alignoth 1.4.2

A tool for creating alignment plots from bam files
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
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443

# Changelog

## [1.4.2](https://github.com/alignoth/alignoth/compare/v1.4.1...v1.4.2) (2026-01-14)


### Bug Fixes

* Allow .vcf files in wizard mode ([#414](https://github.com/alignoth/alignoth/issues/414)) ([e0ea1fb](https://github.com/alignoth/alignoth/commit/e0ea1fbd94d41e87dec8400237b89cc400c2cccb))
* Clamp region to reference bounds generated via around in wizard ([eb3e064](https://github.com/alignoth/alignoth/commit/eb3e064ec03915c0ffb818dc506ed79154c27069))
* Clamp region to reference bounds generated via around in wizard mode ([#415](https://github.com/alignoth/alignoth/issues/415)) ([eb3e064](https://github.com/alignoth/alignoth/commit/eb3e064ec03915c0ffb818dc506ed79154c27069))

## [1.4.1](https://github.com/alignoth/alignoth/compare/v1.4.0...v1.4.1) (2025-11-14)


### Performance Improvements

* Simplify Vega transforms for coverage base counts ([#407](https://github.com/alignoth/alignoth/issues/407)) ([7d094d5](https://github.com/alignoth/alignoth/commit/7d094d5bfea9317e7c29a493c78175d3096652ce))

## [1.4.0](https://github.com/alignoth/alignoth/compare/v1.3.0...v1.4.0) (2025-11-13)


### Features

* Add mismatch display threshold option ([#405](https://github.com/alignoth/alignoth/issues/405)) ([0c77b11](https://github.com/alignoth/alignoth/commit/0c77b110218a026192591fd11b9fee825750af28))


### Bug Fixes

* Strip multiple file extensions from BAM name ([cab3062](https://github.com/alignoth/alignoth/commit/cab3062066115ab4700aa2260118cc0dccd26252))
* Update plot color palettes for color blindness and increase opacity ([#406](https://github.com/alignoth/alignoth/issues/406)) ([ce1bac7](https://github.com/alignoth/alignoth/commit/ce1bac744195088964321513d145ade0358dbedf))

## [1.3.0](https://github.com/alignoth/alignoth/compare/v1.2.1...v1.3.0) (2025-10-30)


### Features

* Add --around-vcf-record option to plot region around VCF record by ([e82e8c3](https://github.com/alignoth/alignoth/commit/e82e8c3a07162271f2767694d46a7fd050b75412))
* Add --around-vcf-record option to plot region around VCF record by index ([#401](https://github.com/alignoth/alignoth/issues/401)) ([e82e8c3](https://github.com/alignoth/alignoth/commit/e82e8c3a07162271f2767694d46a7fd050b75412))

## [1.2.1](https://github.com/alignoth/alignoth/compare/v1.2.0...v1.2.1) (2025-10-30)


### Bug Fixes

* Remove potential coverage plot offset at inital plot rendering ([#399](https://github.com/alignoth/alignoth/issues/399)) ([10e6dad](https://github.com/alignoth/alignoth/commit/10e6dad238b06c971bb4c0c3ae43075a179af251))

## [1.2.0](https://github.com/alignoth/alignoth/compare/v1.1.6...v1.2.0) (2025-10-30)


### Features

* Add tooltip to highlight mark showing name field ([#398](https://github.com/alignoth/alignoth/issues/398)) ([c3242c3](https://github.com/alignoth/alignoth/commit/c3242c3ea7b526e8f46691fdeed9d03788816e2f))


### Bug Fixes

* Clarify highlight input prompt with interval and position examples ([7a6d5fd](https://github.com/alignoth/alignoth/commit/7a6d5fd69bcbc00c4941e3f0a4c05db4ffeaa050))

## [1.1.6](https://github.com/alignoth/alignoth/compare/v1.1.5...v1.1.6) (2025-10-29)


### Bug Fixes

* Check for both .csi and .tbi VCF index files ([#395](https://github.com/alignoth/alignoth/issues/395)) ([dd5059f](https://github.com/alignoth/alignoth/commit/dd5059f89f5963ea9bd30c25d64d1ce67cd1689f))

## [1.1.5](https://github.com/alignoth/alignoth/compare/v1.1.4...v1.1.5) (2025-10-28)


### Bug Fixes

* Write highlight output if VCF or BED is provided ([#393](https://github.com/alignoth/alignoth/issues/393)) ([0ee280f](https://github.com/alignoth/alignoth/commit/0ee280f2b9ff83588a6b62d81af2b203a5e4b450))

## [1.1.4](https://github.com/alignoth/alignoth/compare/v1.1.3...v1.1.4) (2025-10-28)


### Bug Fixes

* Make sure reference start is always interpreted as integer ([#391](https://github.com/alignoth/alignoth/issues/391)) ([291dbb9](https://github.com/alignoth/alignoth/commit/291dbb984006568ed1a8290ad8c1b60540f88ae3))

## [1.1.3](https://github.com/alignoth/alignoth/compare/v1.1.2...v1.1.3) (2025-10-27)


### Bug Fixes

* Create output directory if it does not exist ([#389](https://github.com/alignoth/alignoth/issues/389)) ([43a3c12](https://github.com/alignoth/alignoth/commit/43a3c12583ff4e821de9348427ef33c7f7b9c914))

## [1.1.2](https://github.com/alignoth/alignoth/compare/v1.1.1...v1.1.2) (2025-10-24)


### Bug Fixes

* Ensure correct typing of start field ([#386](https://github.com/alignoth/alignoth/issues/386)) ([bb05b6a](https://github.com/alignoth/alignoth/commit/bb05b6a0605636bc9db77b63bf4ac61f8fbb61cf))

## [1.1.1](https://github.com/alignoth/alignoth/compare/v1.1.0...v1.1.1) (2025-10-21)


### Bug Fixes

* Fixate stack order in coverage plot ([#384](https://github.com/alignoth/alignoth/issues/384)) ([ff45355](https://github.com/alignoth/alignoth/commit/ff45355b6d33cbf23bc051c00159c3d4936aa976))

## [1.1.0](https://github.com/alignoth/alignoth/compare/v1.0.2...v1.1.0) (2025-10-21)


### Features

* Add option to disable embedded JS in generated HTML ([#382](https://github.com/alignoth/alignoth/issues/382)) ([36ba851](https://github.com/alignoth/alignoth/commit/36ba851f0f13afc74e8755b2d595ce16c707f9dc))


### Performance Improvements

* Use indexed reader for VCF highlighting parameters ([#381](https://github.com/alignoth/alignoth/issues/381)) ([4a6bf64](https://github.com/alignoth/alignoth/commit/4a6bf645fded28faf7e497acfbb146516674411c))

## [1.0.2](https://github.com/alignoth/alignoth/compare/v1.0.1...v1.0.2) (2025-10-20)


### Performance Improvements

* Refactor coverage encoding for sparse base tracks and diffs ([#379](https://github.com/alignoth/alignoth/issues/379)) ([3a42840](https://github.com/alignoth/alignoth/commit/3a428404bf8d8ab45a6d5dc331d76c6f684d992b))

## [1.0.1](https://github.com/alignoth/alignoth/compare/v1.0.0...v1.0.1) (2025-10-16)


### Bug Fixes

* Rename test file due to special character preventing crate release ([1998228](https://github.com/alignoth/alignoth/commit/19982284943ca8d2c556bbf3e8a3b45b10bd2e9b))

## [1.0.0](https://github.com/alignoth/alignoth/compare/v0.16.5...v1.0.0) (2025-10-16)


### âš  BREAKING CHANGES

* Update highlight mechanism with multiple highlighting region and VCF and BED options ([#372](https://github.com/alignoth/alignoth/issues/372))

### Features

* Add per-base coverage breakdown to Coverage struct and plot ([#368](https://github.com/alignoth/alignoth/issues/368)) ([5373868](https://github.com/alignoth/alignoth/commit/5373868b177be0586db13ac2ce386af45ba22e38))
* Update highlight mechanism with multiple highlighting region and VCF and BED options ([#372](https://github.com/alignoth/alignoth/issues/372)) ([9adbf16](https://github.com/alignoth/alignoth/commit/9adbf16693438f4dafa35d5faa04d5fde226e216))


### Bug Fixes

* Change area chart interpolation from monotone to step ([cabc396](https://github.com/alignoth/alignoth/commit/cabc396eb859186e011f3685402f68fc69772809))
* Improve read placement by fixing read end-position calculation ([#371](https://github.com/alignoth/alignoth/issues/371)) ([5e0b8ca](https://github.com/alignoth/alignoth/commit/5e0b8ca19451a517e5b8297e6cecdc437e13ddf6))
* Move subtitle to y axis title ([#370](https://github.com/alignoth/alignoth/issues/370)) ([eb029df](https://github.com/alignoth/alignoth/commit/eb029dfab009a6e6ce823af8a751bbeefdadd11f))

## [0.16.5](https://github.com/alignoth/alignoth/compare/v0.16.4...v0.16.5) (2025-10-13)


### Bug Fixes

* Package js libraries into alignoth ([#365](https://github.com/alignoth/alignoth/issues/365)) ([0a890a5](https://github.com/alignoth/alignoth/commit/0a890a5bc3b86a2201f23bf490e3eab97f4c8cb6))

## [0.16.4](https://github.com/alignoth/alignoth/compare/v0.16.3...v0.16.4) (2025-10-10)


### Bug Fixes

* Handle CIGAR operations when calculating coverage ([#363](https://github.com/alignoth/alignoth/issues/363)) ([31d0775](https://github.com/alignoth/alignoth/commit/31d07751bb7d65de080c8e408927e65144062986))

## [0.16.3](https://github.com/alignoth/alignoth/compare/v0.16.2...v0.16.3) (2025-08-25)


### Performance Improvements

* Compress specs using lz-string for HTML output ([#350](https://github.com/alignoth/alignoth/issues/350)) ([65fc73b](https://github.com/alignoth/alignoth/commit/65fc73bd99028f32be867f57560ef9e6b370ff28))

## [0.16.2](https://github.com/alignoth/alignoth/compare/v0.16.1...v0.16.2) (2025-07-08)


### Bug Fixes

* Allow SAM and CRAM files for wizard usage ([#340](https://github.com/alignoth/alignoth/issues/340)) ([70a65e2](https://github.com/alignoth/alignoth/commit/70a65e2547501e222cde75a1bd67fcf7abfa3b39))

## [0.16.1](https://github.com/alignoth/alignoth/compare/v0.16.0...v0.16.1) (2025-05-28)


### Bug Fixes

* Resolve MAPQ border issue in VL specs ([a4a622e](https://github.com/alignoth/alignoth/commit/a4a622e5defa78223a4ab3af4059c151a4775f91))

## [0.16.0](https://github.com/alignoth/alignoth/compare/v0.15.0...v0.16.0) (2025-05-28)


### Features

* Add coverage plot ([#332](https://github.com/alignoth/alignoth/issues/332)) ([0fb3f14](https://github.com/alignoth/alignoth/commit/0fb3f14ae6c484085364dc27f4e0dbc55712eda8))
* Improved visualization for read pairs ([#330](https://github.com/alignoth/alignoth/issues/330)) ([02aaef3](https://github.com/alignoth/alignoth/commit/02aaef3ea4aaa80ef62139059d846d7071b94367))

## [0.15.0](https://github.com/alignoth/alignoth/compare/v0.14.3...v0.15.0) (2025-05-26)


### Features

* Add new wizard mode for interactive plot generation ([#327](https://github.com/alignoth/alignoth/issues/327)) ([25d099e](https://github.com/alignoth/alignoth/commit/25d099edac84a85efc72540006ef96915d95e7e7))

## [0.14.3](https://github.com/alignoth/alignoth/compare/v0.14.2...v0.14.3) (2025-05-15)


### Performance Improvements

* Update release profile ([ef671e3](https://github.com/alignoth/alignoth/commit/ef671e347d700c6419c3f105d766f4d637ca2806))

## [0.14.2](https://github.com/alignoth/alignoth/compare/v0.14.1...v0.14.2) (2025-05-14)


### Performance Improvements

* Improve storage footprint ([9c3dd3f](https://github.com/alignoth/alignoth/commit/9c3dd3fcffa3116793c14115c747786ccc62650b))

## [0.14.1](https://github.com/alignoth/alignoth/compare/v0.14.0...v0.14.1) (2025-05-08)


### Bug Fixes

* Fix library fetching by downgrading reqwest to 0.11 ([dffcc01](https://github.com/alignoth/alignoth/commit/dffcc01dc30f1054ec0b673f7bc879038b410826))
* Fix library fetching by downgrading reqwest to 0.11 ([3ee2348](https://github.com/alignoth/alignoth/commit/3ee2348899ea1e28590d4ced4c1b777052c776d3))

## [0.14.0](https://github.com/alignoth/alignoth/compare/v0.13.0...v0.14.0) (2025-05-06)


### Features

* Add filtering functionality and improve layout for plot controls ([#318](https://github.com/alignoth/alignoth/issues/318)) ([e246dc8](https://github.com/alignoth/alignoth/commit/e246dc8c2dc9677254175938b0eee3437ef0a69b))
* Add interactive read info table and styling to plot page ([#316](https://github.com/alignoth/alignoth/issues/316)) ([493332b](https://github.com/alignoth/alignoth/commit/493332b7955e90178dfe8633f47b029e7a6e7be1))
* Add raw_cigar field to tooltip ([#319](https://github.com/alignoth/alignoth/issues/319)) ([05b6282](https://github.com/alignoth/alignoth/commit/05b6282e61540574e316c4c6757030d2a7fbb5c1))
* Enhanced multi-read selection with shift-click functionality ([#320](https://github.com/alignoth/alignoth/issues/320)) ([b9d6453](https://github.com/alignoth/alignoth/commit/b9d6453af1264c3579d65ee78bbac097ab64a750))


### Bug Fixes

* Adjust control panel margins in html view ([85eacba](https://github.com/alignoth/alignoth/commit/85eacba530776bb58715351562b43d8290a286f8))
* Keep controls fixed at top ([#321](https://github.com/alignoth/alignoth/issues/321)) ([4e8c1a5](https://github.com/alignoth/alignoth/commit/4e8c1a584cf68f29fa779d4a3cba599379d042ba))

## [0.13.0](https://github.com/alignoth/alignoth/compare/v0.12.1...v0.13.0) (2024-09-18)


### Features

* Add manual for plot usage into HTML output ([#269](https://github.com/alignoth/alignoth/issues/269)) ([47d0f1d](https://github.com/alignoth/alignoth/commit/47d0f1df66502ed785dd7b72f48546fa644af4f0))

## [0.12.1](https://github.com/alignoth/alignoth/compare/v0.12.0...v0.12.1) (2024-07-01)


### Bug Fixes

* Fix potentially unplaced read error ([#244](https://github.com/alignoth/alignoth/issues/244)) ([49dc637](https://github.com/alignoth/alignoth/commit/49dc637c446146a1327c4c78c04707ab8bfc77da))
* Fix read placement ([49dc637](https://github.com/alignoth/alignoth/commit/49dc637c446146a1327c4c78c04707ab8bfc77da))

## [0.12.0](https://github.com/alignoth/alignoth/compare/v0.11.0...v0.12.0) (2024-03-05)


### Features

* Show inserted bases in tooltip ([#212](https://github.com/alignoth/alignoth/issues/212)) ([cacadbe](https://github.com/alignoth/alignoth/commit/cacadbed0af23b4d3bbb37cddaf482878944b903))

## [0.11.0](https://github.com/koesterlab/alignoth/compare/v0.10.0...v0.11.0) (2023-11-15)


### Features

* Show warning in plot when reads are downsampled ([#183](https://github.com/koesterlab/alignoth/issues/183)) ([e7587fc](https://github.com/koesterlab/alignoth/commit/e7587fc84c8e9cd4fab9ca3175a7b125a6e772e2))

## [0.10.0](https://github.com/koesterlab/alignoth/compare/v0.9.0...v0.10.0) (2023-10-04)


### Features

* Allow single selection of a read ([#172](https://github.com/koesterlab/alignoth/issues/172)) ([b365680](https://github.com/koesterlab/alignoth/commit/b3656800a95dd8e6f010065c91998a4204de6d9b))

## [0.9.0](https://github.com/koesterlab/alignoth/compare/v0.8.2...v0.9.0) (2023-09-25)


### Features

* Allow displaying user defined aux tags in read tooltip ([#164](https://github.com/koesterlab/alignoth/issues/164)) ([3e969aa](https://github.com/koesterlab/alignoth/commit/3e969aaec2ed8d31c15710a14395dd136028d683))


### Bug Fixes

* Remove unconnected lines for unpaired reads ([#167](https://github.com/koesterlab/alignoth/issues/167)) ([6e25855](https://github.com/koesterlab/alignoth/commit/6e258553e2ea4e9c133ccbc68d12d7820944bffd))

## [0.8.2](https://github.com/koesterlab/alignoth/compare/v0.8.1...v0.8.2) (2023-05-10)


### Bug Fixes

* Fix non-displayed insertions ([#125](https://github.com/koesterlab/alignoth/issues/125)) ([04c91ce](https://github.com/koesterlab/alignoth/commit/04c91ce83ed926e3a36c2e3aaa9742a9a0d796df))

## [0.8.1](https://github.com/koesterlab/alignoth/compare/v0.8.0...v0.8.1) (2023-04-26)


### Bug Fixes

* Reduce vertical mapq border size ([#119](https://github.com/koesterlab/alignoth/issues/119)) ([554288c](https://github.com/koesterlab/alignoth/commit/554288c9c8d77273eefee33c3b6382fb0fbd2aaf))
* Remove duplicated legend ([#117](https://github.com/koesterlab/alignoth/issues/117)) ([9f2412c](https://github.com/koesterlab/alignoth/commit/9f2412c0a7a62fea1bb2d99dc0c673225c69b8d8))
* Remove end offset of 1 ([#120](https://github.com/koesterlab/alignoth/issues/120)) ([6d63973](https://github.com/koesterlab/alignoth/commit/6d639739500eb6ff4c9af923b0455ffcbe90107a))

## [0.8.0](https://github.com/koesterlab/alignoth/compare/v0.7.3...v0.8.0) (2023-04-14)


### Features

* Show length of deletions via tooltip ([#112](https://github.com/koesterlab/alignoth/issues/112)) ([aad66c2](https://github.com/koesterlab/alignoth/commit/aad66c237ded4174510bf4a86d135ba2730b1989))

## [0.7.3](https://github.com/koesterlab/alignoth/compare/v0.7.2...v0.7.3) (2023-03-31)


### Bug Fixes

* Fix wrong read offset when read starts with softclips ([#104](https://github.com/koesterlab/alignoth/issues/104)) ([16153cf](https://github.com/koesterlab/alignoth/commit/16153cf604332effdc05e22329934009d0dbe9db))

## [0.7.2](https://github.com/koesterlab/alignoth/compare/v0.7.1...v0.7.2) (2023-03-22)


### Bug Fixes

* Clamp around parameter according to target length ([#98](https://github.com/koesterlab/alignoth/issues/98)) ([7db5f07](https://github.com/koesterlab/alignoth/commit/7db5f07011d12318de604de375ea55cf6e7ab340))

## [0.7.1](https://github.com/koesterlab/alignoth/compare/v0.7.0...v0.7.1) (2023-03-03)


### Bug Fixes

* Update htslib ([#86](https://github.com/koesterlab/alignoth/issues/86)) ([022a70c](https://github.com/koesterlab/alignoth/commit/022a70c9f9f2b79a650f71a1b72ff495ac739a1c))

## [0.7.0](https://github.com/koesterlab/alignoth/compare/v0.6.2...v0.7.0) (2023-02-08)


### Features

* Add around parameter ([#72](https://github.com/koesterlab/alignoth/issues/72)) ([5cb48fc](https://github.com/koesterlab/alignoth/commit/5cb48fce922cb08ac3530bc6f0bdfb1a8814c4e3))
* Add option to plot full bam file ([#76](https://github.com/koesterlab/alignoth/issues/76)) ([21fafcf](https://github.com/koesterlab/alignoth/commit/21fafcf03ada66ae93fb17e4e1f67d42ede998de))
* Allow highlighting of single base position ([#77](https://github.com/koesterlab/alignoth/issues/77)) ([8d16897](https://github.com/koesterlab/alignoth/commit/8d168970e3dcb0a97fbf9d97a56457be9156d179))
* Allow omitting reference and bam files if cwd only contains one of each ([#74](https://github.com/koesterlab/alignoth/issues/74)) ([e44ec4d](https://github.com/koesterlab/alignoth/commit/e44ec4d6a3a2c73c77f8f303b32c5fcf43dcd082))


### Bug Fixes

* Fix offset of 1 base for reference and reads ([#81](https://github.com/koesterlab/alignoth/issues/81)) ([48fdaaa](https://github.com/koesterlab/alignoth/commit/48fdaaa27e079f9b31146e68044669a559a479bc))

## [0.6.2](https://github.com/koesterlab/alignoth/compare/v0.6.1...v0.6.2) (2023-01-23)


### Bug Fixes

* Remove potential risk of unplaced reads for bam files with very high density ([#63](https://github.com/koesterlab/alignoth/issues/63)) ([b84c9fc](https://github.com/koesterlab/alignoth/commit/b84c9fc52a47143e78071d81f636a9e69554deff))

## [0.6.1](https://github.com/koesterlab/alignoth/compare/v0.6.0...v0.6.1) (2023-01-16)


### Bug Fixes

* Improve error message on missing when bam header doesn't contain given target ([#59](https://github.com/koesterlab/alignoth/issues/59)) ([9bc3f86](https://github.com/koesterlab/alignoth/commit/9bc3f868657cec5998f6268f30656555b8b8893c))

## [0.6.0](https://github.com/koesterlab/alignoth/compare/v0.5.3...v0.6.0) (2022-12-12)


### Features

* Improve identification of base positions ([#48](https://github.com/koesterlab/alignoth/issues/48)) ([5464a3f](https://github.com/koesterlab/alignoth/commit/5464a3f9e9147533010b768705cb52a129814e92))

## [0.5.3](https://github.com/koesterlab/alignoth/compare/v0.5.2...v0.5.3) (2022-12-12)


### Bug Fixes

* Fix highlighting offset ([#42](https://github.com/koesterlab/alignoth/issues/42)) ([1ae9c68](https://github.com/koesterlab/alignoth/commit/1ae9c68cde1c47ddc9411aa9579a1ef97a42f1da))
* Improve error message when bam header doesn't contain given target ([#47](https://github.com/koesterlab/alignoth/issues/47)) ([25df0fd](https://github.com/koesterlab/alignoth/commit/25df0fdba6cb70fb1d17e28123e3b11b77f0f7b9))

## [0.5.2](https://github.com/koesterlab/alignoth/compare/v0.5.1...v0.5.2) (2022-10-26)


### Bug Fixes

* Fix highlighting region for html and json output ([5ce5d17](https://github.com/koesterlab/alignoth/commit/5ce5d172319c523096d3b7baca672f7ca220bf30))

## [0.5.1](https://github.com/koesterlab/alignoth/compare/v0.5.0...v0.5.1) (2022-10-24)


### Bug Fixes

* fix interval position ([#35](https://github.com/koesterlab/alignoth/issues/35)) ([a2ddcfa](https://github.com/koesterlab/alignoth/commit/a2ddcfacbf779d6521596d97107bace77ead13d9))

## [0.5.0](https://github.com/koesterlab/alignoth/compare/v0.4.0...v0.5.0) (2022-09-26)


### Features

* Increase mapq border size ([#27](https://github.com/koesterlab/alignoth/issues/27)) ([f409509](https://github.com/koesterlab/alignoth/commit/f4095091932c6d292e24be73c3f5faa1d0d99418))


### Bug Fixes

* Reverse map color scale ([#25](https://github.com/koesterlab/alignoth/issues/25)) ([d6bac11](https://github.com/koesterlab/alignoth/commit/d6bac1121da17c51290b46f2052ff69de51e914a))

## [0.4.0](https://github.com/koesterlab/alignoth/compare/v0.3.0...v0.4.0) (2022-08-24)


### Features

* Add option to output resulting plot in an html file ([#14](https://github.com/koesterlab/alignoth/issues/14)) ([e36ebc4](https://github.com/koesterlab/alignoth/commit/e36ebc45159262dc0956dd7c202d70747bc2b0f9))
* Resize markers of read plots ([#16](https://github.com/koesterlab/alignoth/issues/16)) ([748d180](https://github.com/koesterlab/alignoth/commit/748d1805c41e5dac164db59feedacf8a50e4035c))

## [0.3.0](https://github.com/koesterlab/alignoth/compare/v0.2.2...v0.3.0) (2022-07-25)


### Features

* Support multiple output formats ([#11](https://github.com/koesterlab/alignoth/issues/11)) ([53bfe08](https://github.com/koesterlab/alignoth/commit/53bfe08f06d1a6e4b81267a23a5da93d76ea4425))

## [0.2.2](https://github.com/koesterlab/alignoth/compare/v0.2.1...v0.2.2) (2022-06-27)


### Bug Fixes

* Fix output of highlight data ([#8](https://github.com/koesterlab/alignoth/issues/8)) ([cd8c42d](https://github.com/koesterlab/alignoth/commit/cd8c42d094fd24ef0fc38b8eb2c6b02a75a28209))

## [0.2.1](https://github.com/koesterlab/alignoth/compare/v0.2.0...v0.2.1) (2022-06-23)


### Bug Fixes

* Fix index out of bounce panic for reads with deletions ([#6](https://github.com/koesterlab/alignoth/issues/6)) ([f412be7](https://github.com/koesterlab/alignoth/commit/f412be7866f9676ed16e5092378187b4b103000e))

## [0.2.0](https://github.com/koesterlab/alignoth/compare/v0.1.0...v0.2.0) (2022-06-22)


### Features

* Add FromStr Implementation for PlotCigar ([ad5ede0](https://github.com/koesterlab/alignoth/commit/ad5ede0c5335ab780a121e0f6b8a04e0243697f3))
* Change outputs to be file paths instead of directories ([9773472](https://github.com/koesterlab/alignoth/commit/97734729fdc8a748fdf30656e795a4836ba76536))


### Bug Fixes

* Fix read placement for positions smaller than 5 ([ad5ede0](https://github.com/koesterlab/alignoth/commit/ad5ede0c5335ab780a121e0f6b8a04e0243697f3))

## 0.1.0 (2022-06-22)


### Miscellaneous Chores

* release 0.1.0 ([d2a9719](https://github.com/koesterlab/alignoth/commit/d2a97197c59aa9465e58025e1a21218a22658896))