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Changelog
1.11.0
(2026-09-14)
Features
Allow passing BAM files via remote URL similar to samtools (
#494
) (
5b9d55d
)
1.10.1
(2026-07-27)
Bug Fixes
Drop redundant y-axis title from coverage track (
#486
) (
8535009
)
1.10.0
(2026-07-22)
Features
Fill available width for HTML plots by default (
#484
) (
15b1f8a
)
1.9.0
(2026-07-20)
Features
Make autocompletion file type aware (
#476
) (
f39de68
)
Bug Fixes
Also replace file extension for index check (
#478
) (
f8a3d72
)
Support bgzipped FASTA references (
#479
) (
970f8e1
)
1.8.0
(2026-07-17)
Features
Add option to clamp reads to region (
#449
) (
6e3d9a2
)
Bug Fixes
Remove stale VCF index before rebuilding after bgzip (
#475
) (
51e9136
)
1.7.0
(2026-07-15)
Features
Allow auto completion for manual path inputs in wizard mode (
#472
) (
58daddc
)
1.6.0
(2026-07-09)
Features
allow specifying multiple bams (will get vstacked) (
#450
) (
d592235
)
Offer to create missing BAM/FASTA/VCF indexes (
#468
) (
d871593
)
Print reproducible command after wizard run (
#469
) (
c6ba421
)
Reorder wizard highlight prompts and unify optional-file selection (
#466
) (
578f34d
)
Retry individual wizard prompts on invalid input (
#467
) (
cf4055d
)
1.5.1
(2026-03-13)
Bug Fixes
Skip reads with empty sequence and non-empty CIGAR (
#447
) (
8c42a8f
)
1.5.0
(2026-02-25)
Features
Show coverage breakdown tooltip with position and base counts (
#440
) (
f4b1ef9
)
1.4.6
(2026-02-05)
Bug Fixes
Preserve full alleles and set legend label limit instead (
#432
) (
051b28b
)
1.4.5
(2026-02-05)
Bug Fixes
Adjust region to be inclusive (
#429
) (
7688911
)
1.4.4
(2026-01-30)
Bug Fixes
Clip reads extending beyond reference bounds (
#422
) (
9e4d955
)
Fix region clamping in wizard mode (
5e94b5f
)
Fix VCF file detection for .vcf.gz extensions (
325f9a7
)
1.4.3
(2026-01-19)
Bug Fixes
Prefix search keys with $ delimiter to avoid false matches (
#417
) (
b5106fa
)
1.4.2
(2026-01-14)
Bug Fixes
Allow .vcf files in wizard mode (
#414
) (
e0ea1fb
)
Clamp region to reference bounds generated via around in wizard (
eb3e064
)
Clamp region to reference bounds generated via around in wizard mode (
#415
) (
eb3e064
)
1.4.1
(2025-11-14)
Performance Improvements
Simplify Vega transforms for coverage base counts (
#407
) (
7d094d5
)
1.4.0
(2025-11-13)
Features
Add mismatch display threshold option (
#405
) (
0c77b11
)
Bug Fixes
Strip multiple file extensions from BAM name (
cab3062
)
Update plot color palettes for color blindness and increase opacity (
#406
) (
ce1bac7
)
1.3.0
(2025-10-30)
Features
Add --around-vcf-record option to plot region around VCF record by (
e82e8c3
)
Add --around-vcf-record option to plot region around VCF record by index (
#401
) (
e82e8c3
)
1.2.1
(2025-10-30)
Bug Fixes
Remove potential coverage plot offset at inital plot rendering (
#399
) (
10e6dad
)
1.2.0
(2025-10-30)
Features
Add tooltip to highlight mark showing name field (
#398
) (
c3242c3
)
Bug Fixes
Clarify highlight input prompt with interval and position examples (
7a6d5fd
)
1.1.6
(2025-10-29)
Bug Fixes
Check for both .csi and .tbi VCF index files (
#395
) (
dd5059f
)
1.1.5
(2025-10-28)
Bug Fixes
Write highlight output if VCF or BED is provided (
#393
) (
0ee280f
)
1.1.4
(2025-10-28)
Bug Fixes
Make sure reference start is always interpreted as integer (
#391
) (
291dbb9
)
1.1.3
(2025-10-27)
Bug Fixes
Create output directory if it does not exist (
#389
) (
43a3c12
)
1.1.2
(2025-10-24)
Bug Fixes
Ensure correct typing of start field (
#386
) (
bb05b6a
)
1.1.1
(2025-10-21)
Bug Fixes
Fixate stack order in coverage plot (
#384
) (
ff45355
)
1.1.0
(2025-10-21)
Features
Add option to disable embedded JS in generated HTML (
#382
) (
36ba851
)
Performance Improvements
Use indexed reader for VCF highlighting parameters (
#381
) (
4a6bf64
)
1.0.2
(2025-10-20)
Performance Improvements
Refactor coverage encoding for sparse base tracks and diffs (
#379
) (
3a42840
)
1.0.1
(2025-10-16)
Bug Fixes
Rename test file due to special character preventing crate release (
1998228
)
1.0.0
(2025-10-16)
⚠ BREAKING CHANGES
Update highlight mechanism with multiple highlighting region and VCF and BED options (
#372
)
Features
Add per-base coverage breakdown to Coverage struct and plot (
#368
) (
5373868
)
Update highlight mechanism with multiple highlighting region and VCF and BED options (
#372
) (
9adbf16
)
Bug Fixes
Change area chart interpolation from monotone to step (
cabc396
)
Improve read placement by fixing read end-position calculation (
#371
) (
5e0b8ca
)
Move subtitle to y axis title (
#370
) (
eb029df
)
0.16.5
(2025-10-13)
Bug Fixes
Package js libraries into alignoth (
#365
) (
0a890a5
)
0.16.4
(2025-10-10)
Bug Fixes
Handle CIGAR operations when calculating coverage (
#363
) (
31d0775
)
0.16.3
(2025-08-25)
Performance Improvements
Compress specs using lz-string for HTML output (
#350
) (
65fc73b
)
0.16.2
(2025-07-08)
Bug Fixes
Allow SAM and CRAM files for wizard usage (
#340
) (
70a65e2
)
0.16.1
(2025-05-28)
Bug Fixes
Resolve MAPQ border issue in VL specs (
a4a622e
)
0.16.0
(2025-05-28)
Features
Add coverage plot (
#332
) (
0fb3f14
)
Improved visualization for read pairs (
#330
) (
02aaef3
)
0.15.0
(2025-05-26)
Features
Add new wizard mode for interactive plot generation (
#327
) (
25d099e
)
0.14.3
(2025-05-15)
Performance Improvements
Update release profile (
ef671e3
)
0.14.2
(2025-05-14)
Performance Improvements
Improve storage footprint (
9c3dd3f
)
0.14.1
(2025-05-08)
Bug Fixes
Fix library fetching by downgrading reqwest to 0.11 (
dffcc01
)
Fix library fetching by downgrading reqwest to 0.11 (
3ee2348
)
0.14.0
(2025-05-06)
Features
Add filtering functionality and improve layout for plot controls (
#318
) (
e246dc8
)
Add interactive read info table and styling to plot page (
#316
) (
493332b
)
Add raw_cigar field to tooltip (
#319
) (
05b6282
)
Enhanced multi-read selection with shift-click functionality (
#320
) (
b9d6453
)
Bug Fixes
Adjust control panel margins in html view (
85eacba
)
Keep controls fixed at top (
#321
) (
4e8c1a5
)
0.13.0
(2024-09-18)
Features
Add manual for plot usage into HTML output (
#269
) (
47d0f1d
)
0.12.1
(2024-07-01)
Bug Fixes
Fix potentially unplaced read error (
#244
) (
49dc637
)
Fix read placement (
49dc637
)
0.12.0
(2024-03-05)
Features
Show inserted bases in tooltip (
#212
) (
cacadbe
)
0.11.0
(2023-11-15)
Features
Show warning in plot when reads are downsampled (
#183
) (
e7587fc
)
0.10.0
(2023-10-04)
Features
Allow single selection of a read (
#172
) (
b365680
)
0.9.0
(2023-09-25)
Features
Allow displaying user defined aux tags in read tooltip (
#164
) (
3e969aa
)
Bug Fixes
Remove unconnected lines for unpaired reads (
#167
) (
6e25855
)
0.8.2
(2023-05-10)
Bug Fixes
Fix non-displayed insertions (
#125
) (
04c91ce
)
0.8.1
(2023-04-26)
Bug Fixes
Reduce vertical mapq border size (
#119
) (
554288c
)
Remove duplicated legend (
#117
) (
9f2412c
)
Remove end offset of 1 (
#120
) (
6d63973
)
0.8.0
(2023-04-14)
Features
Show length of deletions via tooltip (
#112
) (
aad66c2
)
0.7.3
(2023-03-31)
Bug Fixes
Fix wrong read offset when read starts with softclips (
#104
) (
16153cf
)
0.7.2
(2023-03-22)
Bug Fixes
Clamp around parameter according to target length (
#98
) (
7db5f07
)
0.7.1
(2023-03-03)
Bug Fixes
Update htslib (
#86
) (
022a70c
)
0.7.0
(2023-02-08)
Features
Add around parameter (
#72
) (
5cb48fc
)
Add option to plot full bam file (
#76
) (
21fafcf
)
Allow highlighting of single base position (
#77
) (
8d16897
)
Allow omitting reference and bam files if cwd only contains one of each (
#74
) (
e44ec4d
)
Bug Fixes
Fix offset of 1 base for reference and reads (
#81
) (
48fdaaa
)
0.6.2
(2023-01-23)
Bug Fixes
Remove potential risk of unplaced reads for bam files with very high density (
#63
) (
b84c9fc
)
0.6.1
(2023-01-16)
Bug Fixes
Improve error message on missing when bam header doesn't contain given target (
#59
) (
9bc3f86
)
0.6.0
(2022-12-12)
Features
Improve identification of base positions (
#48
) (
5464a3f
)
0.5.3
(2022-12-12)
Bug Fixes
Fix highlighting offset (
#42
) (
1ae9c68
)
Improve error message when bam header doesn't contain given target (
#47
) (
25df0fd
)
0.5.2
(2022-10-26)
Bug Fixes
Fix highlighting region for html and json output (
5ce5d17
)
0.5.1
(2022-10-24)
Bug Fixes
fix interval position (
#35
) (
a2ddcfa
)
0.5.0
(2022-09-26)
Features
Increase mapq border size (
#27
) (
f409509
)
Bug Fixes
Reverse map color scale (
#25
) (
d6bac11
)
0.4.0
(2022-08-24)
Features
Add option to output resulting plot in an html file (
#14
) (
e36ebc4
)
Resize markers of read plots (
#16
) (
748d180
)
0.3.0
(2022-07-25)
Features
Support multiple output formats (
#11
) (
53bfe08
)
0.2.2
(2022-06-27)
Bug Fixes
Fix output of highlight data (
#8
) (
cd8c42d
)
0.2.1
(2022-06-23)
Bug Fixes
Fix index out of bounce panic for reads with deletions (
#6
) (
f412be7
)
0.2.0
(2022-06-22)
Features
Add FromStr Implementation for PlotCigar (
ad5ede0
)
Change outputs to be file paths instead of directories (
9773472
)
Bug Fixes
Fix read placement for positions smaller than 5 (
ad5ede0
)
0.1.0 (2022-06-22)
Miscellaneous Chores
release 0.1.0 (
d2a9719
)
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