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formbio
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laava
LAAVA: Long-read AAV Analysis
MIT License
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Use "ruff check" in CI for deeper static checks
#45
etal
opened
1 week ago
0
Convert vector_type==unspecified to ssAAV or scAAV by heuristic, or remove the option
#44
etal
opened
2 weeks ago
0
Update static images and written definitions to reflect the extended taxonomy of read alignment subtypes
#43
etal
opened
2 weeks ago
0
Implement subtype “reverse-packaging” for ITR-only vector+backbone
#42
etal
opened
2 weeks ago
0
Assign displayed subtype “read-through” for “vector+backbone” in ssAAV and scAAV
#41
etal
opened
2 weeks ago
0
Ensure subtypes "full-gap" and "tandem" are counted and reported properly
#40
etal
opened
2 weeks ago
0
Display scAAV subtypes "snapback", "itr-partial", "complex-AAV" in Table 3, "Assigned AAV read types detailed analysis"
#39
etal
opened
2 weeks ago
0
Use "other-AAV" classification for the unexpected vector type
#38
etal
opened
2 weeks ago
0
Display "chimeric-AAV" and "chimeric non-AAV" (or -vector) as separate rows in Table 1
#37
etal
opened
2 weeks ago
0
Display alignment type "other" as "other-AAV" in Tables 1 and 2
#36
etal
opened
2 weeks ago
0
Run integration tests in CI
#35
etal
opened
2 weeks ago
0
Add map_name to the sequence-error.tsv
#34
bcantarel
opened
2 weeks ago
1
Use a second sentinel file in case 2 input files are missing
#33
etal
closed
2 weeks ago
0
Add Strand to Alignment TSV file
#32
bcantarel
opened
2 weeks ago
1
Take "helper name" input and report unidentified references with their own names in Table 1
#31
etal
opened
2 weeks ago
0
Blc supplementaryanalysis
#30
bcantarel
opened
2 weeks ago
0
Consolidate output TSVs and remove .Rdata output
#29
etal
opened
3 weeks ago
0
Add FASTQ input and position-sorted, indexed BAM output
#28
etal
closed
2 weeks ago
0
Report updates and bugfix
#27
etal
closed
3 weeks ago
0
Accept Sequence and Annotation as Genbank
#26
bcantarel
opened
1 month ago
0
LAAVA accept FastQ as input
#25
bcantarel
closed
2 weeks ago
0
can't use same file twice as input
#24
bcantarel
closed
2 weeks ago
0
Separate container and code path for PDF generation
#23
etal
closed
2 weeks ago
1
Generate IGV-compatible BAM file indexes (.bai) for each BAM output
#22
etal
closed
2 weeks ago
0
Python type annotations and static type checking
#21
etal
opened
1 month ago
0
Consolidate BED, FASTA file input validation
#20
etal
opened
1 month ago
0
Remove intermediate "annotation.txt" and "reference_names.tsv" files from flow
#19
etal
opened
1 month ago
0
Sporadic error in RepCap plot generation
#18
etal
closed
3 weeks ago
1
Split heavy calculations from Rmd into a separate script
#17
etal
closed
1 month ago
1
Enable/disable PDF and HTML report formats independently
#16
etal
opened
1 month ago
0
test: Ensure build/ output directory exists before writing to it
#15
etal
closed
1 month ago
0
Refactor report template vs. scripts
#14
etal
closed
1 month ago
0
Update in-repo documentation
#13
etal
closed
1 month ago
0
Feature request: more annotation in final report
#12
krobison13
opened
1 month ago
2
Test in README.md fails
#11
krobison13
closed
1 month ago
1
Expose more options in workflow; clean up core Python scripts
#10
etal
closed
2 months ago
0
Form Bio workflow MVP
#9
etal
closed
2 months ago
2
Nextflow MVP workflow
#8
etal
closed
3 months ago
3
Update classification figures and definition table
#7
etal
closed
3 months ago
1
Update README
#6
etal
closed
4 months ago
0
Apply remaining AAV WG report recommendations
#5
etal
closed
4 months ago
1
adding seqname
#4
bcantarel
closed
7 months ago
0
Reformat output report as HTML following WG consensus
#3
etal
closed
6 months ago
0
Add MIT license from upstream
#2
etal
closed
7 months ago
0
License, GHA CI, Dockerfile
#1
etal
closed
9 months ago
0