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88 Open 280 Closed
88 Open 280 Closed
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Issues list

work with SQANTi3 to get evaluation result in an easy to parse format.. enhancement New feature or request Testing Testing-related tickets
#411 opened Jan 29, 2025 by diekhans
@diekhans
Running flair collapse with longshot input
#410 opened Jan 22, 2025 by laulambr
3
FLAIR collapse 5'/3' UTR and splice isoform issue bug Something isn't working mod; collapse
#409 opened Jan 21, 2025 by mckalem
3
use argparse in main flair and clean up all argument parsing cleanup Code cleanup and simplification command line Issues related to command line
#408 opened Jan 21, 2025 by diekhans
@diekhans
update development,, pip, docker, pypi, etc building Documentation Update ReadTheDocs manual source install release Issues with source mgt, install, and releases
#407 opened Jan 16, 2025 by diekhans
5 tasks
@diekhans
flair quantify doesn't error exit when it can read one of the input fasta bug Something isn't working Error handling Issues with error handling and logging mod; quantify
#406 opened Jan 15, 2025 by diekhans
@diekhans
Running FLAIR without annotation? enhancement New feature or request
#403 opened Jan 9, 2025 by cafelton
collapse gtf file does not include gene lines enhancement New feature or request mod; collapse
#402 opened Jan 9, 2025 by cafelton
@diekhans
IndexError when running gtf_to_bed.py bug Something isn't working File I/O File parsing and formatting mod; collapse
#401 opened Jan 8, 2025 by shin0727
@diekhans
8
Discrepancy between number of reads from collapse --generate_map and quantification module output Documentation Update ReadTheDocs manual mod; quantify
#400 opened Dec 23, 2024 by pgupta3005
2
GTFs that have a subset of the chromsomes in the BAM cause bed_to_gtf to fail bug Something isn't working mod; collapse
#399 opened Dec 21, 2024 by diekhans
Feature request - flair correct detect junctions using just long reads Documentation Update ReadTheDocs manual enhancement New feature or request mod; correct
#397 opened Dec 17, 2024 by cafelton
@cafelton
Running Flair with many samples Documentation Update ReadTheDocs manual duplicate This issue or pull request already exists enhancement New feature or request mod; collapse
#396 opened Dec 13, 2024 by shenglin-liu
1
Running FLAIR to get annotated transcript IDs bug Something isn't working mod; quantify Need more information Need more information from user
#395 opened Dec 12, 2024 by bmwx410
3
Improve issue template in github enhancement New feature or request source install release Issues with source mgt, install, and releases
#394 opened Dec 10, 2024 by diekhans
All temporary files should got to TMPDIR bug Something isn't working enhancement New feature or request mod; collapse
#393 opened Dec 10, 2024 by diekhans
@diekhans
FLAIR-collapse non-standard chromosome issues mod; collapse
#392 opened Dec 10, 2024 by cafelton
TypeError: 'NoneType' object is not subscriptable - Flair collapse bug Something isn't working mod; collapse
#390 opened Dec 9, 2024 by XieLab-VSU
1
Add FLAIR workflows to Dockstore enhancement New feature or request
#385 opened Nov 20, 2024 by diekhans
convert flair to a distributed application enhancement New feature or request
#383 opened Nov 11, 2024 by diekhans
@diekhans
flair collapse should be able to get reads from BAM as well as going back to FASTQ enhancement New feature or request mod; collapse
#382 opened Nov 10, 2024 by diekhans
1
flair correct guessing the format of junction input is confusing and brittle command line Issues related to command line mod; correct
#381 opened Nov 10, 2024 by diekhans
@diekhans
flair-align --keep_supplementary is incorrectly named command line Issues related to command line mod; align
#380 opened Nov 7, 2024 by diekhans
@diekhans @cafelton
1
exon start coordinate > end coordinate after collapse bug Something isn't working mod; collapse
#379 opened Oct 17, 2024 by YIGUIz
1
FLAIR collapse fails after Minimap2 indexing without clear error bug Something isn't working mod; collapse Need more information Need more information from user
#378 opened Oct 14, 2024 by lucilaviappiani
1
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