| c8bec26 | Kevin Murray | 27 January 2019, 08:03:47 UTC | Update link to published paper | 27 January 2019, 08:03:47 UTC |
| 3cf8a9e | Kevin Murray | 13 October 2016, 05:28:36 UTC | Update link to paper & journal | 13 October 2016, 05:28:36 UTC |
| 4b3a63f | Kevin Murray | 17 September 2016, 06:03:20 UTC | Mention publication in readme | 17 September 2016, 06:03:20 UTC |
| 1f6730e | Kevin Murray | 22 July 2016, 07:08:53 UTC | Add oxlicap | 22 July 2016, 07:08:53 UTC |
| 422b810 | Kevin Murray | 26 May 2016, 10:45:42 UTC | Docs: clearer wording in install docs | 26 May 2016, 10:45:42 UTC |
| c3474b4 | Kevin Murray | 25 May 2016, 00:05:55 UTC | Fix ci by removing static build on tags | 25 May 2016, 00:06:29 UTC |
| 077efaf | Kevin Murray | 22 April 2016, 01:27:51 UTC | kwip-stats: move source file to reflect new name | 22 April 2016, 01:27:51 UTC |
| 522a329 | Kevin Murray | 22 April 2016, 01:22:07 UTC | kwip-stats: remove "Weight" measure, irrelevant | 22 April 2016, 01:22:07 UTC |
| 8fd862d | Kevin Murray | 12 April 2016, 01:48:51 UTC | travis: use trusty builds | 12 April 2016, 01:48:51 UTC |
| 6fe2c6c | Kevin Murray | 12 April 2016, 01:40:57 UTC | Update install instructions for static binaries | 12 April 2016, 01:40:57 UTC |
| 758d5f3 | Kevin Murray | 11 April 2016, 00:24:41 UTC | Readme edits | 11 April 2016, 00:24:41 UTC |
| cbddcdc | Kevin Murray | 11 April 2016, 00:21:45 UTC | Remove old kmerclust code | 11 April 2016, 00:21:45 UTC |
| 176d760 | Kevin Murray | 11 April 2016, 00:09:24 UTC | Add compiled config.hh to gitignore | 11 April 2016, 00:09:24 UTC |
| 06be41a | Kevin Murray | 07 April 2016, 11:19:54 UTC | Use Holy Build Box for static builds | 07 April 2016, 11:19:54 UTC |
| ce9b1db | Kevin Murray | 02 March 2016, 04:02:06 UTC | Use a more modern sphinx | 02 March 2016, 04:02:06 UTC |
| 19037ff | Kevin Murray | 02 March 2016, 03:51:26 UTC | install alabaster in travis CI | 02 March 2016, 03:53:08 UTC |
| 54ff52b | Kevin Murray | 02 March 2016, 03:14:52 UTC | Minor fixes to demo docs | 02 March 2016, 03:14:52 UTC |
| 5a92a36 | Kevin Murray | 02 March 2016, 03:12:42 UTC | Use shell syntax highlighting in demos, rewording | 02 March 2016, 03:12:42 UTC |
| 3185fb3 | Kevin Murray | 02 March 2016, 03:09:26 UTC | Fix bash syntax in rice example | 02 March 2016, 03:09:26 UTC |
| 73c1aed | Kevin Murray | 29 February 2016, 05:20:06 UTC | Move installation docs to docs & link from readme | 29 February 2016, 05:20:06 UTC |
| cdda15d | Kevin Murray | 29 February 2016, 05:07:18 UTC | Update install in readme | 29 February 2016, 05:07:18 UTC |
| d109a13 | Kevin Murray | 12 January 2016, 05:12:25 UTC | Fix static makefile to work with docker image | 12 January 2016, 05:12:25 UTC |
| 2c99d0f | Kevin Murray | 12 January 2016, 05:11:54 UTC | Fixes to install documentation in README | 12 January 2016, 05:11:54 UTC |
| 66582eb | Kevin Murray | 12 January 2016, 04:51:40 UTC | Add optimisation flag to static makefile | 12 January 2016, 04:51:40 UTC |
| 5a8932b | Kevin Murray | 12 January 2016, 04:45:46 UTC | Update travis CI config | 12 January 2016, 04:45:46 UTC |
| 21ec8ec | Kevin Murray | 12 January 2016, 04:07:33 UTC | Rename jenkins script to util/ci-build.sh | 12 January 2016, 04:07:33 UTC |
| aa9ec2e | Kevin Murray | 12 January 2016, 04:06:46 UTC | Biojenkins is decommissioned | 12 January 2016, 04:06:46 UTC |
| b3a5784 | Kevin Murray | 12 January 2016, 02:31:34 UTC | Merge branch 'constify' Closes #10 | 12 January 2016, 02:31:34 UTC |
| e6938fb | Kevin Murray | 12 January 2016, 02:26:39 UTC | Const-ify all khmer::CountingHash refs as needed In all kernel and add_hashtable | 12 January 2016, 02:26:39 UTC |
| ab0ef28 | Kevin Murray | 12 January 2016, 02:25:34 UTC | Const-ify khmer::CountingHash::get_raw_tables meth This is an UPSTREAM patch | 12 January 2016, 02:25:34 UTC |
| be41177 | Kevin Murray | 10 January 2016, 11:24:27 UTC | Rename kwip-entvec to kwip-stats | 10 January 2016, 11:24:27 UTC |
| cd26a8c | Kevin Murray | 10 January 2016, 06:19:29 UTC | Note why we use minCoeff in matrix_is_pos_semidef | 10 January 2016, 06:19:29 UTC |
| 913df63 | Kevin Murray | 10 January 2016, 06:16:47 UTC | Merge branch 'eigenvalues' Calculate eigenvalues & check for PSD | 10 January 2016, 06:16:47 UTC |
| 92ff36b | Kevin Murray | 10 January 2016, 06:16:10 UTC | Warn users on non-PSD kernel matrix | 10 January 2016, 06:16:10 UTC |
| 28763d5 | Kevin Murray | 10 January 2016, 05:52:03 UTC | Merge branch 'eigenvalues' This brings in the Eigen3 implementation of kernel/distance matrices | 10 January 2016, 05:52:03 UTC |
| 906308f | Kevin Murray | 10 January 2016, 05:50:39 UTC | Fix fallback path of eigen3 in cmake module | 10 January 2016, 05:50:39 UTC |
| 3721be8 | Kevin Murray | 10 January 2016, 05:42:58 UTC | Add kmerclust binary back in, it works now | 10 January 2016, 05:42:58 UTC |
| a0cc9d1 | Kevin Murray | 10 January 2016, 05:36:37 UTC | Add Eigen3 in src/ext for ease of installation | 10 January 2016, 05:36:37 UTC |
| 4540baa | Kevin Murray | 10 January 2016, 05:34:05 UTC | Remove old hacking code w/ eigenvalue calculation | 10 January 2016, 05:34:05 UTC |
| 55524e8 | Kevin Murray | 10 January 2016, 05:33:15 UTC | Code I was hacking on originally for the record | 10 January 2016, 05:33:15 UTC |
| df25c06 | Kevin Murray | 10 January 2016, 05:21:38 UTC | Fix labelled square matrix format in print_lsmat | 10 January 2016, 05:21:38 UTC |
| 25c853f | Kevin Murray | 10 January 2016, 05:15:15 UTC | Missed a debugging print | 10 January 2016, 05:15:15 UTC |
| f52d2d3 | Kevin Murray | 10 January 2016, 05:14:27 UTC | Remove debugging prints from kwip-utils.cc | 10 January 2016, 05:14:27 UTC |
| 858ee54 | Kevin Murray | 10 January 2016, 04:50:15 UTC | Check that the kernel matrix exists before use | 10 January 2016, 04:50:15 UTC |
| 741deee | Kevin Murray | 10 January 2016, 04:46:00 UTC | Get eigen working with core kWIP code | 10 January 2016, 04:46:00 UTC |
| e9e569c | Kevin Murray | 15 December 2015, 07:56:28 UTC | initial eigen usage | 08 January 2016, 04:34:47 UTC |
| 0532712 | Kevin Murray | 15 December 2015, 07:33:08 UTC | Fix include dir for eigen3 | 08 January 2016, 04:34:47 UTC |
| c68ec59 | Kevin Murray | 15 December 2015, 07:18:49 UTC | Use 3.0 as min Eigen3 version | 08 January 2016, 04:34:47 UTC |
| c1bc923 | Kevin Murray | 15 December 2015, 07:17:46 UTC | Add Eigen3 to CML | 08 January 2016, 04:34:47 UTC |
| 440b202 | Kevin Murray | 08 January 2016, 04:26:30 UTC | Fixes to static makefile - Add clean rule - Define SEQAN_HAS_GZIP/BZIP2 - KWIP_OBJ depends on the config header | 08 January 2016, 04:26:30 UTC |
| 6e7a58f | Kevin Murray | 08 January 2016, 04:04:09 UTC | Add static binary compilation makefile | 08 January 2016, 04:04:09 UTC |
| 5c7c853 | Kevin Murray | 08 December 2015, 07:09:45 UTC | Bigger image labels for smaller sets | 08 December 2015, 07:09:45 UTC |
| c0ff123 | Kevin Murray | 07 December 2015, 00:38:48 UTC | Fix histogram calculation | 07 December 2015, 00:38:48 UTC |
| a5fb86e | Kevin Murray | 07 December 2015, 00:36:06 UTC | Fix count summing in entvec | 07 December 2015, 00:36:06 UTC |
| be16bb3 | Kevin Murray | 06 December 2015, 07:42:25 UTC | Correct entvec implementation with latest weighting | 06 December 2015, 07:42:25 UTC |
| 4369111 | Kevin Murray | 06 December 2015, 07:23:00 UTC | Merge branch 'preweighting' | 06 December 2015, 07:23:00 UTC |
| 46c97b2 | Kevin Murray | 06 December 2015, 07:22:25 UTC | Fix test with latest kernel matrix calculation | 06 December 2015, 07:22:25 UTC |
| cea7d1b | Kevin Murray | 06 December 2015, 07:17:18 UTC | Use most basic weighting mode, A * B * H | 06 December 2015, 07:17:18 UTC |
| 85625f7 | Kevin Murray | 30 November 2015, 05:41:59 UTC | Reduce hash table size temporarily | 30 November 2015, 05:41:59 UTC |
| 83fa41b | Kevin Murray | 30 November 2015, 05:41:28 UTC | Restructure normalisation code | 30 November 2015, 05:41:28 UTC |
| f8404ae | Kevin Murray | 23 November 2015, 03:44:15 UTC | Use square root of entropy in preweighting kernel | 23 November 2015, 03:44:15 UTC |
| 99dd539 | Kevin Murray | 22 November 2015, 05:22:13 UTC | Calculate kernel as pre-weighted sample vectors | 22 November 2015, 05:22:13 UTC |
| 95efcc1 | Kevin Murray | 03 November 2015, 04:06:56 UTC | use sqrt((v1 * w)^2) as vector norm | 16 November 2015, 23:09:44 UTC |
| 9be5572 | Kevin Murray | 16 November 2015, 23:06:25 UTC | Correct cmake call in install docs | 16 November 2015, 23:09:25 UTC |
| e902508 | Kevin Murray | 16 November 2015, 04:17:11 UTC | Promote kernel types to u32 and double | 16 November 2015, 04:17:11 UTC |
| a83af89 | Kevin Murray | 16 November 2015, 04:00:49 UTC | Strip only known CountGraph ext from filenames | 16 November 2015, 04:00:49 UTC |
| b8fd9c9 | Kevin Murray | 09 November 2015, 05:06:16 UTC | Use correct zlib package name for install docs | 09 November 2015, 05:10:59 UTC |
| 51b97a4 | Kevin Murray | 06 November 2015, 09:43:45 UTC | Typo fix in documentation | 06 November 2015, 09:43:45 UTC |
| a10224c | Kevin Murray | 06 November 2015, 09:26:28 UTC | Fix RST syntax of literal blocks in docs | 06 November 2015, 09:26:28 UTC |
| 3d0d190 | Kevin Murray | 06 November 2015, 09:25:03 UTC | Fix installation documentation in sphinx | 06 November 2015, 09:25:03 UTC |
| b4d10b9 | Kevin Murray | 06 November 2015, 09:22:50 UTC | Fix installation documenation in README | 06 November 2015, 09:22:50 UTC |
| d9d68aa | Kevin Murray | 06 November 2015, 09:13:21 UTC | Merge branch 'khmer-bundled' | 06 November 2015, 09:13:21 UTC |
| 0feed49 | Kevin Murray | 06 November 2015, 09:10:41 UTC | Allow Zlib >= 1.2.3 | 06 November 2015, 09:10:41 UTC |
| 67b036c | Kevin Murray | 06 November 2015, 09:10:05 UTC | Also use clang on travis CI | 06 November 2015, 09:10:05 UTC |
| f35d6d1 | Kevin Murray | 06 November 2015, 09:08:35 UTC | Fix root CML INCLUDE_DIRECTORIES path | 06 November 2015, 09:08:46 UTC |
| c347bef | Kevin Murray | 06 November 2015, 09:07:16 UTC | Use INCLUDE_DIRECTORIES for src/ext in root CML | 06 November 2015, 09:07:16 UTC |
| 824542e | Kevin Murray | 06 November 2015, 09:04:03 UTC | Find ZLIB and use it | 06 November 2015, 09:04:03 UTC |
| 79174c1 | Kevin Murray | 06 November 2015, 08:58:05 UTC | Fix INCLUDE_DIRECTORIES for seqan under src/ext | 06 November 2015, 08:58:05 UTC |
| ed30ca0 | Kevin Murray | 06 November 2015, 08:55:16 UTC | Fix bundling of seqan | 06 November 2015, 08:55:16 UTC |
| fd6f5c0 | Kevin Murray | 06 November 2015, 08:52:47 UTC | Also bundle khmer's bundling of seqan Yo dawg, I hear you like bundling... | 06 November 2015, 08:52:47 UTC |
| 6c2491a | Kevin Murray | 06 November 2015, 08:49:34 UTC | Fix/update CI build script for bundled khmer | 06 November 2015, 08:49:34 UTC |
| b156ab8 | Kevin Murray | 06 November 2015, 08:46:30 UTC | Correct INCLUDE_DIRECTORIES for ext/oxli | 06 November 2015, 08:46:30 UTC |
| f1ad133 | Kevin Murray | 06 November 2015, 08:45:32 UTC | Use 'oxli' not 'khmer' under src/ext Future-proofing, and allows compatiblity with system installed khmer | 06 November 2015, 08:45:55 UTC |
| 5a17036 | Kevin Murray | 06 November 2015, 08:31:20 UTC | Default to using internal copy of khmer | 06 November 2015, 08:42:33 UTC |
| ee0ec5f | Kevin Murray | 06 November 2015, 08:28:58 UTC | Add readme for khmer | 06 November 2015, 08:42:33 UTC |
| b5b1ce3 | Kevin Murray | 06 November 2015, 08:22:46 UTC | Use bundled khmer if we don't find it This is instead of downloading it afresh, which could go wrong. | 06 November 2015, 08:42:33 UTC |
| a797475 | Kevin Murray | 06 November 2015, 08:22:31 UTC | Update readme under src/ext | 06 November 2015, 08:42:33 UTC |
| cad81f6 | Kevin Murray | 06 November 2015, 08:21:32 UTC | Add a readme under src/ext | 06 November 2015, 08:42:33 UTC |
| c862091 | Kevin Murray | 06 November 2015, 08:18:05 UTC | Add khmer version 2.0 under src/ext | 06 November 2015, 08:42:33 UTC |
| 0c503d2 | Kevin Murray | 06 November 2015, 08:41:24 UTC | Fix tests given latest normalisation change | 06 November 2015, 08:41:24 UTC |
| b9daefe | Kevin Murray | 29 October 2015, 08:29:37 UTC | Use khmer version 2.0 in CML download | 29 October 2015, 08:29:37 UTC |
| 40d7ed1 | Kevin Murray | 23 October 2015, 04:48:48 UTC | Fix bug in vector norm calculation | 23 October 2015, 04:48:48 UTC |
| 014b959 | Kevin Murray | 25 September 2015, 02:58:21 UTC | Fix install instructions in README.md | 25 September 2015, 02:58:21 UTC |
| 70d8bed | Kevin Murray | 18 September 2015, 03:39:46 UTC | entvec.cc: Implement Shannon entropy of hashes | 18 September 2015, 03:39:46 UTC |
| c9196da | Kevin Murray | 18 September 2015, 02:32:14 UTC | Calculate weights using SS * WSS in entvec.cc | 18 September 2015, 02:32:14 UTC |
| 5ce5329 | Kevin Murray | 18 September 2015, 02:31:17 UTC | Fix version file based versioning | 18 September 2015, 02:31:17 UTC |
| 882ec52 | Kevin Murray | 15 September 2015, 14:02:13 UTC | Build against v2.0 of khmer | 15 September 2015, 14:02:13 UTC |
| d15ea1e | Kevin Murray | 31 August 2015, 08:48:03 UTC | Minor formatting changes to logging code | 31 August 2015, 08:48:03 UTC |
| 04793ef | Kevin Murray | 31 August 2015, 07:43:59 UTC | Better progress logging for kwip - Use 1-based offsets instead of 0-based - Be a little more verbose | 31 August 2015, 07:43:59 UTC |
| 9bc1712 | Kevin Murray | 30 August 2015, 12:21:22 UTC | Always print version of kWIP when using kwip CLI | 30 August 2015, 12:21:22 UTC |
