predictosaurus 0.7.2

Uncertainty aware haplotype based genomic variant effect prediction
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274

# Changelog

## [0.7.2](https://github.com/fxwiegand/predictosaurus/compare/v0.7.1...v0.7.2) (2025-12-01)


### Bug Fixes

* Convert CDS start to 0-based index ([a5927aa](https://github.com/fxwiegand/predictosaurus/commit/a5927aa91cf7476e929d7912d0a17e794fa08b1b))

## [0.7.1](https://github.com/fxwiegand/predictosaurus/compare/v0.7.0...v0.7.1) (2025-12-01)


### Bug Fixes

* Add max CDS length option and skip long CDSs by default ([#160](https://github.com/fxwiegand/predictosaurus/issues/160)) ([73b7ef5](https://github.com/fxwiegand/predictosaurus/commit/73b7ef5f8b6d795b3f4a84ca1e85d34b5615ee8a))

## [0.7.0](https://github.com/fxwiegand/predictosaurus/compare/v0.6.0...v0.7.0) (2025-11-27)


### Features

* Implement new score method ([#158](https://github.com/fxwiegand/predictosaurus/issues/158)) ([91f17c0](https://github.com/fxwiegand/predictosaurus/commit/91f17c0f14504c730cab4ed8cbb4581cdabdfb46))

## [0.6.0](https://github.com/fxwiegand/predictosaurus/compare/v0.5.0...v0.6.0) (2025-09-07)


### Features

* Add haplotype quantification metrics and store per sample likelihoods derived from VAFs of variants on haplotype ([#126](https://github.com/fxwiegand/predictosaurus/issues/126)) ([6b296a7](https://github.com/fxwiegand/predictosaurus/commit/6b296a7a82de3803e85b2fa8397696221ce5023b))

## [0.5.0](https://github.com/fxwiegand/predictosaurus/compare/v0.4.2...v0.5.0) (2025-09-02)


### Features

* Add --min-vaf parameter to build subcommand ([#141](https://github.com/fxwiegand/predictosaurus/issues/141)) ([5ca19c3](https://github.com/fxwiegand/predictosaurus/commit/5ca19c3a7c9cad5b03b4f68f3c062d25c887af62))


### Bug Fixes

* Add mutex to synchronize score writing in parallel loop ([#135](https://github.com/fxwiegand/predictosaurus/issues/135)) ([1f44ae2](https://github.com/fxwiegand/predictosaurus/commit/1f44ae226de3afbb71698b907d76751cc2c991be))
* Fix contains_variant to take target string argument ([#137](https://github.com/fxwiegand/predictosaurus/issues/137)) ([4a1a9e3](https://github.com/fxwiegand/predictosaurus/commit/4a1a9e3d02e48489a261e8c38cf0c8cbfa84f7eb))
* Gracefully handle ambiguous nucleotide 'N' for amino acid changes ([#133](https://github.com/fxwiegand/predictosaurus/issues/133)) ([f0e72a8](https://github.com/fxwiegand/predictosaurus/commit/f0e72a8cd5940e9bed4806014f2f0615199d67ff))
* Prevent cycles in forward traversal by checking path containment ([#136](https://github.com/fxwiegand/predictosaurus/issues/136)) ([31f0cf4](https://github.com/fxwiegand/predictosaurus/commit/31f0cf4c3e2b1f4e319cd3d1efc3599a6a2a976f))


### Performance Improvements

* Use transaction for writing graphs via DuckDB ([cdc2873](https://github.com/fxwiegand/predictosaurus/commit/cdc28730bd8d82eed60422b43c2139fce2ed8fa4))

## [0.4.2](https://github.com/fxwiegand/predictosaurus/compare/v0.4.1...v0.4.2) (2025-08-20)


### Bug Fixes

* Refactor get_targets to return only chromosomes that are actually ([#132](https://github.com/fxwiegand/predictosaurus/issues/132)) ([1e1c57b](https://github.com/fxwiegand/predictosaurus/commit/1e1c57b976a7e6c21f7708f226d72cefd36f2df6))


### Performance Improvements

* Add threads option and parallelize build and process command ([#130](https://github.com/fxwiegand/predictosaurus/issues/130)) ([8c83f96](https://github.com/fxwiegand/predictosaurus/commit/8c83f96c88e87616755ec46934a044c1db9dcd48))

## [0.4.1](https://github.com/fxwiegand/predictosaurus/compare/v0.4.0...v0.4.1) (2025-08-18)


### Bug Fixes

* Write score output to single TSV file instead of per transcript ([#124](https://github.com/fxwiegand/predictosaurus/issues/124)) ([df0773d](https://github.com/fxwiegand/predictosaurus/commit/df0773d3dfe8748754a4530deb2648f760216c08))

## [0.4.0](https://github.com/fxwiegand/predictosaurus/compare/v0.3.2...v0.4.0) (2025-08-06)


### Features

* Add amino acid distance metrics and Grantham matrix ([adfb9c1](https://github.com/fxwiegand/predictosaurus/commit/adfb9c11c3bc2dda45144c5673f51c3f09ca991c))
* Add distance matrix and calculation for sneath ([b09058c](https://github.com/fxwiegand/predictosaurus/commit/b09058cb43febfa33a272e627de428bfd6de578b))
* Add score storage and output for transcripts ([d0919f2](https://github.com/fxwiegand/predictosaurus/commit/d0919f2397564b90a66051154097957041157fc8))
* Calculate scores for haplotypes ([38be031](https://github.com/fxwiegand/predictosaurus/commit/38be0312f987f5844f87ff925aa371dbfc5fcafb))
* Calculate scores for haplotypes ([12518fa](https://github.com/fxwiegand/predictosaurus/commit/12518fa1bd7a35677436836a1219f47324caacba))
* Calculate stop penalty ([0aa1914](https://github.com/fxwiegand/predictosaurus/commit/0aa19147fb9300892c7403493aed2afe965420c1))
* Finish basic score implementation and restructure part of code ([2ba3d76](https://github.com/fxwiegand/predictosaurus/commit/2ba3d76259076d7428422e99a2924ce2f68f4636))
* Implement Epstein distance matrix and lookup for amino acids ([513c0db](https://github.com/fxwiegand/predictosaurus/commit/513c0db004e143b9f9ecc7571dee1236b661c1ae))
* Implement Miyata distance metric and add tests ([4002801](https://github.com/fxwiegand/predictosaurus/commit/40028018d6af78e02773ff5e8a12889b4d16c5cf))
* Start working on actual score calculation (WIP) ([24a1262](https://github.com/fxwiegand/predictosaurus/commit/24a1262d419169e8fbe283abc62d7e22f3625c02))
* Update phase according to haplotype properly considering coding ([3ae5746](https://github.com/fxwiegand/predictosaurus/commit/3ae5746e7d5a9e08748469c19bbdf3544a67237e))
* Use amino acid distance in score calculation ([70edff7](https://github.com/fxwiegand/predictosaurus/commit/70edff790032fdb75d5652703a343914ecfd4d2f))


### Bug Fixes

* Fix comment name ([0ca41b4](https://github.com/fxwiegand/predictosaurus/commit/0ca41b4445feb599fc0e662242ffbc06af2f4b92))
* Handle stop codons in amino acid distance metrics ([b0913bf](https://github.com/fxwiegand/predictosaurus/commit/b0913bf41dde2ac2c5983a91af7d18a46664e640))
* Penalize stop codons instead of methionine in scoring ([3cf8c29](https://github.com/fxwiegand/predictosaurus/commit/3cf8c29d197b44908231e95dba5683937ed20bc2))
* Remove unused import of std::ptr::write ([8307d35](https://github.com/fxwiegand/predictosaurus/commit/8307d35b227af363dbb030be44b440e5ef540144))

## [0.3.2](https://github.com/fxwiegand/predictosaurus/compare/v0.3.1...v0.3.2) (2025-04-29)


### Bug Fixes

* Remove nodes_in_between check for creating edges ([f1535ad](https://github.com/fxwiegand/predictosaurus/commit/f1535ad857f65319d63a47ad975c5dad6095d580))

## [0.3.1](https://github.com/fxwiegand/predictosaurus/compare/v0.3.0...v0.3.1) (2025-04-29)


### Bug Fixes

* Filter unique paths ([6106aba](https://github.com/fxwiegand/predictosaurus/commit/6106abaf93b85f60d05af801e868573f28f5af5b))

## [0.3.0](https://github.com/fxwiegand/predictosaurus/compare/v0.2.10...v0.3.0) (2025-04-23)


### Features

* Add subcommand for neoantigen prediction via peptides ([#78](https://github.com/fxwiegand/predictosaurus/issues/78)) ([4523e4f](https://github.com/fxwiegand/predictosaurus/commit/4523e4f0026fb616f3ea51bd37bc311efc02818a))


### Bug Fixes

* Cap numerical overshoot when calculating prob_present() ([95180ec](https://github.com/fxwiegand/predictosaurus/commit/95180ecabe51fa4e935d09cb2fec1c92f8d796b7))
* Cap numerical overshoot when calculating prob_present() ([43eefbe](https://github.com/fxwiegand/predictosaurus/commit/43eefbed4014892cad7e3bb69defde516499c815))
* Cap numerical overshoot when calculating prob_present() ([7f2e73c](https://github.com/fxwiegand/predictosaurus/commit/7f2e73c85c8653af2f19a592fd1cf1dc839e8f2f))
* Fix path generation ([862dd5d](https://github.com/fxwiegand/predictosaurus/commit/862dd5dd453185e561bcf7c964e334dadba58ac6))
* Fix path generation ([f440d26](https://github.com/fxwiegand/predictosaurus/commit/f440d262413ffea7022e2ab7c570842986674207))
* Fix weights concatenation ([31d9a12](https://github.com/fxwiegand/predictosaurus/commit/31d9a12fe03d7fd300295b229f502711027fde34))


### Performance Improvements

* Enhance transcript processing with variant detection ([#80](https://github.com/fxwiegand/predictosaurus/issues/80)) ([413db7f](https://github.com/fxwiegand/predictosaurus/commit/413db7f8697b161da019cdfdeae7f6b80525952f))

## [0.2.10](https://github.com/fxwiegand/predictosaurus/compare/v0.2.9...v0.2.10) (2025-02-14)


### Bug Fixes

* Consider splicing for each transcript by joining paths for CDSs ([#72](https://github.com/fxwiegand/predictosaurus/issues/72)) ([5c766c9](https://github.com/fxwiegand/predictosaurus/commit/5c766c9b1c8b0466da46961dad82d4efd5cc5ac2))

## [0.2.9](https://github.com/fxwiegand/predictosaurus/compare/v0.2.8...v0.2.9) (2025-01-17)


### Bug Fixes

* Adjust predictosaurus for non-unique CDS identifiers ([#60](https://github.com/fxwiegand/predictosaurus/issues/60)) ([e9c54ed](https://github.com/fxwiegand/predictosaurus/commit/e9c54ed58b4d33dd978b5d6ea50d8670da441bed))
* Allow  Ns in reverse_complement ([c684ece](https://github.com/fxwiegand/predictosaurus/commit/c684ece0c47cec7ff0a3f7435c73611bf1ee00e6))
* Remove edges between nodes with same position ([8879214](https://github.com/fxwiegand/predictosaurus/commit/8879214419cbb4299da7042e0593228e8b38853e))
* Remove edges between nodes with same position. ([1ab8ede](https://github.com/fxwiegand/predictosaurus/commit/1ab8edecb05bfb90f035ab5d6ac6392bc9b9acb8))
* Remove unused and potentially breaking placeholder nodes ([1d6f6bf](https://github.com/fxwiegand/predictosaurus/commit/1d6f6bf9377086b180cd4d6cf5f22789c7b6d468))
* Reverse reference sequence as expected by amino acid translations ([590c415](https://github.com/fxwiegand/predictosaurus/commit/590c4159498b6276f801af2e42159601faee2bde))

## [0.2.8](https://github.com/fxwiegand/predictosaurus/compare/v0.2.7...v0.2.8) (2025-01-07)


### Miscellaneous Chores

* release 0.2.8 ([1668725](https://github.com/fxwiegand/predictosaurus/commit/1668725766ee90157cb67c3d4c1a30980d0c66bb))

## [0.2.7](https://github.com/fxwiegand/predictosaurus/compare/v0.2.6...v0.2.7) (2025-01-07)


### Bug Fixes

* Ensure `vaf` scale domain is fixed between 0 and 1 ([01fd353](https://github.com/fxwiegand/predictosaurus/commit/01fd353a2a86064a9c5d939b1ea2c979e36a1d2a))

## [0.2.6](https://github.com/fxwiegand/predictosaurus/compare/v0.2.5...v0.2.6) (2024-12-16)


### Bug Fixes

* Create output dir if non existent ([79b1383](https://github.com/fxwiegand/predictosaurus/commit/79b1383075071d506bbfbeff13e2622a5295dd54))
* Fix feature graph generation ([283feec](https://github.com/fxwiegand/predictosaurus/commit/283feec842e031a288dacbdbd1e28fd0a4ebfb5d))

## [0.2.5](https://github.com/fxwiegand/predictosaurus/compare/v0.2.4...v0.2.5) (2024-12-12)


### Bug Fixes

* Remove primary key constraint on nodes table ([e62ac37](https://github.com/fxwiegand/predictosaurus/commit/e62ac3759bfbc9ae410b6101b82f53485d28be1b))

## [0.2.4](https://github.com/fxwiegand/predictosaurus/compare/v0.2.3...v0.2.4) (2024-12-12)


### Bug Fixes

* Fix wrong interpretation of probabilities ([7aeadb4](https://github.com/fxwiegand/predictosaurus/commit/7aeadb4a81462c6b1afd8ec8fba5506d39ac8f23))


### Performance Improvements

* Add indexes for write_graphs tables ([731ea91](https://github.com/fxwiegand/predictosaurus/commit/731ea91120e6ea8aee835aa0a01e02207c566cbf))

## [0.2.3](https://github.com/fxwiegand/predictosaurus/compare/v0.2.2...v0.2.3) (2024-12-10)


### Bug Fixes

* Fix multiple output file creation ([5ec7a40](https://github.com/fxwiegand/predictosaurus/commit/5ec7a40d6faef16745523d309927aa2f374c29e7))

## [0.2.2](https://github.com/fxwiegand/predictosaurus/compare/v0.2.1...v0.2.2) (2024-12-06)


### Bug Fixes

* Improve error messages ([c00a01f](https://github.com/fxwiegand/predictosaurus/commit/c00a01f64d205d53c8837b8381da758c8552199b))
* Improve error messages ([3f41035](https://github.com/fxwiegand/predictosaurus/commit/3f41035a54c39d093eea1c6ee52f2362ec8006df))

## [0.2.1](https://github.com/fxwiegand/predictosaurus/compare/v0.2.0...v0.2.1) (2024-12-06)


### Bug Fixes

* Fix out dir creation ([19dad8d](https://github.com/fxwiegand/predictosaurus/commit/19dad8dfec95fc7d742f645551a4b4c9860b60a3))


### Miscellaneous Chores

* release 0.2.1 ([054d16a](https://github.com/fxwiegand/predictosaurus/commit/054d16af036fb56ec93bb016ca99cc8cc84126fb))

## [0.2.0](https://github.com/fxwiegand/predictosaurus/compare/v0.1.1...v0.2.0) (2024-12-05)


### Features

* Add `--min-prop-present` parameter to build subcommand ([c4542cb](https://github.com/fxwiegand/predictosaurus/commit/c4542cb108d81db203ef1fbb0ab2f55b452ec97f))


### Bug Fixes

* Ignore samples present in calls file that are not present in given observations ([2bff91a](https://github.com/fxwiegand/predictosaurus/commit/2bff91a88314031c99d811b46e87d429da52702f))

## [0.1.1](https://github.com/fxwiegand/predictosaurus/compare/v0.1.0...v0.1.1) (2024-12-04)


### Miscellaneous Chores

* release 0.1.1 ([8551a11](https://github.com/fxwiegand/predictosaurus/commit/8551a110d543be8b84acdfe0f0e0e2692f17ec15))

## 0.1.0 (2024-12-04)


### Features

* Add reverse paths for handling features on reverse strand ([897bd81](https://github.com/fxwiegand/predictosaurus/commit/897bd81193fd062b7adae954e373660ecb511607))
* Add support for features on backward strand ([e6b2141](https://github.com/fxwiegand/predictosaurus/commit/e6b21411d3fdce1b54a36f115e8cb76d099ea030))
* Allow conversion of haplotype path to protein ([3fa2c75](https://github.com/fxwiegand/predictosaurus/commit/3fa2c7598268cf7f197aa8943f25b992fb80780e))
* Calculate 0-based position of variant on reverse strand ([8321619](https://github.com/fxwiegand/predictosaurus/commit/8321619843be637c57aad43d671701a93d85b971))
* Enable serialization and deserialization for Graph ([200b4dd](https://github.com/fxwiegand/predictosaurus/commit/200b4dd8cba77efcd3aef66c0151d0bc845c7488))
* Implement show command ([ba4ea1d](https://github.com/fxwiegand/predictosaurus/commit/ba4ea1d1776fdab0d180a9cb96d5b1c62fca9122))
* Implement show command ([a2f243e](https://github.com/fxwiegand/predictosaurus/commit/a2f243ecca5cafd9f65724e103acece84b4bfac8))
* Implement show command ([3bc8d30](https://github.com/fxwiegand/predictosaurus/commit/3bc8d3080dae4e5106a9b7113e08fa92c514def3))
* Implement show command for HTML format ([4af776b](https://github.com/fxwiegand/predictosaurus/commit/4af776b69a00b41a73ec8d8e874195d61be291cd))
* Implement show command for tsv format ([87be0d9](https://github.com/fxwiegand/predictosaurus/commit/87be0d984711520da761e534b540fca3f7a3b8f6))
* Implement show command for tsv format ([4616bc6](https://github.com/fxwiegand/predictosaurus/commit/4616bc6b70c4df1916f8ff68301fe5f2756ee249))
* Implement show command for tsv format ([f0a8965](https://github.com/fxwiegand/predictosaurus/commit/f0a89655851eaf15628d247d6a5857c825e4f87a))
* Restructure into multiple subcommands ([#13](https://github.com/fxwiegand/predictosaurus/issues/13)) ([4462a23](https://github.com/fxwiegand/predictosaurus/commit/4462a233f037cdccc87ec5acfc40af5f0f69d458))
* Support insertions longer 3 ([252d1d6](https://github.com/fxwiegand/predictosaurus/commit/252d1d64577ab4046b0edc4a2795ba3e2d970932))
* Test graph serialization using serde_json ([5074b49](https://github.com/fxwiegand/predictosaurus/commit/5074b49001a8228c67a3c645ae73469812823cec))
* Use duckdb to write graphs ([#35](https://github.com/fxwiegand/predictosaurus/issues/35)) ([19955ea](https://github.com/fxwiegand/predictosaurus/commit/19955eadaac9d3c0f9dadb7480e8265dca71a285))


### Bug Fixes

* Create path table in bd before writing to it ([c335418](https://github.com/fxwiegand/predictosaurus/commit/c3354189f046ce9a24cd78baa5b5349435a790fe))
* Fix impact color scheme ([b8bed5e](https://github.com/fxwiegand/predictosaurus/commit/b8bed5e733d49863efead1100ad1bb18c15755b9))
* Fix impact for amino acid altering variants ([38548a0](https://github.com/fxwiegand/predictosaurus/commit/38548a0e35ecfa95db48069a0c36012b61365abb))
* Handle variants at start and end of reference ([794a7e0](https://github.com/fxwiegand/predictosaurus/commit/794a7e081eb1775cb1b9c83639c080980efda6b3))
* Refactor field names ([2378127](https://github.com/fxwiegand/predictosaurus/commit/2378127b45be953b96f2f61aef799bf6a8e2f6fa))
* Refine behaviour for invalid EventProbs ([c1a300d](https://github.com/fxwiegand/predictosaurus/commit/c1a300d7ba7f4462e2774a869e31befd0d945c3b))
* Refine behaviour for invalid EventProbs ([4342223](https://github.com/fxwiegand/predictosaurus/commit/4342223da59defd6eb39c76fce4225765dc3efa9))
* Refine behaviour for invalid EventProbs ([ac541b1](https://github.com/fxwiegand/predictosaurus/commit/ac541b1382f5304913c8aae762e663a96e63151d))
* Refine behaviour for invalid EventProbs ([d06b7c4](https://github.com/fxwiegand/predictosaurus/commit/d06b7c45849c604f7dbb9704ddc89290b9c08620))
* Refine behaviour for invalid EventProbs ([89ae172](https://github.com/fxwiegand/predictosaurus/commit/89ae172f7948ff94469d9a0f7dac4b6615690f72))
* Remove duplicate ref nodes for multiple variants with same position ([daf9ee0](https://github.com/fxwiegand/predictosaurus/commit/daf9ee0718050cd4cf9782471f82fa036fd05408))
* Use json5 to serialize and deserialize EventProbs ([3330305](https://github.com/fxwiegand/predictosaurus/commit/333030533326cb24acaec31ff776014a60b7cbc9))