2014, 21:12:48 UTC | col parameter supported in Nonpareil.curve.batch | 13 August 2014, 21:12:48 UTC |
| 48fba90 | Luis M Rodriguez-R | 29 April 2014, 17:40:32 UTC | Nonpareil.R new parameter and output Diversity index is now estimated, returned, and (optionally) plotted | 29 April 2014, 17:40:32 UTC |
| 833e79f | Luis M Rodriguez-R | 17 April 2014, 22:54:10 UTC | .npo output now includes the divide (-d) parameter Logarithmic sampling is resulting in better fits, but the R code must be updated to automatically modify the default value for weights.exp and the data consistency must be updated to reflect the fact that the 20% point is no longer the 20% sampling. | 17 April 2014, 22:54:10 UTC |
| 910e615 | Luis M Rodriguez-R | 04 April 2014, 18:56:21 UTC | Minor bug affecting MPI removed | 04 April 2014, 18:56:21 UTC |
| a9f84cb | Luis M Rodriguez-R | 03 April 2014, 21:23:24 UTC | Extra debugging messages | 03 April 2014, 21:23:24 UTC |
| 99ed97d | Luis M Rodriguez-R | 02 April 2014, 23:10:43 UTC | Reducing clutter | 02 April 2014, 23:10:43 UTC |
| 8458aca | Luis M Rodriguez-R | 02 April 2014, 22:38:24 UTC | Additional debugging messages | 02 April 2014, 22:38:24 UTC |
| 9524b86 | Luis M Rodriguez-R | 31 March 2014, 03:07:14 UTC | v2.304alpha | 31 March 2014, 03:07:14 UTC |
| dcb5ac9 | Luis M Rodriguez-R | 31 March 2014, 03:06:12 UTC | New parameter in Nonpareil.R: col | 31 March 2014, 03:06:12 UTC |
| a98d9b5 | Luis M Rodriguez-R | 31 March 2014, 03:05:57 UTC | New option: -q | 31 March 2014, 03:05:57 UTC |
