|
| 1 | +<a name="0.6.8"></a> |
| 2 | +# [Supports WHO and exon Reduction Types (0.6.8)](https://github.com/nmdp-bioinformatics/py-ard/releases/tag/0.6.8) - 24 Sep 2021 |
| 3 | + |
| 4 | +- Handle cases when there is no typing and when redux fails. |
| 5 | +- added `exon` resolution group |
| 6 | +- added `W` resolution group |
| 7 | +- Fix validation issues with empty alleles, NNNNs, and non-allelic values. |
| 8 | +- pyard-import can refresh MACs and rebuild databases |
| 9 | + |
| 10 | +[Changes][0.6.8] |
| 11 | + |
| 12 | + |
| 13 | +<a name="0.6.6"></a> |
| 14 | +# [handle invalid/blank input (0.6.6)](https://github.com/nmdp-bioinformatics/py-ard/releases/tag/0.6.6) - 29 Jul 2021 |
| 15 | + |
| 16 | +handle cases with no input and redux fails |
| 17 | + |
| 18 | +[Changes][0.6.6] |
| 19 | + |
| 20 | + |
| 21 | +<a name="0.6.5"></a> |
| 22 | +# [updates to pyard-reduce-csv and unit tests (0.6.5)](https://github.com/nmdp-bioinformatics/py-ard/releases/tag/0.6.5) - 17 Jun 2021 |
| 23 | + |
| 24 | + |
| 25 | + Use pyard-reduce-csv command to reduce a CSV file based on a JSON config file. |
| 26 | + Use db_version 3440 in unit test to match behave tests |
| 27 | + Re-run the tests again so local db is used. |
| 28 | + |
| 29 | + |
| 30 | + |
| 31 | +[Changes][0.6.5] |
| 32 | + |
| 33 | + |
| 34 | +<a name="0.6.4"></a> |
| 35 | +# [DRBX Mapping and Cw Serology (0.6.4)](https://github.com/nmdp-bioinformatics/py-ard/releases/tag/0.6.4) - 16 Jun 2021 |
| 36 | + |
| 37 | + - Map DRB3, DRB4 and DRB5 typings to DRBX. #82 |
| 38 | + - Change C to Cw for serology; #84 |
| 39 | + - Return '' for invalid MACs #84 |
| 40 | + |
| 41 | +[Changes][0.6.4] |
| 42 | + |
| 43 | + |
| 44 | +<a name="0.6.3"></a> |
| 45 | +# [0.6.3 release (0.6.3)](https://github.com/nmdp-bioinformatics/py-ard/releases/tag/0.6.3) - 09 Jun 2021 |
| 46 | + |
| 47 | + addresses one-to-many relationship from 2d to lg/lgx |
| 48 | + |
| 49 | +[Changes][0.6.3] |
| 50 | + |
| 51 | + |
| 52 | +<a name="0.6.2"></a> |
| 53 | +# [Fixes serology mappings for broad to include alleles in the split (0.6.2)](https://github.com/nmdp-bioinformatics/py-ard/releases/tag/0.6.2) - 07 Jun 2021 |
| 54 | + |
| 55 | +Fixes serology mappings for broad to include alleles in the split. |
| 56 | + |
| 57 | +[Changes][0.6.2] |
| 58 | + |
| 59 | + |
| 60 | +<a name="0.6.1"></a> |
| 61 | +# [V2 to V3 Mapping (0.6.1)](https://github.com/nmdp-bioinformatics/py-ard/releases/tag/0.6.1) - 04 Feb 2021 |
| 62 | + |
| 63 | + |
| 64 | + - Heuristically predict V3 from V2 when not in exceptional case list |
| 65 | + - Make is_XX a public method on the ARD object |
| 66 | + - Update README and fix bug in pyard-import for importing into Latest |
| 67 | + |
| 68 | + |
| 69 | +[Changes][0.6.1] |
| 70 | + |
| 71 | + |
| 72 | +<a name="0.6.0"></a> |
| 73 | +# [Nomenclature versioning (0.6.0)](https://github.com/nmdp-bioinformatics/py-ard/releases/tag/0.6.0) - 08 Dec 2020 |
| 74 | + |
| 75 | +adds nomenclature versioning, cmdline options, GL string examples |
| 76 | + |
| 77 | +[Changes][0.6.0] |
| 78 | + |
| 79 | + |
| 80 | +<a name="0.5.1"></a> |
| 81 | +# [fix mac expansion (0.5.1)](https://github.com/nmdp-bioinformatics/py-ard/releases/tag/0.5.1) - 30 Nov 2020 |
| 82 | + |
| 83 | +Fix serology mapping and mac expansions |
| 84 | + |
| 85 | +[Changes][0.5.1] |
| 86 | + |
| 87 | + |
| 88 | +<a name="0.4.1"></a> |
| 89 | +# [Upgrade Pandas to 1.1.4 (0.4.1)](https://github.com/nmdp-bioinformatics/py-ard/releases/tag/0.4.1) - 03 Nov 2020 |
| 90 | + |
| 91 | +Update pandas 1.1.4 |
| 92 | + |
| 93 | + - Pandas `1.1.2` doesn't work with Python 3.9. Upgrade Pandas to `1.1.4` which works with Python 3.8 and 3.9 |
| 94 | + |
| 95 | + |
| 96 | +[Changes][0.4.1] |
| 97 | + |
| 98 | + |
| 99 | +<a name="0.4.0"></a> |
| 100 | +# [ Support reduction of serologically typed GL String (0.4.0)](https://github.com/nmdp-bioinformatics/py-ard/releases/tag/0.4.0) - 22 Oct 2020 |
| 101 | + |
| 102 | +Uses WMDA `rel_dna_ser.txt` for the corresponding version of IMGT database to produce serology mapping |
| 103 | + |
| 104 | +[Changes][0.4.0] |
| 105 | + |
| 106 | + |
| 107 | +<a name="0.3.0"></a> |
| 108 | +# [Use sqlite3 database for reference data (0.3.0)](https://github.com/nmdp-bioinformatics/py-ard/releases/tag/0.3.0) - 15 Oct 2020 |
| 109 | + |
| 110 | + Use sqlite3 database for data |
| 111 | + |
| 112 | +Offload MAC codes from memory to sqlite3 database (natively supported by Python) to reduce |
| 113 | +memory footprint. All MAC lookups happen through the db. The alleles and G group expansions |
| 114 | +are still held in memory. |
| 115 | + |
| 116 | +In addition, all generated data is saved as tables in the same database. This leads to one |
| 117 | +file for storing all reference data in a standard format. |
| 118 | + |
| 119 | +This led to drastic reduction in memory usage and startup time. |
| 120 | + |
| 121 | +|Version |First Time| Prebuilt Data| |
| 122 | +|:--|--:|--:| |
| 123 | +| 0.1.0 | 10.5 sec | 4.92 sec| |
| 124 | +| 0.2.0 | 814 msec | 598 msec| |
| 125 | +| 0.3.0 | 24.1 msec | 24.7 msec | |
| 126 | + |
| 127 | +Heap memory used by ARD reference data after `ard = pyard.ARD(3290)` |
| 128 | + |
| 129 | +|Version |Memory (MB) | |
| 130 | +|:--|--:| |
| 131 | +| 0.1.0 | 2977.86 MB | |
| 132 | +| 0.2.0 | 420.76 MB | |
| 133 | +| 0.3.0 | 3.74 MB | |
| 134 | + |
| 135 | + |
| 136 | +[Changes][0.3.0] |
| 137 | + |
| 138 | + |
| 139 | +<a name="0.2.0"></a> |
| 140 | +# [rearrange data in memory (0.2.0)](https://github.com/nmdp-bioinformatics/py-ard/releases/tag/0.2.0) - 14 Oct 2020 |
| 141 | + |
| 142 | +This release rearranges how memory is used especially MAC codes and a lot of cleanup. |
| 143 | + |
| 144 | +[Changes][0.2.0] |
| 145 | + |
| 146 | + |
| 147 | +<a name="0.1.0"></a> |
| 148 | +# [load_mac_file flag to load MAC file (0.1.0)](https://github.com/nmdp-bioinformatics/py-ard/releases/tag/0.1.0) - 01 Oct 2020 |
| 149 | + |
| 150 | + Rename download_mac flag |
| 151 | + |
| 152 | + - Rename `download_mac` ARD flag to `load_mac_file` as it properly describes what it does. |
| 153 | + - Remove dead code |
| 154 | + - Reformat code and fix some comments |
| 155 | + - Version bumped to `0.1.0` |
| 156 | + - Updated `pandas` to `1.1.2` |
| 157 | + |
| 158 | +[Changes][0.1.0] |
| 159 | + |
| 160 | + |
| 161 | +<a name="0.0.21"></a> |
| 162 | +# [fix tests and sorting (0.0.21)](https://github.com/nmdp-bioinformatics/py-ard/releases/tag/0.0.21) - 09 Sep 2020 |
| 163 | + |
| 164 | +fixes test and also a bug in 4th field sorting |
| 165 | + |
| 166 | +[Changes][0.0.21] |
| 167 | + |
| 168 | + |
| 169 | +<a name="0.0.20"></a> |
| 170 | +# [allow P and G as input, fix lg and lgx behavior (0.0.20)](https://github.com/nmdp-bioinformatics/py-ard/releases/tag/0.0.20) - 09 Sep 2020 |
| 171 | + |
| 172 | +This release fixes the behavior of lg and lgx to always reduce to 2-field. |
| 173 | +It also allows P and G alleles as input |
| 174 | + |
| 175 | +[Changes][0.0.20] |
| 176 | + |
| 177 | + |
| 178 | +<a name="0.0.18"></a> |
| 179 | +# [Fixes G-codes expansion (0.0.18)](https://github.com/nmdp-bioinformatics/py-ard/releases/tag/0.0.18) - 29 Jul 2020 |
| 180 | + |
| 181 | +Fixes G-codes expansion when smart sorting. |
| 182 | + |
| 183 | +[Changes][0.0.18] |
| 184 | + |
| 185 | + |
| 186 | +<a name="0.0.17"></a> |
| 187 | +# [Specify path for temporary files (0.0.17)](https://github.com/nmdp-bioinformatics/py-ard/releases/tag/0.0.17) - 22 Jul 2020 |
| 188 | + |
| 189 | +You can specify path when creating ARD object. |
| 190 | +``` |
| 191 | +ard = ARD('3290', data_dir='/tmp/py-ard') |
| 192 | +``` |
| 193 | + |
| 194 | +[Changes][0.0.17] |
| 195 | + |
| 196 | + |
| 197 | +<a name="0.0.16"></a> |
| 198 | +# [version 0.0.16 (0.0.16)](https://github.com/nmdp-bioinformatics/py-ard/releases/tag/0.0.16) - 09 Jul 2020 |
| 199 | + |
| 200 | +update MAC location and version to 0.0.16 |
| 201 | + |
| 202 | +[Changes][0.0.16] |
| 203 | + |
| 204 | + |
| 205 | +<a name="0.0.15.0"></a> |
| 206 | +# [update to MAC location (0.0.15.0)](https://github.com/nmdp-bioinformatics/py-ard/releases/tag/0.0.15.0) - 28 May 2020 |
| 207 | + |
| 208 | + |
| 209 | + |
| 210 | +[Changes][0.0.15.0] |
| 211 | + |
| 212 | + |
| 213 | +<a name="0.0.15"></a> |
| 214 | +# [update to MAC location (0.0.15)](https://github.com/nmdp-bioinformatics/py-ard/releases/tag/0.0.15) - 28 May 2020 |
| 215 | + |
| 216 | +yes |
| 217 | + |
| 218 | +[Changes][0.0.15] |
| 219 | + |
| 220 | + |
| 221 | +<a name="0.0.14"></a> |
| 222 | +# [0.0.14](https://github.com/nmdp-bioinformatics/py-ard/releases/tag/0.0.14) - 14 Apr 2020 |
| 223 | + |
| 224 | +- Support for Python 3.7 |
| 225 | +- Broad XX enhancement |
| 226 | +- p Performance improvements |
| 227 | + |
| 228 | +[Changes][0.0.14] |
| 229 | + |
| 230 | + |
| 231 | +[0.6.8]: https://github.com/nmdp-bioinformatics/py-ard/compare/0.6.6...0.6.8 |
| 232 | +[0.6.6]: https://github.com/nmdp-bioinformatics/py-ard/compare/0.6.5...0.6.6 |
| 233 | +[0.6.5]: https://github.com/nmdp-bioinformatics/py-ard/compare/0.6.4...0.6.5 |
| 234 | +[0.6.4]: https://github.com/nmdp-bioinformatics/py-ard/compare/0.6.3...0.6.4 |
| 235 | +[0.6.3]: https://github.com/nmdp-bioinformatics/py-ard/compare/0.6.2...0.6.3 |
| 236 | +[0.6.2]: https://github.com/nmdp-bioinformatics/py-ard/compare/0.6.1...0.6.2 |
| 237 | +[0.6.1]: https://github.com/nmdp-bioinformatics/py-ard/compare/0.6.0...0.6.1 |
| 238 | +[0.6.0]: https://github.com/nmdp-bioinformatics/py-ard/compare/0.5.1...0.6.0 |
| 239 | +[0.5.1]: https://github.com/nmdp-bioinformatics/py-ard/compare/0.4.1...0.5.1 |
| 240 | +[0.4.1]: https://github.com/nmdp-bioinformatics/py-ard/compare/0.4.0...0.4.1 |
| 241 | +[0.4.0]: https://github.com/nmdp-bioinformatics/py-ard/compare/0.3.0...0.4.0 |
| 242 | +[0.3.0]: https://github.com/nmdp-bioinformatics/py-ard/compare/0.2.0...0.3.0 |
| 243 | +[0.2.0]: https://github.com/nmdp-bioinformatics/py-ard/compare/0.1.0...0.2.0 |
| 244 | +[0.1.0]: https://github.com/nmdp-bioinformatics/py-ard/compare/0.0.21...0.1.0 |
| 245 | +[0.0.21]: https://github.com/nmdp-bioinformatics/py-ard/compare/0.0.20...0.0.21 |
| 246 | +[0.0.20]: https://github.com/nmdp-bioinformatics/py-ard/compare/0.0.18...0.0.20 |
| 247 | +[0.0.18]: https://github.com/nmdp-bioinformatics/py-ard/compare/0.0.17...0.0.18 |
| 248 | +[0.0.17]: https://github.com/nmdp-bioinformatics/py-ard/compare/0.0.16...0.0.17 |
| 249 | +[0.0.16]: https://github.com/nmdp-bioinformatics/py-ard/compare/0.0.15.0...0.0.16 |
| 250 | +[0.0.15.0]: https://github.com/nmdp-bioinformatics/py-ard/compare/0.0.15...0.0.15.0 |
| 251 | +[0.0.15]: https://github.com/nmdp-bioinformatics/py-ard/compare/0.0.14...0.0.15 |
| 252 | +[0.0.14]: https://github.com/nmdp-bioinformatics/py-ard/tree/0.0.14 |
| 253 | + |
| 254 | + <!-- Generated by changelog-from-release --> |
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